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The genome dynamics of rice revealed by sequencing 3,000 varieties

The genome dynamics of rice revealed by sequencing 3,000 varieties
The Genome and Plant Development Laboratory (LGDP, UMR 5096 CNRS/UPVD), just published in Nature Communications an article describing the transpositional dynamics of rice based on the analysis of 3,000 genomes. The authors show that transposable elements (mobile DNA in the genome) contribute significantly to the diversification of the species genome.

Rice, with world production approaching 500 million tons, is the staple food for billions of humans, often among the poorest in the world. It is one of the pillars of food security in Asia, Africa and South America. The sustained production of this cereal, as it is the case for all plants of economic interest, depends on the development of varieties with high agronomic performances. The spread of such high yielding varieties, however, raises the problem of genetic diversity erosion, since selected lines gradually replace traditional varieties.

Eroding genetic diversity

This erosion is now a danger in the context of the acceleration of environmental change, since without sufficient genetic diversity, it will be difficult if not impossible to find new sources of tolerance to the extreme farming conditions (hot, cold, drought, floods ...) that we will face in the near future. Yet rice is one of the oldest cereals, with a multi-millennial history, cultivated today in almost all tropical and subtropical regions of the globe, as well as some temperate zones. The global collection of genetic resources of the species now has more than 100,000 varieties attesting to its strong heritage value, but above all a huge reservoir of genetic diversity that will be very valuable in the context of global change.

Transposable elements contribute significantly to the diversification of the rice genome

Today, there is a very large set of public genomic data in rice., including the full genomic sequence of 3000 cultivated varieties. The processing of such big data (amounting to Terabytes) is in itself a conceptual and technical challenge. The authors of the study therefore developed a new method of processing sequence data, very fast but above all very reliable, to identify all the polymorphisms (genomic variation) associated with the movement of transposable elements. Thanks to this analysis, they found that the differentiation of the genome by transposable elements was very fast and contributed significantly to the genetic diversity of the species since domestication. The authors also show that rice was domesticated three times independently in Asia, whereas it was thought until now that it was domesticated ("invented") only twice.

The results of this study will now allow the identification of new adaptive genetic factors in the existing collection of rice genetic resources and help developing future varieties more tolerant to the environmental stresses that all agrosystems will likely face in the near future.

See also

Carpentier MC, Manfroi E, Wei FJ, Wu HP, Lasserre E, Llauro C, Debladis E, Akakpo R, Hsing YI, Panaud O (2019). Retrotranspositional landscape of Asian rice revealed by 3000 genomes.Nature Communications. 10(1):24. doi: 10.1038/s41467-018-07974-5.