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The genomes of 13 species of wild and cultivated rice revealed: better conserve and harness the genetic diversity of one of the pillars of global food security

The genomes of 13 species of wild and cultivated rice revealed
An international consortium of 16 partners, including the LGDP (UMR 5096 CNRS / UPVD) which recently joined the TULIP LabEx has published in Nature genetics an article describing the comparative sequencing of 13 wild and cultivated rice genomes (genus Oryza). The study reveals the evolutionary dynamics of a plant genome over 15 million years and shows that genes, which were thought to be highly conserved within the same genus, are in fact very dynamic (they appear and disappear at an unexpectedly high rates during evolution). A better knowledge of these genomes is a valuable resource for better exploiting the diversity of rice, thus contributing to the world's food security.

With a world production approaching 500 million tons, rice is the staple food for billions of human beings, often among the poorest on the planet. This cereal is therefore one of the pillars of food security in Asia, Africa and South America. Its sustained production, as it is the case for all plants of economic interest, depends on the development of improved varieties with high agronomic performances.

Maintain genetic diversity


Wild African rice (inner circle) and cultivated rice (outer circle) © Olivier Panaud

The spread of high-yielding varieties, however, poses the problem of eroding genetic diversity, as these varieties gradually replace traditional ones. This erosion constitutes a threat in the context of accelerating environmental changes, since the lack of genetic diversity may seriously diminish our capacity to find new sources of tolerance to the new crop conditions (hot, cold, drought, floods...) that we will face in the near future. Such sources nevertheless exist in natural populations of wild species close to cultivated rice (of the same genus Oryza). A good knowledge of the genome of these species will allow us to better identify and exploit their genetic diversity and thus better fight the effects of climate change to ensure food security.

Characterize the dynamics of genes on evolutionary times

From a fundamental point of view, the genome sequencing of these 13 species helps us better understand the evolution of plant genomes. The genus Oryza is about 15 million years old. Thus, for example, the comparison of available genomes allows us to characterize the dynamics of genes over evolutionary times ranging from a few hundreds of thousands to several million years. One of the surprises of the study is the discovery of the very high rate of appearance of new genes (whose origin remains unknown) in all species. This mechanism could be at the origin of the diversity observed between the species. In addition, the transposable elements (which are non-genic sequences but very frequent in plant genomes) are also very dynamic and actively contribute to the differentiation of genomes. This article helps to better understand the functional impact of these elements and how they contribute to the genesis of biodiversity in plants

See also

Joshua C. Stein et al. ; Genomes of 13 domesticated and wild rices relatives highlight genetic conservation, turnover and innovation across the genus Oryza ; Nature Genetics volume 50, pages285–296 (2018) doi:10.1038/s41588-018-0040-0

Olivier Panaud's website