Xia Jun Hong, Bai Zhiyi, Meng Zining, Zhang Yong, Wang Le, Liu Feng, Jing Wu, Wan Zi Yi, Li Jiale, Lin Haoran, Yue Gen Hua
Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore.
State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
Sci Rep. 2015 Sep 16;5:14168. doi: 10.1038/srep14168.
Natural selection and selective breeding for genetic improvement have left detectable signatures within the genome of a species. Identification of selection signatures is important in evolutionary biology and for detecting genes that facilitate to accelerate genetic improvement. However, selection signatures, including artificial selection and natural selection, have only been identified at the whole genome level in several genetically improved fish species. Tilapia is one of the most important genetically improved fish species in the world. Using next-generation sequencing, we sequenced the genomes of 47 tilapia individuals. We identified a total of 1.43 million high-quality SNPs and found that the LD block sizes ranged from 10-100 kb in tilapia. We detected over a hundred putative selective sweep regions in each line of tilapia. Most selection signatures were located in non-coding regions of the tilapia genome. The Wnt signaling, gonadotropin-releasing hormone receptor and integrin signaling pathways were under positive selection in all improved tilapia lines. Our study provides a genome-wide map of genetic variation and selection footprints in tilapia, which could be important for genetic studies and accelerating genetic improvement of tilapia.
自然选择和为遗传改良进行的选择性育种在一个物种的基因组中留下了可检测的特征。识别选择特征在进化生物学以及检测有助于加速遗传改良的基因方面都很重要。然而，包括人工选择和自然选择在内的选择特征，仅在几种遗传改良鱼类的全基因组水平上得到了识别。罗非鱼是世界上最重要的遗传改良鱼类之一。利用下一代测序技术，我们对47条罗非鱼个体的基因组进行了测序。我们总共鉴定出143万个高质量单核苷酸多态性（SNP），并发现罗非鱼的连锁不平衡（LD）块大小在10 - 100 kb之间。我们在每条罗非鱼品系中检测到了一百多个假定的选择性清除区域。大多数选择特征位于罗非鱼基因组的非编码区域。Wnt信号通路、促性腺激素释放激素受体和整合素信号通路在所有改良罗非鱼品系中都受到正选择。我们的研究提供了罗非鱼遗传变异和选择印记的全基因组图谱，这对于罗非鱼的遗传学研究和加速其遗传改良可能具有重要意义。
