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Research Project: Using Genetic Approaches to Reduce Crop Losses in Rice Due to Biotic and Abiotic Stress

Location: Dale Bumpers National Rice Research Center

Title: Signatures of adaptation in the weedy rice genome

item LI, LIN-FENG - Chinese Academy Of Sciences
item LI, YA-LING - Chinese Academy Of Sciences
item Jia, Yulin
item CAICEDO, ANA - University Of Massachusetts
item OLSEN, KENNETH - Washington University

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/2/2017
Publication Date: 4/3/2017
Citation: Li, L., Li, Y., Jia, Y., Caicedo, A.L., Olsen, K.M. 2017. Signatures of adaptation in the weedy rice genome. Nature Genetics. doi:10.1038/ng.3825.

Interpretive Summary: Weedy rice is a persistent agricultural problem and can lead to the serious reduction of rice production worldwide. Weedy crop relatives are a common and problematic by product of domestication. In this study, to address how exactly the weedy rice strains have originated and to what extend the adaptation shapes the weedy rice genome, we analyzed the whole genome of 183 wild, cultivated, and weedy rice accessions. Through comparing the patterns of genomic variation, we made the following findings: (1) our genome-wide data analyses revealed distinct temporal and spatial origins of three weedy rice strains, with the Black Hull Awaned (BHA) weedy rice diverging from its crop ancestor aus much earlier than those between Straw hull (SH) / Chinese weeds and their crop ancestor indica; (2) only a few genetic changes across the genome can lead to the formation of weedy forms and parallel evolution has resulted in distinct genome structures of the SH and BHA weedy rice; (3) some genomic regions showing footprints of selection are overlapped with our previously identified weediness genetic loci. Our study illustrated that parallel evolution reshaped the weedy rice genome, which present a unique challenge for weedy rice management worldwide.

Technical Abstract: Weedy rice is a common problem of by product of domestication that has evolved multiple times from cultivated and wild rice relatives. Here we use whole genome sequences to examine the origin and adaptation of the two major US weedy red rice strains, with a comparison to Chinese weedy red rice. We find that de-domestication has played a major role in weedy red rice evolution, with relatively few changes required for the emergence of weedy forms and flexibility in underlying genetic mechanisms. Weedy rice strains have likely evolved both early and late during the history of rice cultivation, and represent an under-recognized component of the domestication process.