Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass (<i>Micropterus</i> <i>salmoides</i>)
Chengfei Sun, 1农业农村部热带亚热带水产资源利用与养殖重点实验室, 中国水产科学研究院珠江水产研究所, 广东 广州 510380, 中国, Xinhui Zhang, Junjian Dong, Xinxin You, Yuanyuan Tian, Fengying Gao, He-Tong Zhang, Qiong Shi, Xing Ye, 深圳市华大海洋研究院, 深圳华大海洋科技有限公司, 深圳市海洋生物基因组学重点实验室, 广东省海洋经济动物分子育种重点实验室, 广东 深圳 518081, 中国, 中国科学院大学生命科学学院, 北京 100049, 中国
Abstract
Largemouth bass (<i>Micropterus</i> <i>salmoides</i>) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study, we sequenced 149 largemouth bass fish, including protospecies (imported from the US) and improved breeds (four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection, including several associated with growth (p<i>sst1</i> and <i>grb10</i>), early development (<i>klf9</i>, <i>sp4</i>, and <i>sp8</i>), and immune traits (<i>pkn2</i>, <i>sept2</i>, <i>bcl6</i>, and <i>ripk2</i>). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.