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Research Article

Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection

Weibo Xie, Gongwei Wang, Meng Yuan, Wen Yao, Kai Lyu, Hu Zhao, Meng Yang, Pingbo Li, Xing Zhang, Jing Yuan, Quanxiu Wang, Fang Liu, Huaxia Dong, Lejing Zhang, Xinglei Li, Xiangzhou Meng, Wan Zhang, Lizhong Xiong, Yuqing He, Shiping Wang, Sibin Yu, Caiguo Xu, Jie Luo, Xianghua Li, Jinghua Xiao, Xingming Lian, and Qifa Zhang
  1. National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China

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PNAS September 29, 2015 112 (39) E5411-E5419; first published September 10, 2015; https://doi.org/10.1073/pnas.1515919112
Weibo Xie
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Gongwei Wang
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Meng Yuan
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Wen Yao
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Kai Lyu
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Hu Zhao
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Meng Yang
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Pingbo Li
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Xing Zhang
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Jing Yuan
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Quanxiu Wang
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Fang Liu
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Huaxia Dong
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Lejing Zhang
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Xinglei Li
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Xiangzhou Meng
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Wan Zhang
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Lizhong Xiong
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Yuqing He
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Shiping Wang
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Sibin Yu
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Caiguo Xu
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Jie Luo
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Xianghua Li
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Jinghua Xiao
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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Xingming Lian
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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  • For correspondence: qifazh@mail.hzau.edu.cn xmlian@mail.hzau.edu.cn
Qifa Zhang
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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  • For correspondence: qifazh@mail.hzau.edu.cn xmlian@mail.hzau.edu.cn
  1. Contributed by Qifa Zhang, August 11, 2015 (sent for review July 2, 2015; reviewed by Roberto Tuberosa and Yunbi Xu)

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Significance

Intensive rice breeding over the past 50 y has produced many high-performing cultivars, but our knowledge of the genomic changes associated with such improvement remains limited. By analyzing sequences of 1,479 rice accessions, this study identified genomic changes associated with breeding efforts, referred to as breeding signatures, involving 7.8% of the rice genome. Accumulation of selected regions is positively correlated with yield improvement. The number of selected regions in a line may be used for predicting agronomic potential, and the selected loci may provide useful targets for rice improvement.

Abstract

Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement.

  • rice improvement
  • breeding signature
  • GWAS
  • resequencing

Footnotes

  • ↵1W.X. and G.W. contributed equally to this work.

  • ↵2To whom correspondence may be addressed. Email: qifazh{at}mail.hzau.edu.cn or xmlian{at}mail.hzau.edu.cn.
  • Author contributions: W.X. and Q.Z. designed research; W.X., G.W., M. Yuan, W.Y., K.L., and X. Lian performed research; M. Yuan, W.Y., H.Z., M. Yang, P.L., X.Z., J.Y., Q.W., F.L., H.D., L.Z., Xinglei Li, X.M., W.Z., L.X., Y.H., S.W., S.Y., C.X., J.L., Xianghua Li, and J.X. contributed new reagents/analytic tools; W.X. analyzed data; and W.X., G.W., X. Lian, and Q.Z. wrote the paper.

  • Reviewers: R.T., University of Bologna, Italy; Y.X., Chinese Academy of Agricultural Sciences.

  • The authors declare no conflict of interest.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1515919112/-/DCSupplemental.

Freely available online through the PNAS open access option.

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Breeding signatures of rice improvement
Weibo Xie, Gongwei Wang, Meng Yuan, Wen Yao, Kai Lyu, Hu Zhao, Meng Yang, Pingbo Li, Xing Zhang, Jing Yuan, Quanxiu Wang, Fang Liu, Huaxia Dong, Lejing Zhang, Xinglei Li, Xiangzhou Meng, Wan Zhang, Lizhong Xiong, Yuqing He, Shiping Wang, Sibin Yu, Caiguo Xu, Jie Luo, Xianghua Li, Jinghua Xiao, Xingming Lian, Qifa Zhang
Proceedings of the National Academy of Sciences Sep 2015, 112 (39) E5411-E5419; DOI: 10.1073/pnas.1515919112

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Breeding signatures of rice improvement
Weibo Xie, Gongwei Wang, Meng Yuan, Wen Yao, Kai Lyu, Hu Zhao, Meng Yang, Pingbo Li, Xing Zhang, Jing Yuan, Quanxiu Wang, Fang Liu, Huaxia Dong, Lejing Zhang, Xinglei Li, Xiangzhou Meng, Wan Zhang, Lizhong Xiong, Yuqing He, Shiping Wang, Sibin Yu, Caiguo Xu, Jie Luo, Xianghua Li, Jinghua Xiao, Xingming Lian, Qifa Zhang
Proceedings of the National Academy of Sciences Sep 2015, 112 (39) E5411-E5419; DOI: 10.1073/pnas.1515919112
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