黄河鲤全基因组选择信号分析

Genome-Wide Selection Signature of Yellow River Common Carp Cyprinus carpio haematopterus

黄河鲤是我国重要的水产养殖鱼类,该类群经过长期的遗传改良后,其基因组上可能存在特定的选择信号,研究这些选择信号是筛选功能基因的重要策略之一。笔者对2个黄河鲤遗传改良群体(豫选黄河鲤新品系和福瑞鲤2号养殖群体)和1个未选育群体进行了全基因组重测序,共获得8665728个高质量的单核苷酸多态性(SNP)位点的分型数据,并采用群体间遗传分化指数、核苷酸多态性比值和跨群体复合似然比检验检测受到选择的基因组区域。取前5%的位点作为受选择位点,选择在多种方法中检测到重叠的区域作为候选区域,并对其进行基因注释。结果显示,在黄河鲤基因组上广泛存在选择信号,与未选育群体相比,两个遗传改良群体分别有1434和1333个基因受到选择,豫选黄河鲤新品系群体中受选择的基因富集到了细胞发育、心肌收缩、细胞分化、蛋白质糖基化等相关通路上,福瑞鲤2号养殖群体的受选择基因则与胚胎骨关节发育、细胞膜融合、神经递质分泌有关。将两个遗传改良群体混合,与未选育群体相比,检测到2037个基因受到选择,包括Fabp2、Acaca、Acsl、Cpt1基因等,这些基因显著富集在脂肪合成代谢相关的通路上,如甘油磷脂代谢、脂肪酸合成、脂肪酸代谢和过氧化物酶体增殖物激活受体信号通路。试验结果表明,在不同选育群体中受选择的基因组区域具有特异性,同时检测出与脂肪酸合成代谢相关的重要基因在黄河鲤遗传改良群体中受到选择。试验结果为探索黄河鲤生长性状的遗传改良机制提供新的思路,并有助于促进黄河鲤的基因组选择育种应用。

It is speculated that there should be specific selection signatures in the genetic improvement population of Yellow River common carp Cyprinus carpio haematopterus arising from long-term artificial selection after domestication.Understanding and improvement of the signatures at a genetic level is important to inform future efforts to further improve a fish which is one of the most important commercial species in freshwater culture with a long period of artificial selection.In this study,two genetically modified populations:12 whole sibling families(10)of the new strain of Yellow River common carp(F5)and the culture population of Furui carp No.2(FFRC No.2)and one unselected population were resequenced whole-genome,and a total of 8665728 high-quality SNP sites were obtained by typing data of SNP sites,and the selected genomic regions were detected by the fixation index(Fst),nucleotide diversity(πratio)and cross-population composite likelihood ratio test(XP-CLR).Top 5%of values was used as the threshold signature of artificial selection where were annotated to further identify potential candidate genes.To further control the false positive rates of the detection of selection signatures,genes identified by three methods were used in further enrichment analyses.In total,compared with the reference population,1434 and 1333 genes were potentially selected between two genetic improvement populations,respectively.These candidate genes were enriched in cell development,heart contraction,cell differentiation and protein glycosylation in new strain of Yellow River common carp.The candidate genes were enriched in embryonic skeletal joint development,membrane fusion and neurotransmitter secretion in C.carpio FFRC No.2 strain.Mixing two genetic improvement populations,compared with the reference population,2037 genes were annotated,including Fabp2,Acaca,Acsl and Cpt1.These candidate genes were significantly enriched in several fatty acid metabolism-related pathways,including glycerophospholipid metabolism,fatty acid biosynthesis,fatty acid degradation and peroxisome proliferators activate receptors(PPAR)signaling pathway,which may partly explain the difference between the genetic improvement population and reference population in terms of growth traits.In the current study,a number of regions with signatures of positive selection were identified,and further functional analyses on these regions identified a list of genes involved in fatty acid metabolism.The findings provide a new insight into the mechanism of genetic improvement of growth traits in common carp and contribute to promote the application of genomic selection in breeding of common carp.