Xie Weibo, Wang Gongwei, 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, Zhang Qifa
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):E5411-9. doi: 10.1073/pnas.1515919112. Epub 2015 Sep 10.
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.
在过去50年里，密集的水稻育种显著提高了产量，尤其是在籼稻亚种中，但我们对与此类改良相关的基因组变化的了解一直有限。在本研究中，我们分析了来自73个国家的1479份水稻种质（包括地方品种和现代栽培品种）的低覆盖度测序数据。我们在籼稻亚种中鉴定出两个主要亚群，即籼稻I（IndI）和籼稻II（IndII），它们对应于独立育种产生的两个假定杂种优势群。我们检测到200个区域，覆盖水稻基因组的7.8%，这些区域在IndI和IndII之间存在差异选择，因此被称为育种印记。这些区域包含大量已知的功能基因和与全基因组关联研究揭示的重要农艺性状相关的位点。一个品种的籽粒产量与育种印记的数量呈正相关，这表明一个品系中育种印记的数量可能有助于预测农艺潜力，而所选位点可能为水稻改良提供靶点。
