tag:theconversation.com,2011:/id/topics/plant-breeding-5114/articlesPlant breeding – The Conversation2023-08-04T22:00:28Ztag:theconversation.com,2011:article/2109852023-08-04T22:00:28Z2023-08-04T22:00:28ZIs this the protein plant of the future? New study finds ‘sweetness gene’ that makes lupins tastier<figure><img src="https://images.theconversation.com/files/541155/original/file-20230804-17-98ky3m.jpg?ixlib=rb-1.1.0&rect=10%2C30%2C6699%2C4436&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/pickled-yellow-lupin-beans-bowl-on-2069448974">Shutterstock</a></span></figcaption></figure><p>If you walk into a bar in Italy, you might be served a dish of salty, nutritious snacks: lupin beans, a legume that has been eaten around the Mediterranean and in parts of the Middle East and Africa for thousands of years.</p>
<p>Lupins are very high in protein and fibre, low in carbs, have a low glycaemic index, and they’re easy to grow in a variety of climates. However, some varieties also contain high levels of unpleasantly bitter alkaloids.</p>
<p>In <a href="http://www.science.org/doi/10.1126/sciadv.adg8866">new research</a>, an international team of researchers has for the first time identified the “sweetness gene” responsible for low alkaloid levels. This discovery may make it easier to reliably produce more palatable plants. </p>
<h2>The search for sweetness</h2>
<p>Around 100 years ago, plant breeders in Germany found natural mutations that produced “sweet lupins” with far lower levels of bitter alkaloids. They produced sweet varieties of white lupin (<em>Lupinus albus</em>), narrow-leafed lupin (<em>Lupinus angustifolius</em>, the main type grown in Australia), and the less common yellow lupin (<em>Lupinus luteus</em>).</p>
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<p>Over the past 50 years or so, lupins have become more common as food for farm animals. Sweet lupins are good for this, as they don’t require extensive washing to be usable. They are also increasingly eaten by humans – and we are very sensitive to bitterness.</p>
<p>To find the genetic basis for “sweet” lupins, we used a few approaches.</p>
<h2>A genetic search</h2>
<p>Our colleagues in Denmark studied the biochemistry of the different alkaloids in both bitter and sweet varieties. By looking at the changes in the composition of the alkaloids, we could get an idea of the genes involved.</p>
<p>My own work was on the genetics end. We analysed 227 varieties of white lupin and tested their alkaloid levels.</p>
<p>Then, with colleagues in France, we looked at markers across the lupin genome and tried to associate high and low alkaloid levels with the genetics.</p>
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<img alt="A photo showing white lupin plants with tall stems and white flowers." src="https://images.theconversation.com/files/541158/original/file-20230804-21-77kck2.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/541158/original/file-20230804-21-77kck2.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/541158/original/file-20230804-21-77kck2.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/541158/original/file-20230804-21-77kck2.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/541158/original/file-20230804-21-77kck2.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/541158/original/file-20230804-21-77kck2.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/541158/original/file-20230804-21-77kck2.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">New research has found the ‘sweetness gene’ in white lupins.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/plants-bloom-lupinus-albus-white-lupin-1402412459">Shutterstock</a></span>
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<p>We had clues about where we thought the gene would be, in a certain region of a few dozen genes. There was one we thought looked the most promising, so we designed a lot of DNA markers to work out what sequence varied in that gene.</p>
<p>Eventually we found a very strong link between a change in alkaloid levels and a variation of a single sequence in our gene. </p>
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Read more:
<a href="https://theconversation.com/pulses-are-packed-with-goodness-five-cool-things-you-should-know-about-them-198903">Pulses are packed with goodness: Five cool things you should know about them</a>
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<p>The final test was to find out whether a variation in this gene would also produce sweetness in other types of lupin. In some other plants we would be able to use genetic modification tools to do this, but for various reasons this is difficult in lupins.</p>
<p>Instead, we went to a company called Traitomic who screened a huge number of seeds of narrow-leafed lupin until they found one which naturally had exactly the mutation we were looking for. And when we tested that plant, it had low alkaloids – confirming we really had found the “sweetness gene”.</p>
<h2>A reliable marker</h2>
<p>In practice, growing sweet white lupin can be a bit tricky. There are several different strains that have different low alkaloid genes, and if these strains cross-pollinate, the result can be bitter lupin plants once again.</p>
<p>The research gives a reliable genetic marker for plant breeders to know what strains they are dealing with. This means it will be much easier to consistently grow sweet white lupin.</p>
<p>At the moment most of what is grown in Australia is narrow-leafed lupin, in part because the industry had a hard time keeping the white lupin sweet (and in part because white lupin was plagued by a fungal disease called lupin anthracnose). So perhaps in future we’ll see white lupin make a comeback.</p>
<p>Our vision is more cultivation of the high-protein, hardy lupins for consumption by humans.</p>
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Read more:
<a href="https://theconversation.com/plant-based-patties-lab-grown-meat-and-insects-how-the-protein-industry-is-innovating-to-meet-demand-180859">Plant-based patties, lab-grown meat and insects: how the protein industry is innovating to meet demand</a>
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<img src="https://counter.theconversation.com/content/210985/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Matthew Nelson received funding from Innovate UK to conduct this research while working at the Royal Botanic Gardens, Kew. Three co-authors of the research are employed by biotech company Traitomic, whose technology was used to screen for candidate mutations.</span></em></p>The lupin bean is a nutritional marvel, but its bitter taste has so far made it only a niche food.Matthew Nelson, Plant Geneticist, CSIROLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1987242023-03-08T13:40:36Z2023-03-08T13:40:36ZOnce the Callery pear tree was landscapers’ favorite – now states are banning this invasive species and urging homeowners to cut it down<figure><img src="https://images.theconversation.com/files/513447/original/file-20230303-16-jjphd6.jpg?ixlib=rb-1.1.0&rect=0%2C8%2C1933%2C1283&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Bradford pear trees in bloom along a driveway in Sussex County, Del.</span> <span class="attribution"><a class="source" href="https://flic.kr/p/9xfPoK">Lee Cannon/Flickr</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span></figcaption></figure><p>When people think of spring, they often picture flowers and trees blooming. And if you live in the U.S. Northeast, Midwest or South, you have probably seen a medium-sized tree with long branches, covered with small white blooms – the Callery pear (<em>Pyrus calleryana</em>). </p>
<p>For decades, Callery pear – which comes in many varieties, including “Bradford” pear, “Aristocrat” and “Cleveland Select” – was among the most popular trees in the U.S. for ornamental plantings. Today, however, it’s widely recognized as an <a href="https://www.govinfo.gov/content/pkg/FR-1999-02-08/pdf/99-3184.pdf">invasive species</a>. Land managers and plant ecologists <a href="https://scholar.google.com/citations?user=uRA-SZ0AAAAJ&hl=en&oi=sra">like me</a> are working to eradicate it to preserve biodiversity in natural habitats. </p>
<p>As of 2023, it is illegal to <a href="https://ohiodnr.gov/discover-and-learn/plants-trees/invasive-plants/callery-pear">sell, plant or grow Callery pear</a> in Ohio and <a href="https://www.agriculture.pa.gov/Plants_Land_Water/PlantIndustry/NIPPP/Pages/Callery-Pear.aspx">Pennsylvania</a>, and will become illegal in <a href="https://news.clemson.edu/invasive-bradford-pear-3-other-species-to-be-banned-for-sale-in-sc/">South Carolina</a> on October 1, 2024. <a href="https://news.ncsu.edu/2022/03/bounty-offered-on-bradford-pear-trees/">North Carolina</a> and <a href="https://www.lakeexpo.com/community/community_news/cut-down-your-bradford-pear-and-missouri-conservation-will-send-you-a-free-tree/article_df77978a-b51a-11ec-ab85-b39d20e73240.html">Missouri</a> will give residents free native trees if they cut down Callery pear trees on their property. </p>
<p>How did this tree, once in high demand, become designated by the U.S. Forest Service as “<a href="https://www.invasive.org/weedcd/pdfs/wow/callery_pear.pdf">Weed of the Week</a>”? The devil is in the biological details.</p>
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<figcaption><span class="caption">A Kentucky extension specialist explains why Callery pears initially seemed like a solution, but have proved to be a major problem.</span></figcaption>
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<h2>A quasi-perfect tree</h2>
<p>Botanists brought the Callery pear to the U.S. from Asia <a href="https://arboretum.harvard.edu/stories/the-rise-and-fall-of-the-ornamental-callery-pear-tree/">in the early 1900s</a>. They intentionally bred the horticultural variety to enhance its ornamental qualities. In doing so, they created an arboricultural wunderkind. As The New York Times <a href="https://www.nytimes.com/1964/01/05/archives/bradford-pear-has-many-assets-new-ornamental-fruit-offers-sturdy.html">observed in 1964</a>: </p>
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<p>“Few trees possess every desired attribute, but the Bradford ornamental pear comes unusually to close to the ideal.”</p>
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<p>Modern varieties of Callery pear produce an explosion of white flowers in springtime, followed by deep green summer foliage that turns deep red and maroon in autumn. They also are very tolerant of urban soils, which can be <a href="https://arboretum.harvard.edu/stories/urban-soil-problems-and-promise/">highly compacted</a> and hard for roots to penetrate. The trees grow quickly and have a rounded shape, which made them suitable for planting in rows along driveways and roadsides.</p>
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<a href="https://images.theconversation.com/files/510742/original/file-20230216-22-hkyqya.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Tree with leaves mostly shaded red." src="https://images.theconversation.com/files/510742/original/file-20230216-22-hkyqya.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/510742/original/file-20230216-22-hkyqya.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/510742/original/file-20230216-22-hkyqya.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/510742/original/file-20230216-22-hkyqya.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/510742/original/file-20230216-22-hkyqya.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/510742/original/file-20230216-22-hkyqya.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/510742/original/file-20230216-22-hkyqya.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">A Callery pear turning red in fall.</span>
<span class="attribution"><span class="source">Ryan McEwan</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
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<p>During the post-World War II suburban development boom, Callery pear trees became extremely popular in residential settings. In 2005 the Society of Municipal Arborists named the “Chanticleer” variety the <a href="https://www.concreteconstruction.net/projects/infrastructure/arborists-select-urban-tree-of-the-year_o">urban street tree of the year</a>. But the breeding process that created this and other varieties of Callery pear was producing unexpected results.</p>
<h2>Cloning to produce an American original</h2>
<p>To ensure that each Callery pear tree had bright blooms, red foliage and other desired traits, horticulturists created identical clones through <a href="https://www.britannica.com/topic/graft">a process known as grafting</a>: creating seedlings from cuttings of trees with the desired characteristics. </p>
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<figcaption><span class="caption">Grafting is a method for propagating new fruit trees using buds from existing trees and fusing them onto a branch or stem of another tree, which is called the rootstock.</span></figcaption>
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<p>This approach eliminated the messy complexity of mixing genes during sexual reproduction and ensured that when each tree matured, it would have the characteristics that homeowners desire. Every tree of a specific variety was a genetically identical clone.</p>
<p>Grafting also meant Callery pear trees could not make fruits. Some fruit trees, such as peaches and tart cherries, can <a href="https://extension.umaine.edu/fruit/growing-fruit-trees-in-maine/pollination-requirements/">fertilize their flowers with their own pollen</a>. In contrast, Callery pear is self-incompatible: pollen on an individual tree cannot fertilize flowers on that tree. And since all Callery pears of a specific variety planted in a neighborhood would be identical clones, they would effectively be the same tree. </p>
<p>If a tree can’t produce fruits, it can’t disperse into natural habitats. Gardeners and landscapers thought it was perfectly safe to plant Callery pear near natural habitats, such as prairies, because the species was trapped in place by its reproductive biology. But the tree would break free from its isolation and spread seeds far and wide.</p>
<h2>The great escape</h2>
<p>University of Cincinnati botanist <a href="https://culleylab.com/home-page/members-lab/theresa-culley-pi/">Theresa Culley</a> and colleagues have found that as horticulturalists tinkered with Callery pears to produce new versions, they made the individuals different enough <a href="https://doi.org/10.1007/s10530-008-9386-z">to escape the fertilization barrier</a>. If a neighborhood had only “Bradford” pear trees, then no fruits could be produced – but once someone added an “Aristocrat” pear to their yard, then these two varieties could fertilize each other and produce fruits. </p>
<p>When Callery pear trees in gardens and parks started depositing seeds in nearby areas, wild populations of the trees became established. Those wild trees could pollinate one another, as well as neighborhood trees. </p>
<p>In today’s landscape, Callery pear is astonishingly fertile. The prolific flowering that horticulturists intentionally bred into these varieties now yields tremendous crops of pears each year. Although these little pears are generally not edible by humans, birds feed on the fruit, then fly away and excrete the seeds into natural habitats. Callery pear has become one of the <a href="https://www.fws.gov/program/invasive-species">most problematic invasive species</a> in the eastern United States. </p>
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<h2>A thorny problem</h2>
<p>Like other invasives, Callery pears crowd out native species. Once Callery pear seedlings <a href="https://doi.org/10.1007/s10530-022-02861-z">spread from habitat edges into grasslands</a>, they have advantages that allow them to dominate the site. </p>
<p>In <a href="https://mcewanlab.org/">my research lab</a>, we have found that Callery pear leafs out very early in spring and drops its leaves late in fall. This enables it to <a href="https://doi.org/10.3159/TORREY-D-22-00008.1">soak up more sun than native species</a>. We also have discovered that during invasion, these trees <a href="https://doi.org/10.1016/j.apsoil.2021.103989">alter the soil</a> and release chemicals that suppress the germination of native plants. </p>
<p>Callery pear is highly resistant to natural disturbances. In fact, when <a href="https://www.linkedin.com/in/meg-maloney-51b22b112/">my graduate student Meg Maloney</a> tried to kill the trees by using <a href="https://www.youtube.com/shorts/AeaEsDTnMLw">prescribed fires</a> or applying <a href="https://www.youtube.com/shorts/wtkMey4IItE">liquid nitrogen</a> directly to stumps after cutting the trees down, her efforts failed. Instead, the trees sprouted aggressively and <a href="https://muse.jhu.edu/article/883911#info_wrap">seemingly gained strength</a>.</p>
<p>Once Callery pear has escaped into natural areas, its seedlings produce <a href="https://doi.org/10.21273/HORTTECH04892-21">very sharp, stiff thorns</a> that can puncture shoes or even tires. This makes the trees a menace to people working in the area, as well as to native plants. Another nuisance factor is that when Callery pears bloom, they produce a <a href="https://www.npr.org/2015/04/24/401943000/whats-that-smell-the-beautiful-tree-thats-causing-quite-a-stink">strong odor</a> that many people find unpleasant.</p>
<p>Currently, <a href="https://www.invasive.org/alien/pubs/midatlantic/pyca.htm">directly applying herbicides</a> is the only known control for a Callery pear invasion. But the trees are so successful at spreading that poisoning their seedlings may simply create space for other Callery pear seedlings to establish. It is unclear how habitat managers can escape a confounding ecological cycle of invasion, herbicide application and re-invasion.</p>
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<a href="https://images.theconversation.com/files/513473/original/file-20230304-14-ct0blo.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="An open space studded with Callery pear trees, with dead grasses between the trees." src="https://images.theconversation.com/files/513473/original/file-20230304-14-ct0blo.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/513473/original/file-20230304-14-ct0blo.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/513473/original/file-20230304-14-ct0blo.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/513473/original/file-20230304-14-ct0blo.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/513473/original/file-20230304-14-ct0blo.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/513473/original/file-20230304-14-ct0blo.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/513473/original/file-20230304-14-ct0blo.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">A Callery pear invasion is crowding out native species on this agricultural land, converting it to woodland.</span>
