晋南牛遗传结构特征及选择信号分析

Analysis of Genetic Structure Characteristics andSelection Signal in Jinnan Cattle

【目的】阐明晋南牛的遗传结构特征,通过选择信号检测挖掘与晋南牛经济性状相关的候选基因,探究其在进化过程中的受选择情况。【方法】对晋南牛和红安格斯牛全基因组测序数据进行分析,鉴定2个群体的单核苷酸多态性(single nucleotide polymorphism, SNP)标记,分析其在基因组的位置及其结构特征,基于SNP信息进行主成分分析(PCA)、构建状态同源矩阵(IBS);采用群体遗传分化指数(Fst)和核苷酸多样性比值(θπ)方法联合筛选晋南牛基因组受到强烈选择的区域,并对筛选到的受选择基因进行数量性状基因座(QTL)定位、GO功能和KEGG通路富集分析。【结果】晋南牛群体SNPs位点主要分布于基因间区域,其次位于内含子区域。PCA和IBS分析结果表明,晋南牛和红安格斯牛2个群体间不存在杂交现象,且晋南牛群体中个体间遗传距离较远。通过Fst和θπ联合分析共筛选到188个潜在受选择区域。QTL分析结果表明晋南牛的选择信号多与生长、肉质及抗病性状相关。GO功能和KEGG通路富集分析显示,筛选到晋南牛强受选择的与经济性状相关的候选基因11个,包括组织蛋白酶1(CATHL1)、CATHL3、组织蛋白酶抗菌肽(CAMP)、CATHL4、RAS1激酶抑制因子(KSR1)、梅氏同源框1(MEIS1)、不规则片段极性蛋白1(DVL1)、多梳组无名指1(PCGF1)、RB转录辅助抑制因子1(RB1)、再生家族成员4(REG4)和卷曲类受体7(FZD7),在其外显子区域均检测到了SNP位点;除MEIS1、PCGF1、PZD7基因外,其他基因均存在非同义突变位点,且KSR1基因存在获得终止密码子的突变,CAMP基因存在获得终止密码子的突变和缺失终止密码子的突变;与红安格斯牛相比,晋南牛存在6个特有的受选择基因:CATHL1、CATHL4、CAMP、MEIS1、PCGF1、PZD7,主要与抗病性、生长和骨骼肌发育等相关。【结论】本研究从全基因组水平探究了晋南牛的遗传结构及选择信号特点,筛选出6个可能与晋南牛经济性状相关的候选基因,为后续晋南牛保种选育、特色性状形成的分子机制研究提供理论参考。

【Objective】The purpose of this study was to elucidate the genetic structure characteristics of Jinnan cattle,and explore candidate genes related to economic traits in Jinnan cattle through selection signal detection,in order to explore the selection status during the evolutionary process.【Method】Whole genome sequencing data of Jinnan cattle and Red Angus cattle were analyzed to identify the single nucleotide polymorphism(SNP)marker of the two populations,and analyze its position and structural characteristics in the genome.Principal component analysis(PCA)and identity by state(IBS)matrix were constructed based on SNP information.A combination of population genetic differentiation index(Fst)and nucleotide diversity ratio(θπ)was used to screen the highly selected regions in Jinan cattle genome,and quantitative trait locus(QTL),GO function and KEGG pathway enrichment were analyzed for the selected genes.【Result】The SNPs in Jinnan cattle population were mainly distributed in the intergene region,followed by the intron region.The results of PCA and IBS analysis showed that there was no hybridization between Jinnan cattle and Red Angus cattle,and the genetic distance between individuals in Jinnan cattle was far away.By the combined analysis of Fst andθπ,a total of 188 potential selected regions were screened.QTL analysis showed that the selection signals of Jinnan cattle were mainly related to growth,meat quality and disease resistance traits.GO function and KEGG pathway enrichment analysis showed that 11 candidate genes related to economic traits were selected strongly in Jinnan cattle,including cathepsin 1(CATHL1),CATHL 3,cathepsin antimicrobial peptide(CAMP),CATHL 4,kinase inhibitor of RAS1(KSR1),Meis homeobox 1(MEIS1),irregular fragment polar protein 1(DVL1),polycomb group ring finger 1(PCGF1),RB transcriptional repressor 1(RB1),regenerating family member 4(REG4)and frizzled class receptor 7(FZD7),and SNP sites were detected in the exon region of the genes.In addition to MEIS 1,PCGF 1 and FZD 7 genes,all other genes had non-synonymous mutation sites,and KSR 1 gene had stop gain mutation,and CAMP gene had stop gain and stop loss mutation.Compared with Red Angus cattle,there were 6 unique selected genes(CATHL 1,CATHL 4,CAMP,MEIS 1,PCGF 1 and PZD 7 genes)in Jinnan cattle,which were mainly related to disease resistance,growth and skeletal muscle development.【Conclusion】This study explored the genetic structure and selection signal characteristics of Jinnan cattle from the whole genome level,and screened 6 candidate genes that might be related to the economic traits of Jinnan cattle,providing theoretical reference for the subsequent research on conservation and breeding and the molecular mechanism of characteristic trait formation in Jinnan cattle.