Abstract
The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.
Highlights
The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop
Comparative genomic studies in various lineages show that transposable elements (TEs) contribute significantly to genome diversification, suggesting that TE insertion polymorphisms (TIPs) could be frequent enough in natural populations to serve as a source of adaptive variation[13]
The new strategy we developed consists in first mapping all reads of a given accession onto each TE family represented by a single consensus sequence and mapping the unmapped paired reads onto the rice reference genome, split into 10 kb windows (Fig. 1)
Summary
The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. Comparative genomic studies in various lineages show that TEs contribute significantly to genome diversification, suggesting that TE insertion polymorphisms (TIPs) could be frequent enough in natural populations to serve as a source of adaptive variation[13]. The exhaustive characterization of TIPs in a given gene pool requires genomic data for a comprehensive sample of individuals and at least one good-quality reference genome sequence from which TEs have been well characterized. These resources are available for a few model species.
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