<span class="attribution"><a class="source" href="https://extension.okstate.edu/fact-sheets/the-invasive-callery-pear.html">Oklahoma State University Extension</a>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
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<h2>Banned but not gone</h2>
<p>In response to work by the <a href="https://www.oipc.info/">Ohio Invasive Plants Council</a> and other experts, Ohio has taken the extraordinary step of <a href="https://codes.ohio.gov/ohio-administrative-code/rule-901:5-30-01">banning Callery pear</a> to thwart its ecological invasion into natural habitats. But the trees are common in residential areas across the state and have established vigorous populations in natural habitats. Ecologists will be working well into the future to maintain openness and biodiversity in areas where Callery pear is invading. </p>
<p>In the meantime, homeowners can help. Horticulturists recommend that people who have a Callery pear on their property should <a href="https://dyckarboretum.org/callery-pear-cut-them-down/">remove it and replace it</a> with something that is not an invasive species. Few trees possess every desired attribute, but many <a href="https://moinvasives.org/2018/03/29/plant-this-not-that-10-native-trees-to-plant-in-place-of-callery-pear/">native trees</a> have visually attractive features and will not threaten ecosystems in your region.</p>
<p><em>This article has been updated to reflect current state bans on Callery pear trees as of March 2024.</em></p><img src="https://counter.theconversation.com/content/198724/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Ryan W. McEwan does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>They’re beautiful in bloom, but Callery pear trees crowd out native plants and turn productive open land into woody thickets.Ryan W. McEwan, Professor of Biology, University of DaytonLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1852842022-07-08T12:16:44Z2022-07-08T12:16:44ZCotton breeders are using genetic insights to make this global crop more sustainable<figure><img src="https://images.theconversation.com/files/472873/original/file-20220706-14-c5u37u.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C1908%2C1245&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A cotton field in Lubbock, Texas</span> <span class="attribution"><a class="source" href="https://newsroom.ap.org/detail/CottonAcresAbandoned/1d595485640243258e8e2a4d0e5a7da8/photo">AP Photo/LM Otero</a></span></figcaption></figure><p>Products derived from the cotton plant show up in <a href="https://science.jrank.org/pages/1832/Cotton-Cotton-by-products.html">many items that people use daily</a>, including blue jeans, bedsheets, paper, candles and peanut butter. In the United States cotton is <a href="https://www.ers.usda.gov/topics/crops/cotton-wool/cotton-sector-at-a-glance/">a US$7 billion annual crop</a> grown in 17 states from Virginia to Southern California. Today, however, it’s at risk.</p>
<p>Cotton plants from fields in India, China and the U.S. – the world’s top three producers – all grow, flower and produce cotton fiber very similarly. That’s because they are genetically very similar.</p>
<p>This can be a good thing, since breeders select the best-performing plants and cross-breed them to produce better cotton every generation. If one variety produces the best-quality fiber that sells for the best price, growers will plant that type exclusively. But after many years of this cycle, <a href="https://doi.org/10.1038/s41588-020-0614-5">cultivated cotton all starts to look the same</a>: high-yielding and easy for farmers to harvest using machines, but wildly underprepared to fight disease, drought or insect-borne pathogens.</p>
<p>Breeding alone may not be enough to combat the low genetic diversity of the cultivated cotton genome, since breeding works with what exists, and what exists all looks the same. And genetic modification may not be a realistic option for creating cotton that is useful for farmers, because getting engineered crops approved is expensive and heavily regulated. <a href="https://genetics.tamu.edu/featuring-serina-taluja/">My research</a> focuses on possible solutions that lie at the intersection between these tools.</p>
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<iframe width="440" height="260" src="https://www.youtube.com/embed/QHgNoSYlhYs?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Mechanical harvesting and processing take cotton from field to baled fibers and seeds.</span></figcaption>
</figure>
<h2>How to retool cotton</h2>
<p>In a perfect world, scientists could <a href="https://www.genome.gov/about-genomics/policy-issues/what-is-Genome-Editing">change just a few key components</a> of the cotton genome to make plants more resilient to stresses such as pests, bacteria, fungi and water limitations. And the plants would still produce high-quality cotton fiber. </p>
<p>This strategy isn’t new. Some <a href="https://www.ers.usda.gov/data-products/chart-gallery/gallery/chart-detail/?chartId=99424">88% of the cotton grown in the U.S.</a> has been genetically modified to resist caterpillar pests, which are expensive and hard to manage with traditional insecticides. But as new problems emerge, new solutions will be required that will demand more complex changes to the genome.</p>
<p>Recent advances in plant tissue culture and regeneration make it possible to develop a whole new plant from a few cells. Scientists can use good genes from other organisms to replace the defective ones in cotton, yielding cotton plants with all the resistance genes and all the agriculturally valuable genes. </p>
<p>The problem is that getting regulatory approval for a genetically modified crop to go to market is a <a href="https://geneticliteracyproject.org/gmo-faq/what-does-it-take-to-bring-a-new-gm-product-to-market/">long process</a>, often eight to 10 years. And it’s usually <a href="http://dx.doi.org/10.1080/21645698.2019.1612689">expensive</a>.</p>
<p>But genetic modification isn’t the only option. Researchers today have access to a gigantic amount of data about all living things. Scientists have <a href="https://www.yourgenome.org/facts/timeline-organisms-that-have-had-their-genomes-sequenced/">sequenced the entire genomes of numerous organisms</a> and have annotated many of these genomes to show where the genes and regulatory sequences are within them. Various <a href="https://en.wikipedia.org/wiki/List_of_sequence_alignment_software">sequence comparison tools</a> allow scientists to line up one gene or genome against another and quickly determine where all the differences are.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/472882/original/file-20220706-14-1ef52y.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Map showing U.S. states where cotton was harvested in 2017." src="https://images.theconversation.com/files/472882/original/file-20220706-14-1ef52y.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/472882/original/file-20220706-14-1ef52y.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=464&fit=crop&dpr=1 600w, https://images.theconversation.com/files/472882/original/file-20220706-14-1ef52y.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=464&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/472882/original/file-20220706-14-1ef52y.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=464&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/472882/original/file-20220706-14-1ef52y.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=583&fit=crop&dpr=1 754w, https://images.theconversation.com/files/472882/original/file-20220706-14-1ef52y.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=583&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/472882/original/file-20220706-14-1ef52y.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=583&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Cotton is grown in 13 states across the southern U.S. The western half of this belt has been in drought since 2000.</span>
<span class="attribution"><a class="source" href="https://www.ers.usda.gov/webdocs/charts/99698/CottonAcreage2017.png?v=1148.3">USDA</a></span>
</figcaption>
</figure>
<p>Plants have very large genomes with lots of repetitive sequences, which makes them <a href="http://dx.doi.org/10.3390/biology1020439">very challenging</a> to unpack. However, a team of researchers changed the game for cotton genetics in 2020 by releasing <a href="https://doi.org/10.1038/s41588-020-0614-5">five updated and annotated genomes</a> – two from cultivated species and three from wild species. </p>
<p>Having the wild genomes assembled makes it possible to start using their valuable genes to try to improve cultivated varieties of cotton by breeding them together and looking for those genes in the offspring. This approach combines traditional plant breeding with detailed insights into cotton’s genome.</p>
<p>We now know which genes we need to make cultivated cotton more resistant to disease and drought. And we also know where to avoid making changes to important agricultural genes.</p>
<h2>Analyzing cotton hybrids</h2>
<p>These genomes also make it possible to develop new screening tools to characterize interspecific hybrids – the offspring of two cotton plants from different species. Before this information was available, there were two primary forms of <a href="https://doi.org/10.1534/g3.115.018416">hybrid characterization</a>. Both were based on <a href="https://www.nature.com/scitable/definition/single-nucleotide-polymorphism-snp-148">single nucleotide polymorphisms, or SNPs</a> – differences between species in a single <a href="https://www.cancer.gov/publications/dictionaries/cancer-terms/def/base-pair">base pair</a>, the individual building blocks that make up DNA. Even plants with small genomes have <a href="https://www.darwintreeoflife.org/news_item/genomes-great-and-small-the-diversity-of-plants/">millions of base pairs</a>.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/261105/original/file-20190226-150698-16cc1zu.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/261105/original/file-20190226-150698-16cc1zu.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/261105/original/file-20190226-150698-16cc1zu.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=520&fit=crop&dpr=1 600w, https://images.theconversation.com/files/261105/original/file-20190226-150698-16cc1zu.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=520&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/261105/original/file-20190226-150698-16cc1zu.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=520&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/261105/original/file-20190226-150698-16cc1zu.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=653&fit=crop&dpr=1 754w, https://images.theconversation.com/files/261105/original/file-20190226-150698-16cc1zu.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=653&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/261105/original/file-20190226-150698-16cc1zu.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=653&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Bases are the parts of DNA that store information and give DNA the ability to encode an organism’s visible traits. There are four types of bases in DNA: adenine (A), cytosine (C), guanine (G) and thymine (T).</span>
<span class="attribution"><a class="source" href="http://knowgenetics.org/nucleotides-and-bases/">National Human Genome Research Institute</a>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>SNPs work well if you know exactly where they are located in the genome, if there are no mutations that change the SNPs, and if there are plenty of them. While cotton has SNPs that have been identified and verified in specific regions of the genome, they are few and far between. So characterizing cotton hybrids by focusing exclusively on SNPs would result in incomplete information about those hybrids’ genetic composition.</p>
<p>These new genomes open the door for developing <a href="https://doi.org/10.3390/biology1030460">sequencing-based screening</a> of hybrids, which is something I’ve incorporated into my work. In this approach, scientists still use SNPs as a starting point, but they can also sequence the surrounding DNA. This helps to fill in gaps and sometimes discover new, previously undocumented SNPs.</p>
<p>Sequence-based screening helps scientists make more informed and robust maps of the genomes of hybrids. Determining which parts of the genome are from which parent can give breeders a better idea of which plants to cross together to subsequently create better, more productive cotton in every generation.</p>
<h2>What cotton needs to thrive</h2>
<p>As the world’s population rises toward a <a href="https://www.un.org/en/desa/world-population-projected-reach-98-billion-2050-and-112-billion-2100">projected 9.8 billion by 2050</a>, demand for all agricultural products will also rise. But making cotton plants more productive is not the only goal of genetic improvement. </p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/edolx7n0Uuw?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Beyond the U.S., much of the world’s cotton is grown in low- and middle-income countries.</span></figcaption>
</figure>
<p>Climate change is <a href="https://www.ncei.noaa.gov/access/monitoring/climate-at-a-glance/global/time-series/globe/land_ocean/ann/12/1880-2019">raising average global temperatures</a>, and some important cotton-producing regions like the U.S. Southwest are <a href="https://doi.org/10.1038/s41558-022-01290-z">becoming drier</a>. Cotton is already a crop accustomed to heat – our research plots can thrive in temperatures as high as 102 degrees Fahrenheit (39 C) – but one cotton plant requires about <a href="http://www.ugacotton.com/vault/rer/2003/p72.pdf">10 gallons (38 liters) of water</a> over the course of a four-month growing season to achieve its maximum yield potential. </p>
<p>Researchers have started to search for cultivated cotton that can tolerate drought at the <a href="http://dx.doi.org/10.26717/BJSTR.2020.29.004738">seedling stage</a>, and also in <a href="https://doi.org/10.3390/ijms19061614">hybrid lines</a> and <a href="https://doi.org/10.1007/s11032-015-0422-2">genetically modified lines</a>. Scientists are optimistic that they can develop plants that have higher drought resilience. Along with many other cotton breeders around the world, my goal is to create more sustainable and genetically diverse cotton so that this essential crop can thrive in a changing world.</p><img src="https://counter.theconversation.com/content/185284/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Serina DeSalvio does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Plant breeding, informed by genetic analysis, could be critical to the future of one of the world’s oldest crops.Serina DeSalvio, Ph.D. Candidate in Genetics and Genomics, Texas A&M UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1762542022-02-15T14:12:54Z2022-02-15T14:12:54ZSouth Africa should rethink regulations on genetically modified plants<figure><img src="https://images.theconversation.com/files/443976/original/file-20220202-19-k5pxnl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">New technologies can bolster the production of important crops to feed billions of people.</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>Food security is a <a href="https://www.weforum.org/agenda/2016/01/food-security-and-why-it-matters/">global priority</a> – and it is becoming more urgent in the face of climate change, which is already <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0217148">affecting crop productivity</a>. One way to improve food security is to increase <a href="https://www.frontiersin.org/articles/10.3389/fpls.2021.728328/full">crop yields</a>. </p>
<p>But this is not easy. Research has shown that in the past two decades plant breeders have been unable to <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066428">increase yields of staple crops</a> at the rate at which the world’s population is growing.</p>
<p>New technologies are needed to achieve this rate. Over the past decade several novel technologies have been developed. These are known as <a href="https://www.farm-europe.eu/travaux/new-plant-breeding-techniques-what-are-we-talking-about/">New Breeding Techniques</a> and have the potential to hugely help in growing efforts.</p>
<p>Genome editing is one such technique. It allows the precise editing of genomes – that is, the genetic information an organism contains. Scientists worldwide have <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5733845/">embraced the technology</a>. And countries that adopted New Breeding Techniques early have seen a <a href="https://www.frontiersin.org/articles/10.3389/fbioe.2020.00303/full">significant increase in the development</a> of locally relevant products. Current crops under development include ones resistant to specific diseases and insect pests, that are healthier to eat or which are tolerant of drought or heat stress. </p>
<p>Both small, micro and medium enterprises and the public sector in these countries have been involved in developing and using genome edited crops. This should translate to improved economic growth and employment opportunities. </p>
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Read more:
<a href="https://theconversation.com/what-is-crispr-the-gene-editing-technology-that-won-the-chemistry-nobel-prize-147695">What is CRISPR, the gene editing technology that won the Chemistry Nobel prize?</a>
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</em>
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<p>Whatever approach a country chooses, it must be underpinned by regulation. This ensures a framework for the introduction of new products that benefit consumers and stimulate the bio-economy in a sustainable manner. </p>
<p>South Africa’s authorities have taken what we think is an unfortunate approach to regulating genome-edited plants. <a href="https://www.dalrrd.gov.za/doc/Notice%20SA's%20regulatory%20approach%20for%20NBT's%202021.pdf">In October 2021</a> the government classified genome-edited plants as genetically modified crops. This is based on its interpretation of the definition of a genetically modified organism in a <a href="https://www.gov.za/documents/genetically-modified-organisms-act-0">25-year-old piece of legislation</a> rather than on recent science-based risk analysis considerations.</p>
