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Genomic Variation Associated with Local Adaptation of Weedy Rice During De-domestication

Source: China National Rice Research Institute

Recently, researchers from China National Rice Research Institute (CNRRI) of Chinese Academy of Agriculture Sciences (CAAS), Zhejiang University, Zhejiang Sheng Ting Biotechnology Co., Ltd., University of Virginia and Chinese Academy of Sciences collaboratively published an article entitled Genomic Variation Associated with Local Adaptation of Weedy Rice During De-domestication.

Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem in South and Southeast Asia and Latin America. In China, an emerging threat occurred in Jiangsu, Guangdong, Liaoning and Ningxia of China that causes serious damages to rice quality and yield. Because weedy rice is similar to cultivated rice morphologically, genetically and ecologically, it is difficult to control with herbicide which could lead to serious damages to rice production in the world.

Plant domestication is the process during which wild species are converted into crop plants through artificial selection and has brought about significant alterations of plant traits to meet their desires and benefits. Plant de-domestication is a distinct evolutionary process involving a loss of traits aggregated under domestication, during which domesticated crops are turned into self-sustainable ‘wild-like' plants mainly driven by natural selection. Compared with the well-studied process of domestication, the mechanism of de-domestication has not been thoroughly investigated. Weedy rice could serve as one of the best models to investigate the process of crop de-domestication. To address the underlying adaptive mechanisms of weedy rice, 155 weedy and 76 locally cultivated rice accessions were collected from four representative regions in China that were sequenced to an average 18.2 × coverage.


Phylogenetic and demographic analyses indicated that Chinese weedy rice was de-domesticated independently from cultivated rice and experienced a strong genetic bottleneck. Although evolved from multiple origins, critical genes underlying convergent evolution of different weedy types can be found. The 15 genes are located in adjacent genomic regions (6.0–6.4 Mb of chromosome 7) that cover the seed allergenic gene cluster and Rc may be indispensable for rice de-domestication. Allele frequency analyses suggested that standing variations and new mutations contributed differently to japonica and indica weedy rice. It has been identified that an Mb-scale genomic region presented in weedy rice but not cultivated rice genomes that showed evidence of balancing selection, thereby suggesting that there might be more complexity inherent to the process of de-domestication. These results are helpful to understanding of the adaptive mechanisms of weedy rice during de-domestication and also provided some practical implication for the paddy weed control.

This study was financially supported in part by grants from the China Agriculture Research System (CARS-01-02A), National Science Foundation of China (91435111) and Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP). It also received funding support from Rice Pest Management Research Group of the Agricultural Science and Technology Innovation Program (ASTIP) of CAAS. The research findings have been published in Nature Communication online on May 24, 2017 (DOI: 10.1038/ncomms15323). More details are available on the link below: https://www.nature.com/articles/ncomms15323
By Zhang Jianping