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

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 112; no. 39; pp. E5411 - E5419
• Main Authors: Xie, Weibo, 谢为博, Wang, Gongwei, 王功伟, Yuan, Meng, Yao, Wen, Lyu, Kai, Zhao, Hu, Yang, Meng, Li, Pingbo, Zhang, Xing, Yuan, Jing, Wang, Quanxiu, Liu, Fang, Dong, Huaxia, Zhang, Lejing, Li, Xinglei, Meng, Xiangzhou, Zhang, Wan, Xiong, Lizhong, He, Yuqing, Wang, Shiping, Yu, Sibin, Xu, Caiguo, Luo, Jie, Li, Xianghua, Xiao, Jinghua, Lian, Xingming, 练兴明, Zhang, Qifa, 张启发
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 29.09.2015; National Acad Sciences
• Series: PNAS Plus
• Subjects: Agricultural production; Agronomy; Biological Sciences; Computational Biology; Cultivars; Gene loci; Genetic Markers - genetics; Genetic Variation; Genetics; Genome, Plant - genetics; Genome-Wide Association Study; Genomics; History, 20th Century; History, 21st Century; Oryza - genetics; Oryza - growth & development; Plant breeding; Plant Breeding - history; Plant Breeding - methods; Plant reproduction; PNAS Plus; Regression Analysis; Rice; Selection, Genetic; Subpopulations; GWAS; breeding signature; resequencing; rice improvement
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1515919112

Intensive rice breeding over the past 50 y has dramatically increased productivity especially in theindicasubspecies, 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) andindica II(IndII), in theindicasubspecies, 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 betweenIndIandIndII,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.