<p>As experts in plant biotechnology we fear that this regulatory approach will greatly inhibit the development of improved crops for South African farmers. It will place an unnecessary regulatory burden on bio-innovators. This will discourage local investment for in-house research and development, as well as projects in the public sector. Local entrepreneurs who aim to enhance local crops’ climate resilience or to develop speciality products for niche markets through genome editing will be thwarted by the need to raise disproportionate funding to fulfil current regulations.</p>
<h2>A technological timeline</h2>
<p>Crop plants are improved by generating genetic variation that leads to beneficial traits. Plant breeders traditionally achieved this by crossing different varieties of the same plant species. These approaches alter many genes; the result is that traditionally-bred plants contain both advantageous and deleterious traits. Removing disadvantageous traits before the crop can be commercialised is a costly, time-consuming process.</p>
<p>In the 1980s, transgenic genetic modification technologies were developed. These rely on pieces of DNA from one species being integrated into the genome of a crop. Such genetically modified (GM) plants are highly regulated internationally. In South Africa the <a href="https://www.gov.za/documents/genetically-modified-organisms-act-0">legislation</a> governing these plants came into force in 1999. The use of GM technology in South Africa – and other countries – has been highly successful. </p>
<p>For example, it has led to <a href="https://www.businesslive.co.za/bd/opinion/2022-01-10-government-stance-will-discourage-agribusiness-use-of-new-plant-breeding-technology/">South Africa doubling maize productivity</a>, making it a net exporter of this commodity. This contributes to food security and also generates foreign income, which reduces the country’s trade deficit. </p>
<p>But the regulations governing GM plants are onerous: only large agricultural biotechnology companies have the resources to commercialise them. This is done to the eliminate risk that GM plants containing new DNA are harmful for health or to the environment. </p>
<p>Because of this, all GM plants licensed for commercial use in South Africa come from a small number of international companies. Not a single locally developed product has been commercialised during the past three decades, despite South Africa being an early adopter of the technology. This hampers the development of novel crops and the improvement of traditional crops, especially for emerging and subsistence farmers in sub-Saharan Africa.</p>
<p>That’s why newer tools like genome editing are so exciting. They can be used to introduce genetic variation for crop improvement in a fraction of the time it would take using conventional methods. Some forms of genome editing are transgenic in nature, while others aren’t because they don’t involve the insertion of foreign DNA into a plant. </p>
<p>This approach mimics the effect of traditional plant breeding, but in a highly targeted manner so that only advantageous traits are introduced. For example, genome editing is being used to produce <a href="https://www.frontiersin.org/articles/10.3389/falgy.2021.821107/full">peanuts, soybean and wheat that do not produce allergens</a>.</p>
<p>It’s working well. Despite the technology only being available for a decade, some crops produced using genome editing are already on the market in some countries, including <a href="https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=17345">soybean</a> and <a href="https://www.nature.com/articles/d41587-021-00026-2#">tomatoes</a> which are healthier for human consumption. </p>
<h2>A proposed regulatory approach</h2>
<p>Regulatory authorities around the world have taken either <a href="https://lsspjournal.biomedcentral.com/articles/10.1186/s40504-017-0048-8">a process- or a product-based approach</a> to regulating GM crop safety. A process-based approach examines how the crop was produced; a product-based approach examines the risks and benefits of the GM crop on a case-by-case basis.</p>
<p>We believe that a product-based approach makes most sense. This is because a process-based approach could lead to the strange situation where two identical plants are governed by very different regulations, just because they were produced by different methods. The added regulatory burden imposed by this approach will also hamper innovation in developing new crops.</p>
<p>Our approach would mean that any plant with extra DNA inserted into the genome would be governed as a GM plant. Plants with no extra DNA added and that are indistinguishable from conventionally bred organisms should be regulated like a conventionally produced crop. </p>
<p>This is the most rational way to regulate these different types of organisms, as it adheres to the principles of science-based risk analysis and good governance. </p>
<p>Many countries, among them <a href="https://crispr-gene-editing-regs-tracker.geneticliteracyproject.org/argentina-crops-food/">Argentina</a>, <a href="https://www.reuters.com/world/china/china-drafts-new-rules-allow-gene-edited-crops-2022-01-25/">China</a>, <a href="https://crispr-gene-editing-regs-tracker.geneticliteracyproject.org/japan-crops-food/">Japan</a>, <a href="https://crispr-gene-editing-regs-tracker.geneticliteracyproject.org/united-states-crops-food/">the US</a>, <a href="https://crispr-gene-editing-regs-tracker.geneticliteracyproject.org/australia-crops-food/">Australia</a>, <a href="https://crispr-gene-editing-regs-tracker.geneticliteracyproject.org/brazil-crops-food/">Brazil</a> and <a href="https://www.aatf-africa.org/wp-content/uploads/2021/02/Government-of-Nigeria-approved-National-Biosafety-Guideline-on-Gene-Editing_Lagos_Nigeria_02-08-2021.pdf">Nigeria</a>, have taken this approach. </p>
<p>Science-based risk analysis should return to the heart of regulation: concrete risk thresholds should define regulatory triggers.</p><img src="https://counter.theconversation.com/content/176254/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>James R Lloyd receives funding from the National Research Foundation, South Africa. </span></em></p><p class="fine-print"><em><span>Dave Berger receives funding from the National Research Foundation, South Africa and The Maize Trust, South Africa. </span></em></p><p class="fine-print"><em><span>Dr Priyen Pillay receives funding from the National Research Foundation, South Africa and the Department of Science & Innovation, South Africa. </span></em></p>A regulatory approach will place an unnecessary burden on bio-innovators. This will discourage local investment for in-house R&D, as well as projects in the public sector.James R Lloyd, Associate Professor, Stellenbosch UniversityDave Berger, Professor in Molecular Plant Pathology, University of PretoriaPriyen Pillay, Senior Researcher, Council for Scientific and Industrial ResearchLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1764912022-02-10T13:36:34Z2022-02-10T13:36:34ZWhat makes a fruit flavorful? Artificial intelligence can help optimize cultivars to match consumer preferences<figure><img src="https://images.theconversation.com/files/444872/original/file-20220207-127289-1kiti9b.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C2448%2C1224&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Aroma plays a big role in flavor perception.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/homemade-skin-care-with-fruits-ingredients-royalty-free-image/1356603644">Lina Darjan/500px via Getty Images</a></span></figcaption></figure><p><em>The <a href="https://theconversation.com/us/topics/research-brief-83231">Research Brief</a> is a short take about interesting academic work.</em></p>
<h2>The big idea</h2>
<p>Which flavors and chemical compounds make a particular variety of fruit more appealing to consumers can be identified and predicted using artificial intelligence, according to <a href="https://doi.org/10.1073/pnas.2115865119">our recently published study</a>.</p>
<p>Flavor, defined by scientists as the interaction between <a href="https://doi.org/10.1152/jn.00050.2004">aroma and taste</a>, is chemically complex. The sugars, acids and bitter compounds in food interact with the taste receptors on our tongues to invoke taste, while volatile compounds that interact with olfactory receptors in our noses are responsible for aroma.</p>
<p>Breeding for flavor is a <a href="https://doi.org/10.1111/j.1469-8137.2010.03281.x">difficult task</a> for many different reasons. For one, fruit and vegetable plant breeding programs need to improve several different traits that appeal to both producers and consumers. Creating the optimal genetic combination that covers all these traits is difficult, so breeding programs often deprioritize flavor to focus on improving disease resistance and increasing yield. Plant breeders must also evaluate hundreds to thousands of potential varieties. Testing a single sample in an objective way requires consumer panels of up to 100 people, which can be expensive and impractical to arrange.</p>
<p>To streamline this process, we developed an algorithm to predict how consumers will rank flavor in tomatoes and blueberries. We created a database containing all known compounds associated with flavor in all varieties of these fruits. Then, we compared this database with existing consumer panel ratings on sweetness, sourness, umami and overall flavor and preference of different varieties. By modeling how consumer ratings varied with the chemical makeup of different varieties of these fruits, this allowed us to determine which compounds most influence flavor perception.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/445500/original/file-20220209-1970-1qm7ugo.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Pie charts showing the proportion of chemical compounds that make up consumer panel ratings of overall liking and intensity of sweetness, sourness and flavor in tomatoes and bluberries" src="https://images.theconversation.com/files/445500/original/file-20220209-1970-1qm7ugo.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/445500/original/file-20220209-1970-1qm7ugo.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=384&fit=crop&dpr=1 600w, https://images.theconversation.com/files/445500/original/file-20220209-1970-1qm7ugo.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=384&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/445500/original/file-20220209-1970-1qm7ugo.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=384&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/445500/original/file-20220209-1970-1qm7ugo.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=483&fit=crop&dpr=1 754w, https://images.theconversation.com/files/445500/original/file-20220209-1970-1qm7ugo.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=483&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/445500/original/file-20220209-1970-1qm7ugo.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=483&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Volatile organic compounds are a big part of what consumer panels use to rate flavor in tomatoes and blueberries.</span>
<span class="attribution"><a class="source" href="https://doi.org/10.1073/pnas.2115865119">Vincent Colantonio and Luís Felipe Ferrao</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">CC BY-NC-ND</a></span>
</figcaption>
</figure>
<p>We found that the volatile organic compounds, or chemicals that form a gas, responsible for aroma are a big part of why people like a given variety. Specifically, we estimated that 42% and 56% of the overall preference score of a variety of tomato or blueberry, respectively, was associated with aroma. </p>
<p>Aroma also played a role in perception of sweetness – volatile compounds contributed 33% to 62% of how consumers rated sweetness. </p>
<p>Finally, we were also able to identify several chemical compounds that most contribute to this flavor and sweetness perception in tomatoes and blueberries.</p>
<h2>Why it matters</h2>
<p>Flavor plays an <a href="https://doi.org/10.1177%2F0956797619872191">important role</a> in which varieties of fruit people choose to eat. We believe that our models can help plant-breeding programs develop more flavorful varieties of fruit by making it easier to determine what objectively makes one variety taste better than another without needing to gather large consumer panels. By identifying exactly what influences how people perceive flavor, plant breeders can focus on optimizing for a specific chemical compound instead of a more subjective rating of flavor.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/445523/original/file-20220209-17-1bqnrwq.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Diagram comparing implementing flavor optimization in a plant breeding program to consumer panels." src="https://images.theconversation.com/files/445523/original/file-20220209-17-1bqnrwq.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/445523/original/file-20220209-17-1bqnrwq.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=334&fit=crop&dpr=1 600w, https://images.theconversation.com/files/445523/original/file-20220209-17-1bqnrwq.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=334&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/445523/original/file-20220209-17-1bqnrwq.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=334&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/445523/original/file-20220209-17-1bqnrwq.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=420&fit=crop&dpr=1 754w, https://images.theconversation.com/files/445523/original/file-20220209-17-1bqnrwq.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=420&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/445523/original/file-20220209-17-1bqnrwq.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=420&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Optimizing for flavor using AI could help cut down the cost of traditional plant breeding with consumer panels.</span>
<span class="attribution"><a class="source" href="https://doi.org/10.1073/pnas.2115865119">Vincent Colantonio and Luís Felipe Ferrao</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">CC BY-NC-ND</a></span>
</figcaption>
</figure>
<h2>What still isn’t known</h2>
<p>Because <a href="https://doi.org/10.1093/jn/133.3.829S">genetic and cultural factors</a> greatly influence taste preferences, it’s likely that flavor preferences will also vary among different ethnic and geographic groups. While our results may be representative for the average U.S. consumer, they may not predict consumer preferences as accurately in Asia, for example. Breeding fruit varieties for specific markets might require additional testing of our flavor database.</p>
<h2>What’s next</h2>
<p>Next steps include breeding fruits to increase the key volatile compounds that determine how much a consumer likes a particular variety.</p>
<p>Our team has previously shown that modern commercial varieties of tomatoes contained <a href="https://doi.org/10.1126/science.aal1556">significantly lower levels</a> of many important chemicals that make heirlooms more flavorful. Restoring these chemicals to the same levels as heirlooms and testing whether that makes these commercial varieties more flavorful is an ongoing area of study.</p>
<h2>How we do our work</h2>
<p>Our lab groups have spent decades developing a framework to understand the genetics and biochemistry of fruit flavor. We conduct highly interdisciplinary research with psychologists, food scientists, geneticists, biochemists and plant breeders. </p>
<p>In our research, we start by identifying what chemicals in a fruit are responsible for flavor preferences. We then determine how the plant makes those chemicals and develop a genetic road map to control how the plant produces these chemicals. Finally, we use molecular breeding to produce flavorful varieties that consumers can fully appreciate.</p>
<p>[<em>The Conversation’s science, health and technology editors pick their favorite stories.</em> <a href="https://memberservices.theconversation.com/newsletters/?nl=science&source=inline-science-favorite">Weekly on Wednesdays</a>.]</p><img src="https://counter.theconversation.com/content/176491/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Marcio Resende receives funding from the National Institute of Food and Agriculture. Marcio Resende is also a shareholder at RAPiD Genomics. </span></em></p><p class="fine-print"><em><span>Harry J. Klee receives funding from the National Science Foundation. </span></em></p>Pinpointing the chemical compounds that make a fruit tasty to consumers can help producers breed for even more flavorful crops.Marcio Resende, Assistant Professor of Horticultural Sciences, University of FloridaHarry J. Klee, Professor of Horticultural Sciences, University of FloridaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1645382021-08-22T12:00:20Z2021-08-22T12:00:20ZHow a few good apples spawned today’s top varieties — and why breeders must branch out<figure><img src="https://images.theconversation.com/files/416637/original/file-20210817-14-1a8zceh.jpg?ixlib=rb-1.1.0&rect=54%2C54%2C4834%2C2522&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">You can plant a seed from a delicious Honeycrisp apple from the grocery store — but the fruit that comes from that tree will not be Honeycrisp. </span> <span class="attribution"><span class="source">(Shutterstock)</span></span></figcaption></figure><p>You take a bite out of your midday apple and it’s just perfect: the right amount of crunch, juice, sweet and sour. You imagine saving its hard brown seeds and planting them in the ground. One day you’ll have a whole tree producing apples just like this one. Or will you? </p>
<p>There’s no reason you can’t plant a seed from your delicious Honeycrisp apple from the grocery store — but the fruit that comes from that tree will not be Honeycrisp apples. </p>
<p>Golden Delicious, Red Delicious, Granny Smith and McIntosh are some of the most widely eaten apples in the world, but they were all discovered more than 100 years ago. As the climate changes, pests and diseases attack trees and fruit, and consumer tastes shift, apple breeding could benefit from harnessing the immense amount of genetic diversity that is available. But only if breeders are willing to take a risk and create new varieties using less familiar apples.</p>
