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

Jie Qiu, Yongjun Zhou, Lingfeng Mao, Chuyu Ye, Weidi Wang, Jianping Zhang, Yongyi Yu, Fei Fu, Yunfei Wang, Feijian Qian, Ting Qi, Sanling Wu, Most Humaira Sultana, Ya-Nan Cao, Yu Wang, Michael P. Timko, Song Ge, Longjiang Fan, Yongliang Lu

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.