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Musa genome mapped: that’s bananas!

The completed sequence of the banana’s 11 chromosomes has global implications. Caro Wallace

Musa genome mapped: that’s bananas!

The completed sequence of the banana’s 11 chromosomes has global implications. Caro Wallace

What’s not to love about bananas? Besides being a wildly popular dessert fruit, they are the staple food of millions of people in developing countries.

The current edition of Nature carries a paper that marks a major milestone for both bananas and plant biotechnology.

Some 18 research groups – ten from France, three from USA, one from Switzerland, one from Czech Republic, one from UK, one from Australia and one from Netherlands – have published the first draft sequence of the 523-megabase genome of DH-Pahang, a doubled-haploid genotype of the subspecies malaccensis, that contributed one of the three acuminata genomes of the common dessert banana, Cavendish.

LordKhan

This is the first completed sequence of the 11 chromosomes of banana and it provides the first detailed genetic blueprint of the most important fruit crop in the world and one of the most important food crops after staple cereals and cassava.

This publicly-available finished sequence is anchored to the genetic map, providing both the linear order of the 36,542 genes and their positions on the 11 banana chromosomes.

The new Nature paper unravels the major features of the banana genome in terms of nucleotide composition and repeats.

Nucleotides are the basic building blocks of nucleic acids, such as DNA and RNA. They are organic compounds made up of a nitrogenous base, a sugar, and a phosphate group – the way they line up in the nucleic acid queue has a huge impact on the function they perform.

The new paper also unravels the major features of the banana in terms of gene content and variability.

The research bridges a large gap in genome evolution studies and sheds new light on the monocot lineage (flowering plants are divided into two classes, monocots and dicots, mainly based on whether they have one or two cotyledons in the seeds respectively).

The paper compares the banana genome with three members of grass family, rice, sorghum, Brachypodium, one non-graminaceous monocot, date-palm and a dicot, Arabidopsis to reveal 7,674 gene clusters that are common to all six species, thus representing ancestral gene families.

To put that number in context, more than 326 or 377 clusters are needed to show human individuals are more similar to individuals in their own population group than to individuals in different population groups.

The genome sequence of Arabidopsis, a dicot weed widely used in research, was the first genetic code of a plant to be released, in November 2000.

Rice, a monocot of grass family (which includes maize, wheat, barley and sorghum) was the next important genome to be released in 2005.

And now finally, in 2012, we have the banana genome - arguably the most important of these in terms of its global significance.

Quality control

As already mentioned, bananas and plantains are the staple food of millions of people in developing countries, especially in Eastern and Western Africa.

Exposing the complete genetic code of banana will help speed up the ongoing breeding efforts to develop new cultivars with improved fruit quality and disease-resistance. Until now, such improvements have required years of crossing between male and female flowers from banana parents because of the high levels of male sterility among the commercially-favoured triploid banana cultivars.

(Triploid bananas have three sets of chromosomes and hence cannot pair up into even numbered groups – that makes them sterile, and most sterile plants produce no seeds. Banana fruit from triploid varieties is therefore seedless).

Breeding for feeding

For molecular breeding in any crop species, not only the gene sequence but the sequence information linked to the complete genetic map of the genome is required to exploit the full potential of the sequences.

If breeders transfer one gene to the progeny during breeding they need to understand which neighbouring genes will come tagging along – and not every neighbour is a good one.

Skely

Using the newly-released sequence data, banana biotechnologists can isolate genes and regulatory sequences more easily and use them to over-express or under-express genes for desirable traits and functions.

This will have implications for transgenics (the branch of biology concerned with the transfer of genes to other species) and cisgenics (a cisgene is a natural gene coding for a trait from the crop plant itself or from a crossable species used in conventional breeding).

The new sequence is of inestimable significance to banana researchers and is bound to yield tangible results from the standpoint of offering food security and combating malnutrition in the tropical world – one of the many health issues addressed by the Bill and Melinda Gates Foundation program on Global health improvement.

One of the Grand Challenges in Global Health focuses on nutrition and one of the funded programs aims to improve the nutritional status in Uganda and surrounding countries through the generation of edible bananas acceptable to farmers and consumers, with significantly increased fruit levels of pro-vitamin A and iron.

Defend and serve

To understand the full significance of the publication of the banana sequence, one maybe needs to read the epic 2011 article in The New Yorker by Mike Peed concerning the demise of the Cavendish banana (which currently makes up 99% of exported bananas).

That same article also profiles the devastating disease known to scientists as Fusarium Tropical Race Four (a fungal disease commonly known as Panama disease) and often referred to as the “H.I.V. of banana plantations”.

Fusarium oxysporum f. sp. cubense (Foc), the causal pathogen of Fusarium wilt of banana is a soil-borne fungus that kills the banana cells and colonises the dead tissue.

There are no long-term chemical or physical measures to control it. Due to the low fertility and long generation times of conventional breeding with Musa germplasm, exploitation of resistance genes that have been identified in diploid banana species has been slow.

Transgenics offers a very promising alternative strategy for the improvement of commercial Fusarium-resistant banana varieties.

The published sequence has identified many of the defence-related genes and this fact is specifically important because the sequenced DH-Pahang is highly resistant to this dreaded fungus.

On hearing about the new paper, my colleague James Dale, Director of Tropical Crops and Biocommodities at Queensland University of Technology, said:

“Tropical Race 4 is the greatest threat to Cavendish and other banana production in the world. Malaccensis has resistance and is very important source of resistance genes against this disease.

We are already testing some of these genes in a field trial in North Australia and we had used alternative methods to isolate these genes. Now we have an easier way of accessing them.

To put it mildly, we are very pleased to see the publication of the banana sequence.