<h2>An orchard of clones</h2>
<p>Apples, like other fruiting plants, start with flowers. The flowers on an apple tree require pollen from another tree in order to set fruit. That fruit will look like the tree it is growing on, but the seeds inside of it now contain two copies of DNA in each cell, one from the tree it grew on and one from the tree the pollen came from. </p>
<p>Crabapple trees are sometimes planted among cultivated apples in commercial orchards to provide pollen. If the apple you picked off a grocery store shelf wasn’t pollinated by a crabapple tree, it could have been pollinated by another apple variety. So, if you plant an apple seed, you might get something really delicious and tasty, which is exactly what apple breeders aim for when they make targeted crosses between two apple trees. But most likely you will not. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A researcher dusts pollen onto an apple flower." src="https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=503&fit=crop&dpr=1 600w, https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=503&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=503&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=632&fit=crop&dpr=1 754w, https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=632&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=632&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The flowers on an apple tree require pollen from another to set fruit. That can be done by hand, or by pollinators, such as bees.</span>
<span class="attribution"><span class="source">(Beatrice Amyotte)</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>The odds of getting something delicious aren’t great even when you know who the two parents are. <a href="https://orgprints.org/id/eprint/13698/1/220-225.pdf">One German apple breeding program started with 52,000 seeds</a> and it was only after 26 years that it finally released three new apple varieties.</p>
<p>If we can’t plant their seeds, how is it possible to grow more Granny Smith apple trees? The secret is clonal propagation. </p>
<p>Clonal propagation involves taking a cutting of wood that includes a bud from a desirable tree to grow a new tree, called a clone. Any apple orchard composed of one variety, like Gala, Granny Smith or Honeycrisp, is actually an orchard of clones. </p>
<figure class="align-center ">
<img alt="Small pots of apple seedlings in a greenhouse." src="https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Planting an apple seed will give you a seedling that has two parents: the tree the fruit came from, and the tree the pollen came from.</span>
<span class="attribution"><span class="source">(Beatrice Amyotte)</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Clonal propagation is so successful that <a href="https://doi.org/10.3732/ajb.1000522">more than 75 per cent of perennial fruit crops are grown this way</a>. But this means that only a handful of apple varieties are grown worldwide.</p>
<p>For example, <a href="https://agriculture.canada.ca/en/canadas-agriculture-sectors/horticulture/market-information-infohort/apple-reports?menupos=01.02.02.05">according to Canadian Apple Storage Reports</a>, Canada’s top four apple varieties (McIntosh, Ambrosia, Honeycrisp and Gala) were responsible for over 50 per cent of apple production, based on weight, for the 2020-21 crop year. </p>
<h2>Closely related</h2>
<p><a href="https://doi.org/10.1038/s41438-020-00441-7">In a recent study</a>, my colleagues and I looked at <a href="https://www.ars.usda.gov/northeast-area/geneva-ny/plant-genetic-resources-unit-pgru/docs/apple-collection/">one of the most diverse collections of apples in the world</a>, located in Geneva, N.Y. <a href="http://www.pubhort.org/aps/74/v74_n2_a4.htm">This living collection contains thousands of apple trees</a>, including both the domesticated apple we eat and its wild relatives. </p>
<p>Apple varieties have to be preserved in living collections because they are clonally propagated and not grown from seed, so <a href="https://doi.org/10.2135/cropsci2019.05.0353">collections like the one in Geneva are critical to conserving and maintaining apple diversity</a>. </p>
<p>Our research found that some of the most popular apples are often used in apple breeding, with both Red Delicious and Golden Delicious having over 60 putative first-degree relatives (parent, sibling, offspring) in the collection. </p>
<p>Sometimes using a commercially successful parent works well. For example, Gala is the offspring of Golden Delicious, and Red Delicious is one of its grandparents. </p>
<p>In our study, we found seven of the top eight apple varieties in the United States were interconnected by a series of first-degree relationships. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Diagram showing the relationships of the top nine apple varieties" src="https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=486&fit=crop&dpr=1 600w, https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=486&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=486&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=611&fit=crop&dpr=1 754w, https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=611&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=611&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Network of first-degree relationships with the top eight apple varieties sold in the United States. Each apple is represented by a dot and each line represents a first-degree relationship.</span>
<span class="attribution"><a class="source" href="https://doi.org/10.1038/s41438-020-00441-7">(Zoë Migicovsky, modified)</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>The only exception was Honeycrisp, an apple variety with a unique and crisp texture. <a href="https://doi.org/10.1038/hortres.2017.3">Honeycrisp’s parents were commercially unsuccessful</a>: Keepsake and a University of Minnesota selection called MN1627, which is no longer available and not in the apple collection we studied. However, if it were, Honeycrisp would be linked to the remaining top apples because one of the parents of MN1627 was Golden Delicious. </p>
<h2>Missed apple-tunities</h2>
<p>By using the same handful of parents repeatedly in apple breeding, we are missing out on a lot of the unusual and wonderful variation that is out there. Commercial orchards have the same apple variety planted side by side. But <a href="http://www.cultivatingdiversity.org">our research orchard in Kentville, N.S.,</a> has more than 1,000 unique apple trees. Walking among these trees in the fall, you can see, smell and taste the possibilities. </p>
<p>All the Honeycrisps in the world can be traced back to one single tree. Plant diversity is the foundation of crop improvement, and by expanding the breeding pool, apple breeders can introduce new traits for consumers and improve crop resilience in response to a changing climate. </p>
<p>Apple breeding is about taking two parents, dusting the pollen from one tree onto the flower of another and creating something brand new. This is the same process that happens (with the help of bees) to the trees that grow the apples you buy at the grocery store. So if you were to plant a seed from one of them in your garden? Well, who knows how far the apple would fall from the tree.</p><img src="https://counter.theconversation.com/content/164538/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Zoë Migicovsky receives funding from National Science Foundation Plant Genome Research Program 1546869.</span></em></p>Apple breeders have created crisp, juicy and tasty fruits, but the limited varieties leave crops vulnerable to diseases, pests and climate change. Introducing new traits could improve crop resilience.Zoë Migicovsky, Postdoctoral fellow, Faculty of Agriculture, Dalhousie UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1300412020-01-30T13:13:31Z2020-01-30T13:13:31ZModern tomatoes are very different from their wild ancestors – and we found missing links in their evolution<figure><img src="https://images.theconversation.com/files/312304/original/file-20200128-81416-1odt8n2.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C5000%2C2971&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Tomatoes' ancestors looked very different.</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/flatlay-fresh-colorful-ripe-fall-summer-1124959727"> Foxys Forest Manufacture/Shutterstock</a></span></figcaption></figure><p><em>The Research Brief is a short take on interesting academic work.</em></p>
<p><strong>The Big Idea:</strong> The tomato’s path from wild plant to household staple is much more complex than researchers have long thought. For many years, scientists believed that humans domesticated the tomato in two major phases. First, native people in South America cultivated blueberry-sized wild tomatoes about 7,000 years ago to breed a plant with a cherry-sized fruit. Later, people in <a href="https://en.wikipedia.org/wiki/Mesoamerica">Mesoamerica</a> bred this intermediate group further to form the large cultivated tomatoes that we eat today. </p>
<p>But in a 2020 study, we show that the cherry-sized tomato likely <a href="https://doi.org/10.1093/molbev/msz297">originated in Ecuador around 80,000 years ago</a>. No human groups were domesticating plants that long ago, so this implies that it started as a wild species, although people in Peru and Ecuador probably cultivated it later. </p>
<p>We also found that two subgroups from this intermediate group spread northward to Central America and Mexico, possibly as weedy companions to other crops. As this happened, their fruit traits changed radically. They came to look more like wild plants, with smaller fruits than their South American counterparts and higher levels of citric acid and beta carotene. </p>
<p>We were surprised to find that modern cultivated tomatoes seem most closely related to this wild-like tomato group, which is still found in Mexico, although farmers don’t deliberately cultivate it. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/312295/original/file-20200128-81341-1aqkfhm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/312295/original/file-20200128-81341-1aqkfhm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/312295/original/file-20200128-81341-1aqkfhm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=109&fit=crop&dpr=1 600w, https://images.theconversation.com/files/312295/original/file-20200128-81341-1aqkfhm.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=109&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/312295/original/file-20200128-81341-1aqkfhm.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=109&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/312295/original/file-20200128-81341-1aqkfhm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=137&fit=crop&dpr=1 754w, https://images.theconversation.com/files/312295/original/file-20200128-81341-1aqkfhm.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=137&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/312295/original/file-20200128-81341-1aqkfhm.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=137&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Average fruit size in the cultivated tomato in comparison with its semi-domesticated and fully wild relatives.</span>
<span class="attribution"><span class="source">Hamid Razifard</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p><strong>Why it matters:</strong> This research has direct implications for crop improvement. For example, some intermediate tomato groups have high levels of glucose, which makes the fruit sweeter. Breeders could use those plants to make cultivated tomatoes more attractive to consumers. </p>
<p>We also saw signals that some varieties in this intermediate group had traits that promoted disease resistance and drought tolerance. Those plants could be used to breed hardier tomatoes.</p>
<p><strong>What still isn’t known:</strong> We don’t know how the intermediate group of tomatoes spread from South America to Central America and Mexico. Birds may have eaten the fruits and excreted the seeds elsewhere, or humans may have cultivated or traded them.</p>
<p>Another question is why this intermediate group “regressed” and lost so many domestication traits once it spread north. Natural selection in new northern habitats may have actively favored tomatoes with more wild-like traits. It also could be that humans weren’t breeding these plants and selecting for domestication traits, such as large fruits, which may require plants to use more energy than they would put into fruiting naturally.</p>
<p><strong>How we do our work:</strong> We <a href="https://scholar.google.com/citations?user=tNvKhWwAAAAJ&hl=en">reconstruct tomato history</a> by <a href="https://scholar.google.com/citations?user=E_vnipYAAAAJ&hl=en">sequencing the genomes</a> of wild, intermediate and domesticated tomato varieties. We also carry out population genomic analyses, in which we use models and statistics to deduce the changes that have occurred to tomatoes over time.</p>
<p>This work involves writing a lot of computer codes to analyze large amounts of data and look at patterns of variation in DNA sequences. We also work with other scientists to grow tomato samples and record data on many traits, such as fruit size, sugar content, acid content and flavor compounds. </p>
<p><strong>What else is happening in the field:</strong> Feeding a growing human population will require improving crop yields and quality. To do this, scientists need to know more about plant genes that are involved in phenomena such as fruit development and flavor and disease resistance. </p>
<p>For example, research led by <a href="http://lippmanlab.labsites.cshl.edu/people/">Zachary Lippman</a> at the <a href="https://www.cshl.edu/">Cold Spring Harbor Laboratory</a> in New York is using genome editing to manipulate traits that can help improve tomato yield. By tweaking genes native to two popular varieties of tomato plants, they have devised a rapid method to make the plants flower and produce ripe fruit more quickly. This means more plantings per growing season, which increases yield. It also means that the plant can be grown in latitudes more northerly than currently possible – an important attribute as the Earth’s climate warms.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/Jem3hP734uA?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Gene editing has produced tomatoes that flower and ripen weeks earlier.</span></figcaption>
</figure>
<p><strong>What’s next for you:</strong> Our research provides an atlas of candidates for future tomato gene function studies. We now can identify which genes were important at each stage of domestication history, and discover what they do. We also can search for beneficial alleles, or variants of specific genes, that may have been lost or diminished as the tomato was domesticated. We want to find out whether some of those lost variants could be used to improve growth and desirable traits in cultivated tomatoes.</p><img src="https://counter.theconversation.com/content/130041/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Hamid Razifard receives funding from National Science Foundation of USA. </span></em></p><p class="fine-print"><em><span>Ana Caicedo receives funding from the National Science Foundation (NSF) of the USA and the National Institute of Food and Agriculture (NIFA) of the USA. </span></em></p>Through genetic detective work, scientists have identified missing links in the tomato’s evolution from a wild blueberry-sized fruit in South America to the larger modern tomato of today.Hamid Razifard, Postdoctoral Researcher in Biology, UMass AmherstAna Caicedo, Associate Professor of Biology, UMass AmherstLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1267632019-11-28T03:37:53Z2019-11-28T03:37:53ZThe case of the pirated blueberries: courts flex new muscle to protect plant breeders’ intellectual property<figure><img src="https://images.theconversation.com/files/304187/original/file-20191128-176618-zrwazf.jpg?ixlib=rb-1.1.0&rect=0%2C8%2C3640%2C2572&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Not all blueberries are the same. A variety called Ridley 1111 is at the centre of an important lawsuit for intellectual property and plants.</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>A few weeks ago, the Federal Court of Australia ordered <a href="https://www.abc.net.au/news/2019-11-08/federal-court-decision-on-blueberry-case-a-wake-up-call/11685158">a farmer in New South Wales</a> to pay A$290,000 to a blueberry-producing company because he had grown and sold a proprietary variety of the fruit without permission. </p>
<p>At issue in the blueberry case were questions of intellectual property. Who owns the plant varieties that are commercialised in Australia and other countries? Who can grow them? If you are the owner of a particular variety, how can you prove someone else has grown it without your permission, and what can you do about it? </p>
<p>The case is an important one in an area of law that may affect how we develop new varieties of plants. This type of work is important to address challenges such as food security and climate change adaptation.</p>
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Read more:
<a href="https://theconversation.com/will-patenting-crops-help-feed-the-hungry-3405">Will patenting crops help feed the hungry?</a>
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<p>Australia’s intellectual property law was changed last February to give courts more options to protect plant breeders’ rights. This case is one of the first to take those revisions into account, which give courts more options to impose sanctions for infringements.</p>
<p>The plant breeders’ rights system works like a patent or trademark for plant varieties: when breeders create a new variety, they can register it and obtain exclusive rights to grow and sell it. </p>
<p>The system is designed to encourage breeders – who may include scientists, companies, or growers themselves – to develop innovative plant varieties. In other words, the possibility of commercial exclusivity functions as a profit incentive. </p>
<h2>The case of Ridley 1111</h2>
<p>The recent case (<em>Mountain Blue Orchards v. Chellew</em>) was about a blueberry variety named Ridley 1111. It has appealing characteristics for growers and consumers alike: the berries ripen early and have a notable dark blue colour and firmness. </p>
<p>The NSW-based growers Mountain Blue Orchards obtained plant breeders’ rights for Ridley 1111 in September 2010. </p>
