几个中国地方猪群体遗传结构和产仔数性状选择信号分析  

Population Genetic Structure and Selection Signatures Associated with Litter Size Trait in Several Chinese Indigenous Pig Breeds

作　　者：路玉洁 莫家远 綦文晶 朱思燃 杨丽丽 刘巧玲 卜亚歌 兰干球[1] 梁晶[1] LU Yujie;MO Jiayuan;QI Wenjing;ZHU Siran;YANG Lili;LIU Qiaoling;BU Yage;LAN Ganqiu;LIANG Jing(College of Animal Science & Technology, Guangxi University, Nanning 530004, China)

机构地区：[1]广西大学动物科学技术学院,南宁530004

出　　处：《畜牧兽医学报》2022年第2期360-369,共10页ACTA VETERINARIA ET ZOOTECHNICA SINICA

基　　金：国家现代农业产业技术体系(nycytxgxcxtd-15-01);广西创新驱动发展专项(桂科AA17204029);广西科技重大专项(桂科AA17292002)。

摘　　要：旨在对几个中国地方猪品种进行群体遗传结构分析,并筛选与中国地方猪产仔数相关的基因组选择信号及候选基因。本研究下载了6个中国地方品种猪共计102头个体的Illumina PorcineSNP60芯片数据,构建了包括19头迪庆藏猪、16头明光小耳猪、16头五指山猪在内的低产仔数组和包括11头姜曲海猪、20头蓝塘猪、20头梅山猪在内的高产仔数组,经质控和基因型填充后,使用软件进行亲缘关系分析、主成分分析、连锁不平衡衰减分析、群体遗传结构分析、进化树构建和选择信号分析,并对受选择位点进行基因定位和功能富集分析。对数据进行质控和基因型填充后共获得33285个SNPs位点,6个中国地方猪品种间个体的亲缘关系较远,品种内个体亲缘关系较近;6个群体的LD衰减速度都非常快,依次为梅山猪<蓝塘猪<姜曲海猪<明光小耳猪<五指山猪或迪庆藏猪;梅山猪群体内存在3个亲缘关系较高的小群体,明光小耳猪有部分个体与迪庆藏猪聚集在一起,各个猪种在进化树的距离与其地理距离较为一致。选择信号分析共筛选到176个受选择的SNPs位点,在其上、下游12.68 kb范围内共检测到66个候选基因,富集到6条信号通路。通过文献查阅发现5个可能与繁殖性状相关的基因,其中CHD7与生长发育迟缓和生殖器异常相关,FBXO43与繁殖力相关并且影响呈圆周运动的精子数量,RUNX1控制雌激素、雄激素和前列腺素的分泌,STRBP与卵巢发育有关,TEDDM1在附睾中特异性表达。CHD7、FBXO43、RUNX1、STRBP和TEDDM1基因可能作为中国地方猪产仔数性状的候选基因。The aim of this study was to analyze the population genetic structure of several Chinese indigenous pig breeds,and detect genomic selection signals and candidate genes related to litter size.The Illumina PorcineSNP60 microarray data of 102 pigs from 6 Chinese indigenous breeds was used,and constructed a low litter size group including 19 Diqing Tibetan pigs,16 Mingguang Xiaoer pigs and 16 Wuzhishan pigs,and a high litter size group including 11 Jiangquhai pigs,20 Lantang pigs and 20 Meishan pigs.After quality control and genotype imputation,softwares were used for genetic relationship analysis,principal component analysis,linkage disequilibrium attenuation analysis,population genetic structure analysis,phylogenetic tree construction and selection signal analysis,and gene localization and functional enrichment analysis of selected sites were carried out.A total of 33285 SNPs was obtained after data quality control and genotype imputation.The genetic relationships among the 6 Chinese indigenous pig breeds were far,whereas the relationships of individuals within breeds were close.The LD decay rates of the 6 populations were very fast,which were Meishan pig<Lantang pig<Jiangquhai pig<Mingguang Xiaoer pig<Wuzhishan pig or Diqing Tibetan pig in order.There were 3 subpopulations with high internal genetic relationship in Meishan pig population,and some individuals of Mingguang Xiaoer pig were clustered with Diqing Tibetan pig.The distance of each pig breed in the phylogenetic tree was consistent with the corresponding geographical distance.A total of 176 SNPs were detected by the selection signal analysis,and 66 candidate genes were obtained in their upstream and downstream range of 12.68 kb,which were enriched into 6 signaling pathways.Through literature review,five genes might be related to reproductive traits,among which CHD7 was related to growth retardation and genital abnormalities,FBXO43 was related to reproductive ability and affected the number of sperm in circular motion,RUNX1 affected the secretion of estroge

关 键 词：群体遗传结构 产仔数 选择信号 SNP位点 候选基因 

分 类 号：S828.2[农业科学—畜牧学]