Structural variation involving transposable elements associated with grain width in cultivated rice.
Résumé
Rice, Oryza sativa, is the staple food for half the world population. It is the first crop whose genome has been sequenced in 2005. This model species benefits from various genomic ressources among which genome sequences of 3000 rice varieties that were publicly released in 2014 [1]. This provides a unique opportunity to unravel the genetic diversity of the crop with accessions from 89 countries, distributed
into 5 varietal groups – indica, japonica, aus/boro, basmati/sandri and intermediate.
Transposable elements (TE) are mobile genetic elements abundant in plant genomes. Knowledge of their impact on the structure, function and evolution of genome, these mobile entities can provide a more precise picture of rice genome dynamics on a shorter evolutionary scale (posterior to the domestication) because their transposition rate is higher than base substitutions.
We have developped a pipeline, nammed TRACKPOSON, to detect all retrotransposons insertions in the 3000 genomes dataset [2]. With these results, to understand the funtional impact of TE on this crop, we performed a genome-wide association study (TE-GWAS, [3]) with different agronomic traits. We found a significant association between an insertion of TE and rice grain width. If the TE is present, the grain is larger.
For further analysis, we sequenced 2 phylogenetically related rice varieties (one thin grain and one large grain) with Nanopore technologies. Thanks to long-read sequencing, after assembly and genomic analysis, we validated the insertions of TE. In addition, we observed that the insertion region is part of a larger insertion, possibly an introgression from another rice variety (appears to be an ancestral wild rice). Analyses of introgression are underway to annotate the genes, insertions of TE insertion and genomic comparision between the 2 cultivated rice varieties.
In parallel, genetic analysis is underway by crossing the two rice plants together and creating a
rice population for futures analysis.
References
[1] The 3,000 rice genomes project. The 3,000 rice genomes project. GigaScience, 3(1):7, December 2014.
[2] Marie-Christine Carpentier, Ernandes Manfroi, Fu-Jin Wei, Hshin-Ping Wu, Eric Lasserre, Christel Llauro, Emilie Debladis, Roland Akakpo, Yue-Ie Hsing, and Olivier Panaud. Retrotranspositional landscape of Asian rice revealed by 3000 genomes. Nature Communications, 10(1):24, December 2019.
[3] Roland Akakpo, Marie‐Christine Carpentier, Yue Ie Hsing, and Olivier Panaud. The impact of transposable elements on the structure, evolution and function of the rice genome. New Phytologist, 226(1):44–49, April 2020.
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