Published online 26 December 2010 | Nature | doi:10.1038/news.2010.698

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Smorgasbord of genomes for food lovers

Drafts of cacao and strawberry sequences unveiled.

Strawberries and chocolate anyone?Strawberries and chocolate anyone?P. LEFEVRE/ISTOCKPHOTO

Genome gastronomes rejoice! Today sees the publication of genome sequences behind two of the tastiest treats: the cacao tree, whose beans yield chocolate, and the woodland strawberry.

Earlier this year, a team backed by food giant Mars unveiled a preliminary sequence of the cacao tree Theobroma cacao. Now a team partly supported by rival chocolate company Hershey has become the first to get a genome of the valuable plant into a peer-reviewed journal1.

Led by researchers at the Agricultural Research for Development (CIRAD) centre in Montpellier, France, the genome, published in Nature Genetics, looks at the Belizean Criollo variety of the crop. "The Criollo is one of the two varieties that provide fine favour chocolate," says Claire Lanaud, a geneticist at CIRAD and last author on the paper. "We chose this variety also because we are very interested in the genes involved in quality traits."

Criollo is also extremely homozygous — it has matching copies of most of its genes on each pair of chromosomes. This is an important factor in producing a high quality genome sequence.

Flavour saver

Although fine cocoa commands a high price, Criollo is not a great crop for farmers; it is susceptible to disease and its yields are not the best.

"In plantations, people are using a hybrid between this Criollo variety and other cocoa genotypes," says Lanaud. This hybrid is called Trinitario, created by crossing Criollo crossed with the more common Forastero variety. But the hybridization reduces "the high flavour quality of this ancestral Criollo variety", she says. Consequently, "it is very important to try to have a better knowledge of the genetic determinants of the quality traits of the cocoa".

Lanaud's team found scores of genes potentially involved in the production of lipids, flavonoids and terpenoids, responsible for much of the taste of chocolate. T. cacao had some 84 candidate genes involved in lipid biosynthesis, compared with 71 in the well-studied but less flavoursome plant thale cress (Arabidopsis thaliana), and 96 involved in flavonoid biosynthesis, versus just 36 in Arabidopsis.

The paper also highlights genes potentially involved in disease resistance. These may eventually allow breeders to improve the quality and yields of the cocoa varieties.

In contrast to the French-led team, the Mars-backed researchers, who were also supported by the US Department of Agriculture, chose a more widely-farmed hybrid variety of Forastero, known as Matina 1-6, for their sequence (online at www.cacaogenomedb.org).

Having two cacao genomes will be "particularly valuable" and should provide additional candidate genes for important traits, says Brian Scheffler, research leader of the Stoneville, Mississippi-based Genomics and Bioinformatics Research Unit at the US Department of Agriculture's Agricultural Research Service, who worked on that effot.

"Breeding disease-resistant varieties is one of the major goals of our group's breeding team. They are already making significant progress in attaining this goal," he says. "With genomic information from two divergent varieties, they should be able to proceed more rapidly."

An initial draft of his team's sequence was unveiled in September this year, although Lanaud says that it has not been possible to directly compare the two versions, as the Mars-sequence appears to have a number of fragments that were inverted when the genome was assembled.

"There indeed might be chromosomal inversions distinguishing these varieties, because they are distantly related," responds Scheffler. "But determining that will probably require refinements to the assemblies of both genomes, and additional data."

Strawberry genomes forever

The genome of the woodland strawberry, also known as the wild or alpine strawberry, is also published today in Nature Genetics2. Fragaria vesca — the fleshy shoot tips of which are technically neither fruit nor berry — has a relatively small genome. The authors of the new paper on its genome note that it takes up very little space, potentially making it a good candidate for further study in the lab.

This could open the way to studies on flavour and disease resistance in the cultivated strawberry Fragaria x ananassa, and even in other relatives of the plant such as apples and peaches, all members of the Rosaceae family. 

  • References

    1. Argout, X. et al. Nature Genetics advance online publication doi:10.1038/ng.736 (2010).
    2. Shulaev, V. et al. Nature Genetics advance online publication doi:10.1038/ng.740 (2010).

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  • #60752

    I think one of the key things is that some genes and their corresponding protein have specific amino acid residues that are essential to their function and are thus highly conserved by evolution (i.e. all humans who have a functioning version of that gene will have those codons exactly or codons for very conservative substitution).

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