<p>This March, Mountain Blue filed a claim before the Federal Court. They alleged that a grower based near Grafton in NSW named Jason Chellew had obtained, grown, and sold Ridley 1111 blueberries without authorisation. </p>
<p>Earlier this month, the Federal Court found in Mountain Blue’s favour. The court ordered Chellew to destroy the infringing plants and pay Mountain Blue A$290,000 in damages. This sum included compensatory damages, additional damages, interest, and litigation costs. </p>
<h2>How do you prove someone has pirated your plants?</h2>
<p>Establishing infringement for plant varieties is more difficult than for products protected with other kinds of intellectual property. </p>
<p>If someone is using your trademarked brand name, or is selling a widget that you patented, it is relatively straightforward to show infringement by deconstructing these things into their component elements. </p>
<p>In contrast, plants are complex living organisms that change based on human and non-human influences alike. </p>
<p>DNA testing played a role in the Ridley 1111 case, but this alone may not be enough to prove infringement. A protected variety may have only minor genetic differences from other varieties. Likewise, two individual plants of the same variety may have tiny genetic differences due to random mutations. </p>
<p>Furthermore, plant breeders’ rights infringement may occur at a small scale over diffuse areas, making it difficult for rights owners to enforce their rights. </p>
<p>Finally, it is difficult to collect evidence of possible infringement. If plants are grown on private property they can be hard to see, and third parties may be reluctant to help. Rights owners may also be wary of possible adverse business or public image consequences from pursuing a case. </p>
<h2>A new kind of damages</h2>
<p>Another difficulty in plant breeders’ rights infringement cases relates to the limits of how much impact even a successful case might have.</p>
<p>Until last February, courts could only award damages based on a calculation of the actual loss suffered by the rights owner. It can be difficult to put a number on this loss, which meant that many in the agricultural industry saw plant breeders’ rights infringement as having few practical consequences. </p>
<p>The Ridley 1111 case is a sign that this may be changing, however. It is one of the first the Federal Court has considered since February’s comprehensive amendments to Australian intellectual property law, which now allows judges to award additional damages. </p>
<p>Courts can now consider several factors when setting damages in an infringement case, including how flagrant the infringement is and the need to deter future infringements. This brings plant breeders’ rights into line with other forms of intellectual property law such as patents and trademarks.</p>
<p>The resulting penalties can now be much higher. This could encourage growers to pursue licensing deals with the owners of protected varieties, when in the past they might have risked a lawsuit to save on royalty payments. </p>
<p>However, this assumes growers are aware of the possibility of heightened penalties, and that rights owners can prove that infringement actually occurred. </p>
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Read more:
<a href="https://theconversation.com/to-feed-the-world-in-2050-we-need-to-build-the-plants-that-evolution-didnt-127316">To feed the world in 2050 we need to build the plants that evolution didn't</a>
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<h2>Encouraging innovation</h2>
<p>What effect will these changes have on the ground? It is probably too ambitious to argue that these changes alone will lead to increased innovation in plant breeding, as some industry groups have claimed.</p>
<p>The development of new plant varieties involves significant investments of time and other resources. What’s more, breeding often relies on substantial collaborations between the private sector and public or academic research institutions. </p>
<p>So while the possibility of obtaining additional damages in an infringement action may have some effect, other factors will continue to affect the development of new plant varieties. </p>
<p>These include the ongoing need for governmental support of plant breeding initiatives, the development of effective partnerships between the public and private sectors, and an accurate understanding of the kinds of crops that would be best suited to Australia’s climatic and agronomic peculiarities and to the desires of Australian consumers.</p><img src="https://counter.theconversation.com/content/126763/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>David J Jefferson holds the position of Postdoctoral Research Fellow with the ARC Laureate Project 'Harnessing Intellectual Property to Build Food Security' at the University of Queensland School of Law. </span></em></p>Bigger penalties for pirating plants could help encourage growers to develop new varieties.David Jefferson, Research Fellow, The University of QueenslandLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1123062019-02-25T19:08:45Z2019-02-25T19:08:45ZEarly sowing can help save Australia’s wheat from climate change<figure><img src="https://images.theconversation.com/files/260573/original/file-20190224-195873-57g5o.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Timing is of the essence when it comes to growing wheat.</span> <span class="attribution"><span class="license">Author provided</span></span></figcaption></figure><p>Climate change has already <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.13604">reduced yields for Australian wheat growers</a>, thanks to increasingly unreliable rains and hostile temperatures. But our new research offers farmers a way to adapt.</p>
<p>By sowing much earlier than they currently do, wheat growers can potentially increase yields again. However, our study <a href="https://www.nature.com/articles/s41558-019-0417-9">published today in Nature Climate Change</a> shows that to do this they need new varieties that allow them more leeway to vary their sowing dates in the face of increasingly erratic rainfall.</p>
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Read more:
<a href="https://theconversation.com/changing-climate-has-stalled-australian-wheat-yields-study-71411">Changing climate has stalled Australian wheat yields: study</a>
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<p>Sowing wheat is a matter of delicate timing. Seeds of current varieties need to be planted at just such a time so that, months later, the plants flower during a window of just 1-2 weeks, known as the <a href="https://www.sciencedirect.com/science/article/pii/S0378429017306895">optimal flowering period</a>.</p>
<p>In Australia’s wheat belt this window is generally in early spring. At this time the soil is moist after the cool, wet winter; days are getting longer and sunnier; maximum temperatures are still relatively low; and frosts are less frequent. If crops flower outside the optimal window, yields decline sharply.</p>
<h2>Crops and colonies</h2>
<p>When Europeans first started trying to grow wheat in Australia, they used varieties that were suited to the cool, wet climate of northern Europe, where the optimal flowering period is in summer. These varieties were much too slow to flower in Australian conditions, and yields were very low. Wheat breeder <a href="http://adb.anu.edu.au/biography/farrer-william-james-6145">William Farrer</a> used faster-developing wheats from India to create the <a href="https://www.nma.gov.au/defining-moments/resources/federation-wheat">Federation</a> variety, which revolutionised wheat production in Australia, earning Farrer the ultimate honour of <a href="https://www.williamfarrerhotel.com.au/">having a pub named after him</a>.</p>
<p>Federation wheat is a “spring wheat”, moving rapidly through its life cycle regardless of when it is planted. If you sow it earlier, it flowers earlier. For more than a century Australian wheat breeders have bred spring wheats, allowing growers to adjust their sowing time to get their crops to flower during the optimal period. Anzac Day has traditionally been the start of sowing season, after autumn rains have wet the soil enough for seeds to germinate.</p>
<p>Here is where climate change is causing a problem. If farmers sow later than mid-May, the wheat is likely to miss its spring flowering window. But southern Australia has experienced <a href="https://journals.ametsoc.org/doi/full/10.1175/JCLI-D-12-00035.1">declining April and May rainfall</a>, making it harder for growers to <a href="https://rmets.onlinelibrary.wiley.com/doi/abs/10.1002/joc.1833">sow and establish crops at the right time</a>. This in turn means crops flower too late the following spring, meaning yields are reduced by drought and heat.</p>
<p>Growers could start sowing earlier, and use stored soil water from summer rain (which hasn’t declined and has even <a href="http://www.publish.csiro.au/cp/CP11268">increased at some locations</a>), but current spring wheat varieties would flower too early to yield well. For farmers to sow earlier, they need a different sort of wheat in which development is slowed down by an environmental cue. One such environmental cue is called <a href="https://en.wikipedia.org/wiki/Vernalization">vernalisation</a>. Plants that are sensitive to vernalisation will not flower until they have experienced a period of cold temperatures. These strains are thus called “winter wheats”.</p>
<p>Ironically enough, the wheat varieties that Europeans first brought to Australia were winter wheats, but they were further slowed by sensitivity to <a href="https://en.wikipedia.org/wiki/Photoperiodism">day length</a> which made them too slow to reach the earlier flowering times needed in the hotter, drier colony.</p>
<p>But this problem can be sidestepped by using a “fast winter wheat”, which is sensitive to vernalisation but not to day length. Our <a href="https://www.sciencedirect.com/science/article/pii/S0378429018300819">previous research</a> showed that this type of wheat was very suited to Australian conditions – it can be sown early but still flower at the right time. In fact, the vernalisation requirement means that this wheat can be sown over a much broader range of dates and experience fluctuating temperatures, and still flower at the right time. </p>
<h2>Yielding results</h2>
<p>In our new research, we developed different lines of wheat that varied in their response to vernalisation and day length, and grew them across the wheat belt to compare which ones would yield best at earlier sowing times. </p>
<p>We found that a fast winter wheat performed best over most of the wheatbelt, and on average yielded 10% more than spring wheat when they flower at the same time. </p>
<p>We then used computer simulations to investigate how these crops would perform at the scale of an entire farm. Our results showed that if Australian growers had access to adapted winter varieties in addition to spring varieties, they could start sowing earlier in seasons where there was an opportunity. If the rains come early, farmers can use the winter wheat; if they come late they can switch to the spring wheat, which yields better than winter wheat at late sowing times.</p>
<p>This would mean that more area of crop would be planted on time, and yields would increase as a result. If realised, this could increase national wheat production by about 20%, or roughly 7.1 million tonnes.</p>
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Read more:
<a href="https://theconversation.com/australias-farming-future-can-our-wheat-keep-feeding-the-world-14678">Australia's farming future: can our wheat keep feeding the world?</a>
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<p>The main hurdle is that growers do not currently have access to suitable winter wheats. Breeding companies have <a href="https://www.agtbreeding.com.au/news/longsword-opens-the-sowing-window-in-medium-to-low-rainfall-areas-across-australia">started work on them</a>, but it will be several years before suitably high-quality varieties become available.</p>
<p>Australian growers urgently need to keep pace with climate change. Although Australia only produces 4% of the world’s wheat, it accounts for 10% of exports and is thus important in determining global supply and price. If global wheat supply is low, prices rise, and it becomes unaffordable for many of the world’s poorest people, potentially causing malnutrition and civil unrest. Steeply rising wheat prices were <a href="http://www.fao.org/3/a-I7695e.pdf">among the factors</a> behind the food riots that broke out in more than 40 countries in 2007-08, which helped to trigger the Arab Spring uprisings of 2010-12.</p>
<p>The world’s poorest people deserve to be able to buy wheat. But Australian wheat farmers also need to earn a decent living and stay internationally competitive. The only way to meet all these needs is to keep production costs low – and increasing yields by sowing the right wheat cultivars for Australia’s changing climate is one way to go about it.</p><img src="https://counter.theconversation.com/content/112306/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>James Hunt receives funding from the Grains Research & Development Corporation (GRDC). </span></em></p>Australian wheat growers need to boost yields to stay competitive in the face of climate change. They could do this by sowing earlier, but need new varieties of wheat to help them do it.James Hunt, Associate Professor, La Trobe UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/770452017-05-08T12:00:18Z2017-05-08T12:00:18ZScientists have mapped the DNA of tea – and it could stave off a pending crisis<figure><img src="https://images.theconversation.com/files/168356/original/file-20170508-20732-jvnxuo.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://unsplash.com/@ravipinisetti?photo=ySQXoZLAsmc">Ravi Pinisetti/Unsplash</a></span></figcaption></figure><p>The world’s <a href="http://www.fao.org/economic/est/est-commodities/tea/en/">most popular drink</a> (after water) is under threat. We already know much about the threat of climate change to staple crops such as wheat, maize and rice, but the impact on tea is just coming into focus. Early research indicates that tea grown in some parts of Asia could see <a href="https://www.scientificamerican.com/article/global-warming-changes-the-future-for-tea-leaves/">yields decline</a> by up to 55% thanks to drought or excessive heat, and the quality of the tea is also falling.</p>
<p>The intensive use of pesticides and chemical fertilisers in tea plantations has also led to <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2984095/">soil degradation</a> at an average annual rate of 2.8%. This also causes chemical runoff into waterways, which can lead to serious problems for human health and the environment.</p>
<p>However, hope may be on the horizon now that scientists at the Kunming Institute of Botany at the Chinese Academy of Sciences have <a href="http://bit.ly/2q7zvyi">sequenced the entire tea genome</a>. Mapping the exact sequence of DNA in this way provides the foundation for extracting all the genetic information needed to help breed and speed up development of new varieties of the tea plant. And it could even help improve the drink’s flavour and nutritional value.</p>
<p>In particular, the whole tea tree genome reveals the genetic basis for tea’s tolerance to environmental stresses, pest and disease resistance, flavour, productivity and quality. So breeders could more precisely produce better tea varieties that produce higher crop yields and use water and nutrients more efficiently. And they could do this while widening the genetic diversity of tea plants, improving the overall health of the tea plant population.</p>
<p>This is also an important milestone for scientists because it provides a deeper understanding of the complex evolution and the functions of key genes associated with stress tolerance, tea flavour and adaptation. </p>
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<img alt="" src="https://images.theconversation.com/files/168363/original/file-20170508-20738-eu82um.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/168363/original/file-20170508-20738-eu82um.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/168363/original/file-20170508-20738-eu82um.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/168363/original/file-20170508-20738-eu82um.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/168363/original/file-20170508-20738-eu82um.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/168363/original/file-20170508-20738-eu82um.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/168363/original/file-20170508-20738-eu82um.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">Mmm, you can really taste the flavonoids.</span>
<span class="attribution"><a class="source" href="https://stocksnap.io/photo/B6CJ1F4MSR">Matthew Henry/Stocksnap</a></span>
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<p>The new tea genome is very large, with nearly 37,000 genes – more than four times the size of the coffee plant genome. The process of evolution by natural selection has already helped the tea plant develop hundreds of genes related to resisting environmental stress from drought and disease.</p>
<p>These genes are like molecular markers that scientists can identify when selecting plants for use in breeding. This will allow them to be more certain that the next generation of plants they produce will have the genes and so the traits they want, speeding up <a href="https://link.springer.com/article/10.1007/s10681-010-0169-0">the breeding process</a>. Sequencing the genome also raises the possibility of using <a href="https://theconversation.com/how-gm-crops-can-help-us-to-feed-a-fast-growing-world-71112">genetic modification</a> (GM) technologies to turn on or enhance desirable genes (or turn off undesirable ones). </p>
<p>The same principles could also be used to enhance the nutritional or medicinal value of certain tea varieties. The genome sequence includes genes associated with biosynthesis. This is the production of the proteins and enzymes involved in creating the compounds that make tea so drinkable, such as <a href="http://www.ccsenet.org/journal/index.php/jfr/article/viewFile/45729/24980">flavonoids, terpenes and caffeine</a>. These are closely related to the aroma, flavour and quality of tea and so using genetic breeding techniques could help improve the taste of tea and make it more flavourful or nutritional.</p>
