Retrotranspositional landscape of Asian rice revealed by 3000 genomes

Marie-Christine Carpentier (1) , Ernandes Manfroi , Fu-Jin Wei , Hshin-Ping Wu , Eric Lasserre (1) , Christel Llauro (1) , Emilie Debladis (1) , Roland Akakpo (1) , Yue-Ie Hsing (2) , Olivier Panaud (1)

1 LGDP - Laboratoire Génome et développement des plantes
2 Academia Sinica

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 TRACK-POSON 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.

Domaines: Sciences du Vivant [q-bio]

Marie-Christine Carpentier, Ernandes Manfroi, Fu-Jin Wei, Hshin-Ping Wu, Eric Lasserre, et al.. Retrotranspositional landscape of Asian rice revealed by 3000 genomes. Nature Communications, 2019, 10 (1), ⟨10.1038/s41467-018-07974-5⟩. ⟨hal-02098307⟩