Genomic variation associated with local adaptation of weedy rice during de-domestication

TLDR

De‑domestication converts domesticated crops into wild‑like forms, a unique evolutionary process. Weedy rice (Oryza sativa f. spontanea) serves as a model to dissect the molecular mechanisms of de‑domestication. We sequenced 155 weedy and 76 locally cultivated rice accessions from four Chinese regions at ~18.2× coverage to analyze their genomes.

Abstract

De-domestication is a unique evolutionary process by which domesticated crops are converted into 'wild predecessor like' forms. Weedy rice (Oryza sativa f. spontanea) is an excellent model to dissect the molecular processes underlying de-domestication. Here, we analyse the genomes of 155 weedy and 76 locally cultivated rice accessions from four representative regions in China that were sequenced to an average 18.2 × coverage. Phylogenetic and demographic analyses indicate that Chinese weedy rice was de-domesticated independently from cultivated rice and experienced a strong genetic bottleneck. Although evolving from multiple origins, critical genes underlying convergent evolution of different weedy types can be found. Allele frequency analyses suggest that standing variations and new mutations contribute differently to japonica and indica weedy rice. We identify a Mb-scale genomic region present in weedy rice but not cultivated rice genomes that shows evidence of balancing selection, thereby suggesting that there might be more complexity inherent to the process of de-domestication.