<p>For example, we could also remove the caffeine biosynthetic genes from the tea plant to help breeding of low or non-caffeine varieties. By boosting certain compounds at the same time, we could make tea healthier and develop entirely new flavours to make caffeine tea more appealing.</p>
<p>An estimated 5.56m tons of tea is commercially grown on more than 3.8m hectares of land (<a href="http://www.top-news.top/news-12896789.html">as of 2014</a>). And its huge cultural importance, as well as its economic value, mean securing a sustainable future for tea is vitally important for millions of people. So the first successful sequencing of the tea genome is a crucial step to making tea plants more robust, productive and drinkable in the face of massive environmental challenges.</p><img src="https://counter.theconversation.com/content/77045/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Chungui Lu does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Sequencing the tea plant’s genome could help scientists breed new varieties that thrive in the degrading soil of tea farms.Chungui Lu, Professor of Sustainable Agriculture., Nottingham Trent UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/642062016-10-24T01:59:53Z2016-10-24T01:59:53ZWith the familiar Cavendish banana in danger, can science help it survive?<figure><img src="https://images.theconversation.com/files/142716/original/image-20161021-1763-13xoceb.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Facing down a future with no bananas.</span> <span class="attribution"><a class="source" href="https://www.flickr.com/photos/35652152@N07/28004881235">Chris Richmond</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">CC BY-NC-ND</a></span></figcaption></figure><p>The banana is the world’s most popular fruit crop, with <a href="http://www.fao.org/economic/worldbananaforum/statistics/en/">over 100 million metric tons produced annually</a> in over 130 <a href="http://www.fao.org/docrep/019/i3627e/i3627e.pdf">tropical and subtropical countries</a>. Edible bananas are the result of a genetic accident in nature that created the seedless fruit we enjoy today. </p>
<p>Virtually all the bananas sold across the Western world belong to the <a href="http://www.dpi.nsw.gov.au/__data/assets/pdf_file/0007/251899/Banana-growing-guide-cavendish-bananas-1.pdf">so-called Cavendish subgroup</a> of the species and are <a href="http://doi.org/10.1093/aob/mcm191">genetically nearly identical</a>. These bananas are sterile and <a href="http://www.dpi.nsw.gov.au/__data/assets/pdf_file/0006/251898/Banana-growing-guide-cavendish-bananas-Complete.pdf">dependent on propagation via cloning</a>, either by using suckers and cuttings taken from the underground stem or through modern tissue culture.</p>
<p>The familiar bright yellow Cavendish banana is ubiquitous in supermarkets and fruit bowls, but it is in imminent danger. The vast worldwide monoculture of genetically identical plants leaves the Cavendish <a href="http://dx.doi.org/10.1371/journal.ppat.1005197">intensely vulnerable to disease outbreaks</a>. </p>
<p>Fungal diseases severely devastated the banana industry once in history and it could soon happen again if we do not resolve the cause of these problems. Plant scientists, including us, are working out the genetics of wild banana varieties and banana pathogens as we try to prevent a Cavendish crash. </p>
<h2>The cautionary tale of ‘Big Mike’</h2>
<p>One of the most prominent examples of genetic vulnerability comes from the banana itself. Up until the 1960s, Gros Michel, or “Big Mike,” was the prime variety grown in commercial plantations. Big Mike was so popular with consumers in the West that the banana industry established ever larger monocultures of this variety. Thousands of hectares <a href="http://www.apsnet.org/publications/apsnetfeatures/Pages/PanamaDiseasePart1.aspx">of tropical forests</a> in Latin America were converted into <a href="http://www.penguinrandomhouse.com/books/299017/banana-by-dan-koeppel/9780452290082">vast Gros Michel plantations</a>.</p>
<p>But Big Mike’s popularity led to its doom, when a pandemic whipped through these plantations during the 1950s and ‘60’s. A fungal disease called Fusarium wilt or Panama disease nearly wiped out the Gros Michel and brought the global banana export industry to the <a href="http://www.agriculturedefensecoalition.org/sites/default/files/pdfs/3T_2000_Banana_Destructive_Panama_Disease_2000.pdf">brink of collapse</a>. A soilborne pathogen was to blame: The fungus <em>Fusarium oxysporum</em> f.sp. <em>cubense</em> (Foc) <a href="http://dx.doi.org/10.1094/PHYTO-04-15-0101-RVW">infected the plants’ root and vascular system</a>. Unable to transport water and nutrients, the plants wilted and died.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/142717/original/image-20161021-1778-1ihcafz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/142717/original/image-20161021-1778-1ihcafz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/142717/original/image-20161021-1778-1ihcafz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/142717/original/image-20161021-1778-1ihcafz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/142717/original/image-20161021-1778-1ihcafz.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/142717/original/image-20161021-1778-1ihcafz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/142717/original/image-20161021-1778-1ihcafz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/142717/original/image-20161021-1778-1ihcafz.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">A cross-section of a banana plant, infected with the fungus that causes Fusarium wilt.</span>
<span class="attribution"><span class="source">Gert Kema</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>Fusarium wilt is <a href="http://www.promusa.org/Fusarium+wilt">very difficult to control</a> – it spreads easily in soil, water and infected planting material. Fungicide applications in soil or in the plant’s stem are as of yet ineffective. Moreover, the fungus can persist in the soil for several decades, thus prohibiting replanting of susceptible banana plants. </p>
<h2>Is history repeating itself?</h2>
<p>Cavendish bananas are resistant to those devastating Fusarium wilt Race 1 strains, so were able to replace the Gros Michel when it fell to the disease. Despite being less rich in taste and logistical challenges involved with merchandising this fruit to international markets at an acceptable quality, <a href="http://www.apsnet.org/publications/apsnetfeatures/Documents/2005/PanamaDisease2.pdf">Cavendish eventually replaced Gros Michel</a> in commercial banana plantations. The <a href="http://www.fao.org/fileadmin/templates/est/COMM_MARKETS_MONITORING/Bananas/Documents/Banana_Information_Note_2014-_rev.pdf">entire banana industry</a> was restructured, and to date, Cavendish accounts for <a href="http://www.fao.org/docrep/007/y5102e/y5102e04.htm">47 percent of the bananas grown worldwide</a> and <a href="http://www.newyorker.com/magazine/2011/01/10/we-have-no-bananas">99 percent of all bananas sold commercially for export</a> to developed countries. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/142718/original/image-20161021-1763-1fza2aq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/142718/original/image-20161021-1763-1fza2aq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/142718/original/image-20161021-1763-1fza2aq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=800&fit=crop&dpr=1 600w, https://images.theconversation.com/files/142718/original/image-20161021-1763-1fza2aq.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=800&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/142718/original/image-20161021-1763-1fza2aq.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=800&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/142718/original/image-20161021-1763-1fza2aq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1005&fit=crop&dpr=1 754w, https://images.theconversation.com/files/142718/original/image-20161021-1763-1fza2aq.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1005&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/142718/original/image-20161021-1763-1fza2aq.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1005&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Bananas in Costa Rica affected by Black Sigatoka.</span>
<span class="attribution"><span class="source">Gert Kema</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>But the Cavendish unfortunately has its own weaknesses – most prominently susceptibility to <a href="http://apsjournals.apsnet.org/doi/abs/10.1094/PDIS.2003.87.3.208">a disease called Black Sigatoka</a>. The fungus <em>Pseudocercospora fijiensis</em> attacks the plants’ leaves, causing cell death that affects photosynthesis and leads to a reduction in fruit production and quality. If Black Sigatoka is left uncontrolled, <a href="http://doi.org//10.1111/j.1364-3703.2010.00672.x">banana yields can decline</a> by <a href="http://www.apsnet.org/edcenter/intropp/lessons/fungi/ascomycetes/Pages/BlackSigatoka.aspx">35 to 50 percent</a>.</p>
<p>Cavendish growers currently manage Black Sigatoka through a combination of pruning infected leaves and <a href="http://doi.org/10.17660/ActaHortic.2009.828.16">applying fungicides</a>. Yearly, it can take 50 or more applications of chemicals to control the disease. Such heavy use of fungicides has negative impacts on the environment and the occupational health of the banana workers, and increases the costs of production. It also helps select for survival the strains of the fungus with <a href="http://www.frac.info/working-group/banana-group">higher levels of resistance to these chemicals</a>: As the resistant strains become more prevalent, the disease gets harder to control over time.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/142816/original/image-20161024-15958-1gmv13y.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/142816/original/image-20161024-15958-1gmv13y.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/142816/original/image-20161024-15958-1gmv13y.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=278&fit=crop&dpr=1 600w, https://images.theconversation.com/files/142816/original/image-20161024-15958-1gmv13y.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=278&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/142816/original/image-20161024-15958-1gmv13y.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=278&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/142816/original/image-20161024-15958-1gmv13y.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=350&fit=crop&dpr=1 754w, https://images.theconversation.com/files/142816/original/image-20161024-15958-1gmv13y.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=350&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/142816/original/image-20161024-15958-1gmv13y.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=350&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Aerial spraying of fungicides on a banana plantation.</span>
<span class="attribution"><span class="source">Gert Kema</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>To further aggravate the situation, Cavendish is also now under attack from <a href="http://dx.doi.org/10.1094/PHYTO-04-15-0101-RVW">a recently emerged strain of Fusarium oxysporum</a>, known as Tropical Race 4 (TR4). First identified in the early 1990s in Taiwan, Malaysia and Indonesia, TR4 has since spread to many Southeast Asian countries and <a href="http://dx.doi.org/10.1094/PDIS-12-14-1356-PDN">on into the Middle East</a> and <a href="http://dx.doi.org/10.1094/PDIS-09-13-0954-PDN">Africa</a>. If TR4 makes it to Latin America and the Caribbean region, the export banana industry in that part of the world could be in big trouble.</p>
<p>Cavendish varieties have shown <a href="http://dx.doi.org/10.1038/504195a">little if any resistance against TR4</a>. Growers are relying on temporary solutions – trying to <a href="http://www.promusa.org/Fusarium+wilt">prevent it</a> from entering new regions, using clean planting materials and limiting the transfer of potentially infected soil between farms.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/142714/original/image-20161021-1796-1on3qw6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/142714/original/image-20161021-1796-1on3qw6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/142714/original/image-20161021-1796-1on3qw6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/142714/original/image-20161021-1796-1on3qw6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/142714/original/image-20161021-1796-1on3qw6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/142714/original/image-20161021-1796-1on3qw6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/142714/original/image-20161021-1796-1on3qw6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/142714/original/image-20161021-1796-1on3qw6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Cavendish banana trees in China infected with new fungal disease TR4.</span>
<span class="attribution"><span class="source">Andre Drenth, UQ</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>Black Sigatoka and Panama disease both cause serious production losses and are difficult to control. With the right monitoring in place to rapidly intervene and halt their spread, the risks and damage imposed by these diseases can be considerably reduced, as has been <a href="http://www.musalit.org/seeMore.php?id=14394">recently shown in Australia</a>. But current practices don’t provide the durable solution that’s urgently needed.</p>
<h2>Getting started on banana genetic research</h2>
<p>If there’s a lesson to be learned from the sad history of Gros Michel, it’s that reliance on a large and genetically uniform monoculture is a risky strategy that is prone to failure. To reduce the vulnerability to diseases, we need more genetic diversity in our cultivated bananas. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/140963/original/image-20161008-21433-5f2wkn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/140963/original/image-20161008-21433-5f2wkn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/140963/original/image-20161008-21433-5f2wkn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/140963/original/image-20161008-21433-5f2wkn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/140963/original/image-20161008-21433-5f2wkn.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/140963/original/image-20161008-21433-5f2wkn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/140963/original/image-20161008-21433-5f2wkn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/140963/original/image-20161008-21433-5f2wkn.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Local banana varieties in southern China.</span>
<span class="attribution"><span class="source">Andre Drenth, UQ</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>Over a thousand species of banana have been recorded in the wild. Although most do not have the desired agronomic characteristics – such as high yields of seedless, nonacidic fruits with long shelf life – that would make them a direct substitute for the Cavendish, they are an untapped genetic resource. Scientists could search within them for resistance genes and other desirable traits to use in engineering and breeding programs.</p>
<p>To date, though, there’s been little effort and insufficient funding for collecting, protecting, characterizing and <a href="http://dx.doi.org/10.17660/ActaHortic.2011.897.4">utilizing wild banana genetic material</a>. Consequently, while almost every other crop used for food production has been significantly improved through plant breeding over the last century, the banana industry has yet to benefit from genetics and plant breeding.</p>
<p>But we have started taking the first steps. We now know the <a href="http://dx.doi.org/10.1038/nature11241">genome sequences of the banana</a> and the fungi that <a href="http://dx.doi.org/10.1371/journal.pone.0095543">cause Fusarium wilt</a> and <a href="http://dx.doi.org/10.1371/journal.pgen.1005904">Sigatoka</a>. These studies helped illuminate some of the molecular mechanisms by which these fungal pathogens cause disease in the banana. That knowledge provides a basis for <a href="http://dx.doi.org/10.1371/journal.pgen.1005904">identifying disease-resistant genes</a> in wild and cultivated bananas.</p>
<p>Researchers <a href="http://dx.doi.org/10.1371/journal.pgen.1005876">now have the tools</a> to <a href="https://www.google.co.in/patents/WO2011005090A1?cl=en">identify resistance genes</a> in wild bananas <a href="http://dx.doi.org/10.1073/pnas.1002910107">or other plant species</a>. Then they can use classical plant breeding or genetic engineering to transfer those genes into desired cultivars. Scientists can also use these tools to further study the dynamics and evolution of banana pathogens in the field, and monitor changes in their resistance to fungicides.</p>
<p>Availability of the latest tools and detailed genome sequences, coupled with long-term visionary research in genetics, engineering and plant breeding, can help us keep abreast of the pathogens that are currently menacing the Cavendish banana. Ultimately we need to increase the pool of genetic diversity in cultivated bananas so we’re not dependent on single clones such as the Cavendish or the Gros Michel before it. Otherwise we remain at risk of history repeating itself.</p><img src="https://counter.theconversation.com/content/64206/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>André Drenth receives funding from Horticulture Innovation Australia </span></em></p><p class="fine-print"><em><span>Gert Kema is a senior scientist and professor of tropical phytopathology at Wageningen University and Research. He receives funding for his R&D program on banana, see <a href="http://www.panamadisease.org">www.panamadisease.org</a>. He also co-founded two companies dealing with banana and owns shares in Yellow Pallet, a company that produces transport pallets from banana fiber. </span></em></p><p class="fine-print"><em><span>Ioannis Stergiopoulos does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Every single Cavendish banana plant worldwide is genetically identical. This vast monoculture sets them up for disastrous disease outbreaks. But researchers have ideas on how to protect the crop.Ioannis Stergiopoulos, Assistant Professor of Plant Pathology, University of California, DavisAndré Drenth, Professor of Agriculture and Food Sciences, The University of QueenslandGert Kema, Special Professor of Phytopathology, Wageningen UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/604682016-06-23T14:47:29Z2016-06-23T14:47:29ZHow science can genetically strengthen endangered plants and agriculture<figure><img src="https://images.theconversation.com/files/127707/original/image-20160622-7175-1w2bhnq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Somatic embryogenesis is only used in selected agroforestry industries like sugarcane.</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>As the human population swells – and in the face of a changing and unpredictable climate – the demand for natural resources increases. This leads to distressing rates of deforestation to prepare land for agriculture, medicinal and forestry products. Related to this is an alarming reduction in species worldwide.</p>
