民猪全基因组序列测定与分析  

Determination and analysis of the whole genome sequence of Min pig

作　　者：张冬杰[1,2] 何鑫淼 王文涛[1,2] 汪亮 刘娣[1,2] ZHANG Dongjie;HE Xinmiao;WANG Wentao;WANG Liang;LIU Di(Institute of Animal Husbandry Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086,China)

机构地区：[1]黑龙江省农业科学院畜牧研究所,哈尔滨150086 [2]农业农村部种养结合重点实验室,哈尔滨150086

出　　处：《东北农业大学学报》2018年第11期9-17,共9页Journal of Northeast Agricultural University

基　　金：黑龙江省科技攻关项目(GC12B311);黑龙江省科研机构创新能力提升专项(YC2016D001);国家生猪产业技术体系项目(CARS-37)

摘　　要：民猪是我国优良地方猪品种,具有高繁殖、耐粗饲、抗逆和肉质优良等特性,但遗传背景模糊。为合理保护和利用民猪资源,利用Illumina Hiseq2000测序平台,采用双末端测序方法,测定10头民猪和4头东北野猪全基因组序列,统计分析SNPs和InDel标记信息,利用NCBI数据库中已知的50个不同个体的SNPs信息作主成分分析并构建分子进化树,使用θπ和Fst两个参数筛选民猪和东北野猪基因组内受选择基因。结果表明,民猪基因组内检测8 255 874个SNPs,大量的SNPs发生在基因间区及内含子区;与猪dbSNP数据库相比,新发现7 739 173个SNPs;检测到739 647个InDel位点,其中纯合多于杂合位点。民猪在遗传距离上介于亚洲猪种和欧洲猪种之间,说明民猪在品种形成过程中,曾引入欧洲猪血统,东北野猪则与亚洲家猪和亚洲野猪聚为一类,符合其地理分布。民猪基因组内共181个基因受到选择,涉及能量代谢、脂质转运、脊椎及视神经发育等。东北野猪基因组内共411个基因受到选择,涉及神经系统、免疫应答、繁殖、线粒体能量代谢等。Min pig is a famous indigenous pig breed in China.It has the characteristics of high reproduction,rough feeding,good resistance and meat quality.But,its genetic background is fuzzy.In order to protect and utilize the Min pig resources more reasonably in the future,the Illumina Hiseq2000sequencing platform and the dual terminal sequencing method were used to determine the complete genome sequences of10Min pigs and four northeast wild boars.SNPs and InDel marker information were analyzed.SNPs information of Min pig,Northeast wild boar and50different individuals which came from NCBI database were analyzed together by principal component analysis.The phylogenetic tree was constructed,too.Using two parameters ofθπand Fst,the selected genes were screened in the genome of Min pig and Northeast wild boar.The results showed that there were8255874SNPs in Min pig genome and a large number of SNPs were occurred in the intergenic region and intron region.7739173were newly discovered SNPs comparing with dbSNP database of pigs.At the same time,739647InDel loci were detected.Homozygous InDel loci were more than hetero-zygous InDel loci.Min pig was existed between the Asian pig breeds and the European pig breeds in the genetic distance.It meaned that the Min pig had been introduced into the European pig breeds in the course of breed formation,while the northeast wild boar was clustered with the Asian pig and the Asian wild boar,conforming to its geographical distribution.181candidate genes were selected from the Min pig genome,which involved energy metabolism,lipid transport,spine and optic nerve development.411candidate genes were selected from northeast wild boar genome,including nervous system,immune response,reproduction,mitochondrial energy metabolism and so on.

关 键 词：民猪 SNPS INDEL 主成分分析 分子进化树 

分 类 号：S813.3[农业科学—畜牧学]