title: Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.
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.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Gongwei
authors.initials: G
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Meng
authors.initials: M
authors.lastname: Yuan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Yao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Lyu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Hu
authors.initials: H
authors.lastname: Zhao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Meng
authors.initials: M
authors.lastname: Yang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Pingbo
authors.initials: P
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Xing
authors.initials: X
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Yuan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Quanxiu
authors.initials: Q
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Fang
authors.initials: F
authors.lastname: Liu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Huaxia
authors.initials: H
authors.lastname: Dong
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Lejing
authors.initials: L
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Xinglei
authors.initials: X
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Xiangzhou
authors.initials: X
authors.lastname: Meng
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Wan
authors.initials: W
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Lizhong
authors.initials: L
authors.lastname: Xiong
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yuqing
authors.initials: Y
authors.lastname: He
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Shiping
authors.initials: S
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Sibin
authors.initials: S
authors.lastname: Yu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Caiguo
authors.initials: C
authors.lastname: Xu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Luo
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Xianghua
authors.initials: X
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Jinghua
authors.initials: J
authors.lastname: Xiao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China qifazh@mail.hzau.edu.cn xmlian@mail.hzau.edu.cn.
authors.forename: Xingming
authors.initials: X
authors.lastname: Lian
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China qifazh@mail.hzau.edu.cn xmlian@mail.hzau.edu.cn.
authors.forename: Qifa
authors.initials: Q
authors.lastname: Zhang
mesh_terms: D019295:Computational Biology; D005819:Genetic Markers / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study; D049673:History, 20th Century; D049674:History, 21st Century; D012275:Oryza / Q000235:genetics* / Q000254:growth & development*; D000069600:Plant Breeding / Q000266:history* / Q000379:methods*; D012044:Regression Analysis; D012641:Selection, Genetic
chemical_list: D005819:Genetic Markers
keywords: GWAS; breeding signature; resequencing; rice improvement