<p>This can only be ameliorated through urgent, intensive and sustainable agroforestry and conservation initiatives. This involves the conservation of natural forests as well as renewable plantation efforts. But to date only a scattering of such projects are in place worldwide. </p>
<p>Conservation and renewable plantation efforts are trailing behind the rate of resource exploitation and species disappearance. The problem is worsened by the vast number of endangered plant species. Once disturbed from their natural habitat, they can’t easily be reintroduced. This is because many of them do not readily produce seeds, or their seeds cannot be stored to ensure longevity of the species. The result is a decreasing gene pool. </p>
<p>This poses further risks, as vulnerable species become marginalised. They are only suitable to shrinking ranges and more susceptible to disease. To intensify conservation while enhancing agroforestry, smarter plant breeding practices are required.</p>
<p>Traditional breeding has allowed for the identification, selection and propagation of plants with a superior genetic makeup, or genotype, from a given plant population. But traditional methods often fail to isolate the required superior characteristics of a species. They can also take more than five or six breeding cycles before a valuable trait is established and maintained in a plant population. The process can take decades for perennial plants, like trees. </p>
<p>Plant biotechnology is increasingly being used to complement traditional screening and <a href="https://agricultureandfoodsecurity.biomedcentral.com/articles/10.1186/2048-7010-1-7">breeding practices</a>. Plants can be grown in test tubes under controlled laboratory conditions. Advances in biochemistry and genetics have also ushered in an understanding of the factors that influence plant growth. </p>
<p>Together these developments have created the opportunity to precisely identify and mass propagate superior plant varieties within a fraction of the time of traditional methods. On top of this, if required, the precise altering of the genetic makeup of plants is now also possible. This enables plant genomes to be radically enhanced so that superior genotypes can be created, maintained and propagated. </p>
<h2>Preserving valuable genes</h2>
<p>Maintaining superior genetics for valuable traits is fundamental in agroforestry. But to maintain superior genetics, seed production is rarely an option. In producing a seed, the sexual cross between genetically different male and female parent plants results in the dilution of valuable genes. This often leads to offspring with unpredictable genetics. </p>
<p>For the agroforestry industry to succeed, genotypes with predictably fast growth rates, high yields, and disease and drought resistance are needed. This will ensure land-use efficiency is maximised, which in turn will decrease ecological disturbance and protect indigenous plant species and sensitive natural forests. </p>
<p>One method that holds promise for preserving valuable genes is somatic embryogenesis. This is the ability to produce viable embryos from virtually any plant organ, while avoiding sexual crossing. Such embryos, when encased in alginate gel, constitute a synthetic seed. They retain all the valuable properties of the cloned parent plant. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/127715/original/image-20160622-7175-1ufxsyv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/127715/original/image-20160622-7175-1ufxsyv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/127715/original/image-20160622-7175-1ufxsyv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/127715/original/image-20160622-7175-1ufxsyv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/127715/original/image-20160622-7175-1ufxsyv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/127715/original/image-20160622-7175-1ufxsyv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/127715/original/image-20160622-7175-1ufxsyv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/127715/original/image-20160622-7175-1ufxsyv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Somatic embryogenesis is the ability to produce viable embryos from virtually any plant organ, while avoiding sexual crossing.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
</figcaption>
</figure>
<h2>Creating synthetic seeds</h2>
<p>Somatic embryos may form naturally in certain plants, but can potentially be induced in any plant species and from any plant organ outside its normal biological context. This is done by altering the balance of plant hormones – the language signal in plants that controls all developmental processes. </p>
<p>Our <a href="https://www.researchgate.net/publication/294106816_Using_synergistic_exogenous_phytohormones_to_enhance_somatic_embryogenesis_from_leaf_explants_of_a_Eucalyptus_grandis_clone">research</a> investigated the potential of inducing somatic embryos from leaves of the commercially important Eucalyptus tree. These are an important source of global timber products. Intensive efforts are under way to screen and select preferred genotypes to support environmental sustainability. </p>
<p>Somatic embryos mimic seeds without the lengthy breeding cycle. The germinated products are essentially clones of the parent plant from which the embryos were induced. So somatic embryogenesis allows for superior genotypes to be preserved. It also allows for the propagation of plant species that were previously excluded from standard propagation practices like traditional plant breeding or plant tissue culture. </p>
<p>There are other benefits too. The easily transported embryos constitute known genetics and growth properties. They could also potentially be cryopreserved, that is frozen to ultra-low temperatures indefinitely in liquid nitrogen. Importantly, because of the conditions under which they are induced, they are disease-free.</p>
<p>Despite its many uses somatic embryogenesis is only being used in selected agroforestry industries like sugarcane, certain conifer and forestry plantations and in a <a href="http://www.academia.edu/1615682/Somatic_embryogenesis_for_crop_improvement">few ornamental plants</a>. But its potential as a medium for genetic enhancement cannot be ignored, especially given recent advances in gene editing.</p>
<h2>Gene editing</h2>
<p>With the drive to sequence whole genomes of commercially important, rare or valuable plant species, scientists are presented with an opportunity to identify, understand the functions of and edit specific gene sequences to enhance plant properties. </p>
<p>To date, one hurdle to the success of the process has been the choice of organ when genetically editing plants. </p>
<p>This is why somatic embryos could be very useful for gene editing. As embryos they contain both root and shoot meristems – the precursors to a complete plant. If genes are edited at this embryonic stage, then as the embryo divides to form the complete plant all cells of the entire plant will carry the edited genome. </p>
<p>The advent of highly accurate gene editing methods has provided scientists with the opportunity to improve forestry, agricultural and threatened plant species. This can be done in a precise, targeted and reproducible manner. One such example is the <a href="https://www.neb.com/tools-and-resources/feature-articles/crispr-cas9-and-targeted-genome-editing-a-new-era-in-molecular-biology">Crispr/Cas9 system</a>. This is a highly specific gene editing method that can be used to precisely replace whole gene sequences.</p>
<p>The potential exists to genetically insert tolerance to pests, disease, drought, floods and other pressures of a changing climate. Such precise gene editing will greatly benefit from readily available, disease-free embryos. In the near future, gene editing of synthetic seeds will allow extensive improvement of agricultural and forestry crops.</p>
<h2>Planning for the future</h2>
<p>The only historical limitation of somatic embryogenesis lay in the possibility of unplanned mutations arising from the embryo induction process. But advanced molecular screening techniques have mitigated this. </p>
<p>In time, we should expect to see greater use of enhanced, tolerant plant genotypes through specific gene editing of somatic embryos and synthetic seeds. What remains to be done is fervent research into the underlying mechanisms of somatic embryogenesis, their efficient conversion into synthetic seeds and successful cryopreservation. This should be done using a greater number of plant species for more efficient, productive, tolerant and sustainable agroforestry plantations, and in conservation programmes.</p><img src="https://counter.theconversation.com/content/60468/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Muhammad Nakhooda receives funding from National Research Foundation and Cape Peninsula University of Technology Research Fund. </span></em></p>Smarter plant breeding practices are crucial in a world where climate change, deforestation and species reduction are an increasing problem.Muhammad Nakhooda, Senior Lecturer in Biotechnology, Cape Peninsula University of TechnologyLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/395322015-04-10T09:47:51Z2015-04-10T09:47:51ZNot all GMO plants are created equally: it’s the trait, not the method, that’s important<figure><img src="https://images.theconversation.com/files/77560/original/image-20150409-15231-13zm7ko.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Cornfield, GMO or not?</span> <span class="attribution"><a class="source" href="https://www.flickr.com/photos/katieharbath/4809776181">Katie Harbath</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">CC BY-NC-SA</a></span></figcaption></figure><p>Many people have strong opinions about genetically modified plants, also known as genetically modified organisms or GMOs. But sometimes there’s confusion around what it means to be a GMO. It also may be much more sensible to judge a plant by its specific traits rather than the way it was produced – GMO or not. </p>
<p>This article is not about judging whether GMOs are good or bad, but rather an explanation of how plants with modified genomes are made. (There are non-plant GMOs, but in this article we will only refer to plant GMOs.) First of all, it’s necessary to define what we mean by a GMO. For the purposes of this discussion, I’m defining GMOs as plants whose genetic information (found in their genomes) has been modified by human activity.</p>
<h2>Humans have changed the genomes of virtually all the plants in the grocery store</h2>
<p>If we think of GMOs as plants that have genomes modified by humans, then quite a lot of the plants sold in any grocery store fit that description. But many of these modifications didn’t occur in the lab. Farmers select plants with superior, desirable traits to cultivate in a process known as <a href="http://dx.doi.org/10.1104/pp.126.1.8">agricultural evolution</a>. Thousands of years of traditional agricultural breeding has changed plant genomes from those of their original wild ancestors. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/77381/original/image-20150408-18057-56zb3w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/77381/original/image-20150408-18057-56zb3w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/77381/original/image-20150408-18057-56zb3w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=402&fit=crop&dpr=1 600w, https://images.theconversation.com/files/77381/original/image-20150408-18057-56zb3w.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=402&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/77381/original/image-20150408-18057-56zb3w.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=402&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/77381/original/image-20150408-18057-56zb3w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=505&fit=crop&dpr=1 754w, https://images.theconversation.com/files/77381/original/image-20150408-18057-56zb3w.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=505&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/77381/original/image-20150408-18057-56zb3w.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=505&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Wild cabbage doesn’t look much like its domesticated version, broccoli.</span>
<span class="attribution"><a class="source" href="https://www.flickr.com/photos/nturland/7291619104">Nicholas Turland</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">CC BY-NC-ND</a></span>
</figcaption>
</figure>
<p>Broccoli, for example, is not a naturally occurring plant. It’s been bred from <a href="http://dx.doi.org/10.1007/BF02862698">undomesticated <em>Brassica oleracea</em></a> or ‘wild cabbage’; domesticated varieties of <em>B. oleracea</em> include both broccoli and cauliflower. Broccoli, along with any seedless variety of fruit (<a href="http://www.popsci.com/scitech/article/2008-06/can-fruit-be-saved">including what you think of as bananas</a>), and most of the crops grown on farms today would not exist without human intervention. </p>
<p>However, these aren’t the plants that people typically think of when they think of GMOs. It’s easy to understand how farmers can breed better plants on farms (by choosing to plant seeds from the biggest or best-yielding plants, for example, imposing <a href="http://learn.genetics.utah.edu/content/selection/artificial/">artificial selection</a> on the crop species) so even though this activity changes plant genomes in ways nature wouldn’t have, most people don’t consider these plants GMOs.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/77383/original/image-20150408-18086-ja40u2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/77383/original/image-20150408-18086-ja40u2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/77383/original/image-20150408-18086-ja40u2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=399&fit=crop&dpr=1 600w, https://images.theconversation.com/files/77383/original/image-20150408-18086-ja40u2.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=399&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/77383/original/image-20150408-18086-ja40u2.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=399&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/77383/original/image-20150408-18086-ja40u2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=501&fit=crop&dpr=1 754w, https://images.theconversation.com/files/77383/original/image-20150408-18086-ja40u2.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=501&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/77383/original/image-20150408-18086-ja40u2.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=501&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Scientists training in marker-assisted backcrossing selection technique.</span>
<span class="attribution"><a class="source" href="https://www.flickr.com/photos/icrisat/7595881154">ICRISAT/CT. Hash</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc/4.0/">CC BY-NC</a></span>
</figcaption>
</figure>
<h2>Creating “lab” GMOs</h2>
<p>Once plant genes had been studied enough, researchers could turn to <a href="http://dx.doi.org/10.1104/pp.108.118232">backcrossing</a>. This technique involves breeding the offspring back with the parents to try to get a desired, stable combination of parental traits. Genes previously linked to desirable plant traits, such as higher yield or pest-resistance, could be identified and screened for using molecular biology techniques and linkage maps. These maps lay out the relative position of genes along a chromosome, based on how often they are passed along together to offspring. Closer genes tend to travel together. </p>
<figure class="align-left zoomable">
<a href="https://images.theconversation.com/files/77563/original/image-20150409-15219-t69s2g.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/77563/original/image-20150409-15219-t69s2g.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/77563/original/image-20150409-15219-t69s2g.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=901&fit=crop&dpr=1 600w, https://images.theconversation.com/files/77563/original/image-20150409-15219-t69s2g.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=901&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/77563/original/image-20150409-15219-t69s2g.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=901&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/77563/original/image-20150409-15219-t69s2g.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1132&fit=crop&dpr=1 754w, https://images.theconversation.com/files/77563/original/image-20150409-15219-t69s2g.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1132&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/77563/original/image-20150409-15219-t69s2g.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1132&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Tiny experimental trees grown from lab-cultured cells in which researchers inserted new genes.</span>
<span class="attribution"><a class="source" href="http://www.ars.usda.gov/is/graphics/photos/k5011-19.htm">Scott Bauer</a></span>
</figcaption>
</figure>
<p>Researchers used molecular markers – specific, known gene sequences, present in the linkage maps – to select individual plants that contained both the new marker gene and the greatest proportion of other favorable genes from the parents. The combinations of genes passed to offspring are always due to random recombination of the parents’ genes. Researchers weren’t able to drive particular combinations themselves, they had to work with what arose naturally; so in this <a href="http://dx.doi.org/10.1098/rstb.2007.2170">marker-assisted selection</a> approach, there’s a lot of effort and time spent trying to find plants with the best combinations of genes.</p>
