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

• Published in: Nature communications Vol. 8; no. 1; p. 15323
• Main Authors: Qiu, Jie, Zhou, Yongjun, Mao, Lingfeng, Ye, Chuyu, Wang, Weidi, Zhang, Jianping, Yu, Yongyi, Fu, Fei, Wang, Yunfei, Qian, Feijian, Qi, Ting, Wu, Sanling, Sultana, Most Humaira, Cao, Ya-Nan, Wang, Yu, Timko, Michael P., Ge, Song, Fan, Longjiang, Lu, Yongliang
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 24.05.2017; Nature Publishing Group; Nature Portfolio
• Subjects: 45; 45/23; 631/181/735; 631/449/2669; Adaptation; Crops; Domestication; Environmental science; Evolution; Genomes; Humanities and Social Sciences; multidisciplinary; Mutation; Phylogenetics; Plant sciences; Rice; Science; Science (multidisciplinary); China
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms15323

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. De-domestication is the process by which cultivated plants adopt characteristics similar to that of their wild predecessors. Here Qiu et al . re-sequence de-domesticated weedy rice and matched cultivated varieties and identify genetic variants indicative of convergent evolution across multiple de-domestication events.