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

• DOI: 10.1073/pnas.1515919112
• Publication Date: 2015-09-11T05:21:54Z
• Authors: 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
• Keywords: Genetic Markers; 0301 basic medicine; 2. Zero hunger; Computational Biology; Genetic Variation; Oryza; History, 20th Century; History, 21st Century; Plant Breeding; 03 medical and health sciences; Regression Analysis; Selection, Genetic; Genome, Plant; Genome-Wide Association Study

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.