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 () and Yongliang Lu ()
Additional contact information
Jie Qiu: Institutue of Crop Science & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University
Yongjun Zhou: China National Rice Research Institute, Chinese Academy of Agricultural Sciences
Lingfeng Mao: Institutue of Crop Science & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University
Chuyu Ye: Institutue of Crop Science & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University
Weidi Wang: Institutue of Crop Science & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University
Jianping Zhang: China National Rice Research Institute, Chinese Academy of Agricultural Sciences
Yongyi Yu: Institutue of Crop Science & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University
Fei Fu: Institutue of Crop Science & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University
Yunfei Wang: Zhejiang Sheng Ting Biotechnology Co., Ltd.
Feijian Qian: Zhejiang Sheng Ting Biotechnology Co., Ltd.
Ting Qi: Institutue of Crop Science & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University
Sanling Wu: Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University
Most Humaira Sultana: Institutue of Crop Science & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University
Ya-Nan Cao: Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Zhejiang University
Yu Wang: University of Virginia
Michael P. Timko: University of Virginia
Song Ge: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences
Longjiang Fan: Institutue of Crop Science & Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University
Yongliang Lu: China National Rice Research Institute, Chinese Academy of Agricultural Sciences

Nature Communications, 2017, vol. 8, issue 1, 1-12

Abstract: 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.

Date: 2017
References: Add references at CitEc
Citations: View citations in EconPapers (4)

Downloads: (external link)
https://www.nature.com/articles/ncomms15323 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms15323

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/ncomms15323

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().