<p>In this system, a laboratory needs to screen the genomes, using molecular biology methods to look for particular gene sequences for desirable traits in the bred offspring. Sometimes a lab even breeds the plants in cases using <a href="http://www.elsevier.com/books/plant-tissue-culture-theory-and-practice/bhojwani/978-0-444-81623-8">tissue culture</a> – a way to propagate many plants simultaneously while minimizing the resources needed to grow them. </p>
<h2>Inserting non-plant genes into GMOs</h2>
<p>In the early 1980s, the plant biotechnology era began with <em>Agrobacterium tumifaciens</em>. This bacterium naturally infects plants and, in the wild, creates tumors by transferring DNA between itself and the plant it has infected. Scientists use this natural property to <a href="http://dx.doi.org/10.2225/vol1-issue3-fulltext-1">transfer genes</a> to plant cells from an <em>A. tumifaciens</em> bacterium modified to contain a gene of interest.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/77384/original/image-20150408-18075-1gialxm.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/77384/original/image-20150408-18075-1gialxm.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/77384/original/image-20150408-18075-1gialxm.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=760&fit=crop&dpr=1 600w, https://images.theconversation.com/files/77384/original/image-20150408-18075-1gialxm.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=760&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/77384/original/image-20150408-18075-1gialxm.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=760&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/77384/original/image-20150408-18075-1gialxm.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=956&fit=crop&dpr=1 754w, https://images.theconversation.com/files/77384/original/image-20150408-18075-1gialxm.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=956&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/77384/original/image-20150408-18075-1gialxm.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=956&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption"><em>Agrobacterium tumefaciens</em> as they begin to infect a carrot cell.</span>
<span class="attribution"><a class="source" href="http://commons.wikimedia.org/wiki/File:Agrobacterium-tumefaciens.png">A G Matthysse, K V Holmes, R H G Gurlitz</a></span>
</figcaption>
</figure>
<p>For the first time, it was possible to insert specific genes into a plant genome, even genes that do not come from that species – or even from a plant. <em>A. tumifaciens</em> does not affect all plants, however, so researchers went on to develop DNA-transferring methods inspired by this system which would work without it. They include microinjection and “gene guns,” where the desired DNA was <a href="http://dx.doi.org/10.1038/325274a0">physically injected</a> into the plant, or covered tiny particles that were literally <a href="http://dx.doi.org/10.1016/0167-7799(88)90023-6">shot into the nuclei of plant cells</a>.</p>
<p>A recent review <a href="http://dx.doi.org/10.1111/tpj.12413">summarizes eight new methods for altering genes in plants</a>. These are molecular biology techniques that use different enzymes or nucleic acid molecules (DNA and RNA) to make changes to a plant’s genes. One route is to alter the sequence of a plant’s DNA. Another is to leave the sequence alone but make other <a href="http://dx.doi.org/10.1016/j.pbi.2010.12.002">epigenetic modifications</a> to the structure of a plant’s DNA. For instance, scientists could add arrangements of atoms called methyl groups to some of the nucleotide building blocks of DNA. These epigenetic modifications, while not altering the order of the DNA or of genes, <a href="http://www.nature.com/scitable/topicpage/the-role-of-methylation-in-gene-expression-1070">change how genes can be expressed</a> and thus the observable traits a plant has. </p>
<h2>GMO doesn’t mean glyphosate-resistant</h2>
<p>Calling a plant a genetically modified organism means only that – its genome has been modified by the activity of humans. But lots of people conflate the idea of a GMO plant with one that’s been created to be resistant to the herbicide glyphosate, also known by the brand name Roundup. It’s true that the most well-known GMO crops currently grown contain a gene that makes them resistant to glyphosate, which allows farmers to spray the chemical to kill weeds while allowing their crop to grow. But that’s just one example of a gene inserted into a plant. </p>
<p>It’s sensible to evaluate GMOs not on how they are made, but rather on <a href="http://dx.doi.org/10.1111/tpj.12413">what new traits the modified plants have</a>. For instance, while it can be argued that glyphosate resistance in plants is not good for the environment because of <a href="http://dx.doi.org/10.1186/2190-4715-24-24">increased use of the pesticide</a>, other GMOs are unlikely to cause this problem. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/77380/original/image-20150408-18089-zab3i7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/77380/original/image-20150408-18089-zab3i7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/77380/original/image-20150408-18089-zab3i7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=399&fit=crop&dpr=1 600w, https://images.theconversation.com/files/77380/original/image-20150408-18089-zab3i7.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=399&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/77380/original/image-20150408-18089-zab3i7.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=399&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/77380/original/image-20150408-18089-zab3i7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=501&fit=crop&dpr=1 754w, https://images.theconversation.com/files/77380/original/image-20150408-18089-zab3i7.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=501&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/77380/original/image-20150408-18089-zab3i7.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=501&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Golden rice (on the right) compared to white rice.</span>
<span class="attribution"><a class="source" href="http://commons.wikimedia.org/wiki/File:Golden_Rice.jpg">International Rice Research Institute</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
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<p>For example, it’s difficult see how the controversial <a href="http://dx.doi.org/10.1104/pp.125.3.1157">golden rice</a>, which has been engineered to produce vitamin A in the rice grains to be more nutritious, is worse for the environment than ordinary rice. GMOs have been developed to express a pesticide permitted in organic farming: <a href="http://www2.ca.uky.edu/entomology/entfacts/ef130.asp">Bt toxin</a>, an insecticide naturally produced by the bacterium <em>Bacillus thuringiensis</em>. While this may reduce pesticide use, it may also lead to the <a href="http://dx.doi.org/10.1186/2190-4715-24-24">evolution of Bt-resistant insects</a>. And there are GMOs which have improved storage characteristics or nutritional content, like <a href="http://dx.doi.org/10.3733/ca.v054n04p6">“Flavr Savr” tomatoes</a>, or <a href="http://m.apnews.com/ap/db_289563/contentdetail.htm?contentguid=YOuzt2GL">pineapples that contain lycopene, and tomatoes that contain anthocyanins</a>. These compounds are ordinarily found in other fruits and are thought to have <a href="http://dx.doi.org/10.1016/S0002-8223(00)00420-X">health benefits</a>. </p>
<figure class="align-left zoomable">
<a href="https://images.theconversation.com/files/77565/original/image-20150409-15244-12bc0db.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/77565/original/image-20150409-15244-12bc0db.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/77565/original/image-20150409-15244-12bc0db.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=800&fit=crop&dpr=1 600w, https://images.theconversation.com/files/77565/original/image-20150409-15244-12bc0db.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=800&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/77565/original/image-20150409-15244-12bc0db.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=800&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/77565/original/image-20150409-15244-12bc0db.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1005&fit=crop&dpr=1 754w, https://images.theconversation.com/files/77565/original/image-20150409-15244-12bc0db.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1005&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/77565/original/image-20150409-15244-12bc0db.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1005&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">GMOs that include different species’ genes make some people uncomfortable.</span>
<span class="attribution"><a class="source" href="https://www.flickr.com/photos/elizaio/5608032236">elizaIO</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
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<p>The so-called <a href="https://e-class.teilar.gr/modules/document/file.php/FP103/3.pdf">“fish tomato”</a> contains an antifreeze protein (gene name <em>afa3</em>), found naturally in winter flounder, that increases frost tolerance in the tomato plant. The tomato doesn’t actually contain fish tissue, or even necessarily DNA taken from fish tissue – just DNA of the same sequence present in the fish genome. The Afa3 protein is produced from the <em>afa3</em> gene in the tomato cells using the same machinery as other tomato proteins. </p>
<p>Is there any fish in the tomato plant? Whether DNA taken from one organism and put into another can change the species of the recipient organism is an interesting philosophical debate. If a single gene from a fish can make a “fish tomato” a non-plant, <a href="http://www.iflscience.com/plants-and-animals/almost-150-our-genes-may-have-come-microbes">are we human beings, who naturally contain over a hundred non-human genes,</a> truly human?</p><img src="https://counter.theconversation.com/content/39532/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Elizabeth Bent receives funding from the Ontario Ministry of Agriculture and Food, and the Natural Sciences and Engineering Research Council of Canada. She consults to her own company, Renaissance Biological Solutions, Inc. She is a molecular biologist and microbiologist, and does not work with or research genetically modified plants, or have relationships with any company or organization promoting the use of genetically modified plants. </span></em></p>People have been changing plant genomes ever since agriculture got started thousands of years ago. Here are the high-tech ways researchers insert new genes into plants now.Elizabeth Bent, Research Associate, University of GuelphLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/298582014-08-13T12:48:38Z2014-08-13T12:48:38ZCounter crop patents by freeing seeds to feed the world<figure><img src="https://images.theconversation.com/files/56406/original/2pj4tczv-1407938378.jpg?ixlib=rb-1.1.0&rect=52%2C86%2C1020%2C618&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Free the seed!</span> <span class="attribution"><span class="source">Irwin Goldman</span>, <span class="license">Author provided</span></span></figcaption></figure><p>Today, just three companies – Monsanto, DuPont and Syngenta – account for about half of all commercial seed sales. More and more, agricultural patents are used to increase the control these and similar companies wield over access to the seeds with which farmers feed the world and – especially in the Global South – themselves and their families. </p>
<p>But it was not always this way. Improving crops through plant breeding has always been a core part of farming and gardening. Farmers would freely exchange their seed with others in order to identify characteristics that could be beneficial in their particular soil or climate conditions. Grow them, cross-breed them, pick the best, then grow and cross-breed them again. Scientific plant breeders do essentially the same thing, and free exchange of seeds and the freedom to use them for the breeding of additional varieties has been a key component of agricultural progress. </p>
<p>Over the past 20 years the growth of the free and <a href="http://opensource.org/osd-annotated">open source software</a> movement, whose poster child is the operating system <a href="http://www.linuxfoundation.org/about">Linux</a>, has provided an alternative to proprietary software from megacorps such as Microsoft, Apple and IBM, and a means to protect against <a href="http://endsoftpatents.org/">software patents</a>. Taking inspiration from this, we have created a similar organisation, the Open Source Seed Initiative (<a href="http://www.opensourceseedinitiative.org/">OSSI</a>), whose aim is to free the seed – that is, to make sure that the genes in at least some plant seeds can never be locked away from use by intellectual property rights. </p>
<p>OSSI kicked off its outreach activities on the University of Wisconsin campus on April 17 this year, with members – plant breeders, seed companies, and sustainability advocates – rallying to share seeds with each other and with the community. They then took a pledge to keep that seed freely available to anyone who wants to use it. </p>
<p>We chose April 17 as it had been designated as the <a href="http://viacampesina.org/en/index.php/actions-and-events-mainmenu-26/17-april--day-of-peasants-struggle-mainmenu-33/1564-april-17th-international-day-of-farmers-struggles-in-defence-of-peasants-and-farmers-seeds">International Day of Struggles in Defence of Peasants’ and Farmers’ Seeds</a>, announced by landless and peasant farmers groups worldwide in response to the growing struggles they face with commercialised agriculture and the increased patenting of seeds. </p>
<p>OSSI’s <a href="http://www.opensourceseedinitiative.org/about/ossi-pledge/">Open Source Seed Pledge</a> commits anyone who receives and uses OSSI seed to keep that seed, and any seed derivatives that are bred from that seed, freely available for use by others: </p>
<blockquote>
<p>By opening this packet, you pledge that you will not restrict others’ use of these seeds and their derivatives by patents, licenses, or any other means. You pledge that if you transfer these seeds or their derivatives you will acknowledge the source of these seeds and accompany your transfer with this pledge.</p>
</blockquote>
<p>This pledge is OSSI’s equivalent of the idea that underpins the open source software movement, in the form of the General Public Licence, or <a href="http://www.gnu.org/licenses/#GPL">GPL</a>. The GPL states that the software is free to use, but any modifications to it or other software derived from it must be licensed under the GPL too, ensuring the benefits accrue to the public and continue to be free. </p>
<p>Importantly, that’s “free” as in freedom, not “free” as in you don’t have to pay for it. Because just as we need free speech to be able to say what needs to be said, we also need free seed to be able to breed what needs to be bred.</p>
<p>This OSSI pledge to freely share is essential. A patented seed cannot be saved, or replanted, or shared by farmers and gardeners. There is no standard research exemption for patented material, so plant breeders at universities and small seed companies usually cannot use patented seed to breed the new crop varieties that should be sustainable alternatives to the conventional cultivars of the big commercial firms. The yield and productivity increases of the last sixty years began with academic, government, and public interest scientific institutions breeding and developing the crop varieties that now feed billions of people worldwide. The fruits of their research – the seed – were freely available to all. Today much research work is being done by major agro-tech businesses, and their products must be purchased.</p>
<p>In order to continually improve our crops to feed the world’s rapidly growing population, farmers and plant breeders need access to the best genetic resources. But increasingly that access is being limited due to seed patenting and licensing. OSSI creates a pool of genetic resources that are freely available for all to use, share, save, replant, and breed, and are a conduit through which seeds can be widely distributed. These seeds can never be wholly owned or their use restricted. In addition, OSSI serves an educational mission to promote awareness of germplasm access for farmers, gardeners, and plant breeders and to foster a conversation about plant breeders’ continued “freedom to operate.” </p>
<p>Among the 36 varieties of 14 species shared on April 17 were <a href="http://www.wildgardenseed.com/product_info.php?products_id=63">Wrinkled Crinkled Crumpled cress</a> from Frank Morton of Wild Garden Seed in Oregon, <a href="http://coloradomaltingcompany.com/FULL_PINT_MALT.html">Full Pint malting barley</a> from <a href="http://cropandsoil.oregonstate.edu/content/pat-hayes">Pat Hayes</a> of Oregon State University, <a href="http://www.highmowingseeds.com/organic-non-gmo-seeds-midnight-lightning-zucchini.html">Midnight Lightning zucchini</a> from Vermont’s High Mowing Organic Seeds, and Sovereign carrots from the University of Wisconsin’s Irwin Goldman. </p>
<p>Most of the OSSI varieties are available as organic seed and were bred with organic growers and gardeners in mind. Within a month, OSSI received more than 400 orders from 16 countries. Clearly there is a hunger for seed that is not just agronomically good, but also fair. In the future OSSI hopes to offer a certified brand that can be used in seed catalogues to identify “free seed” to those who agree that what the world needs is more free and open source seeds, not patented and indentured seeds.</p>
<p>OSSI is itself a seed that we have planted, and we wait with hope to see how it grows.</p><img src="https://counter.theconversation.com/content/29858/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Irwin Goldman is on the board of the Open Source Seed Initiative, which is in the process of obtaining not-for-profit status in the US.</span></em></p><p class="fine-print"><em><span>Jack Kloppenburg does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Today, just three companies – Monsanto, DuPont and Syngenta – account for about half of all commercial seed sales. More and more, agricultural patents are used to increase the control these and similar…Jack Kloppenburg, Professor of Community & Environmental Sociology, University of Wisconsin-MadisonIrwin Goldman, Professor and Chair, Department of Horticulture, University of Wisconsin-MadisonLicensed as Creative Commons – attribution, no derivatives.