基于SNP芯片分析的蓝塘猪遗传群体结构  

Population structure of Lantang pig evaluated using SNP chip

作　　者：王晨[1] 马宁 郭春和[1] 袁仁强 曾检华 宋德清 张惠文 陈瑶生[1] 刘小红[1] WANG Chen;MA Ning;GUO Chun-he;YUAN Ren-qiang;ZENG Jian-hua;SONG De-qing;ZHANG Hui-wen;CHEN Yao-sheng;LIU Xiao-hong(School of Life Sciences,Sun Yat-sen University/State Key Laboratory of Biocontrol and Resources Utilization,Guangzhou 510006,China;Zijing Dongrui Agricultural and Livestock Co.,Ltd.,Heyuan 517447,China;Guangdong YIHAO Food Co.,Ltd.,Guangzhou 510620,China)

机构地区：[1]中山大学生命科学学院/有害生物控制与资源利用国家重点实验室,广东广州510006 [2]紫金东瑞农牧发展有限公司,广东河源517447 [3]广东壹号食品股份有限公司,广东广州510620

出　　处：《广东农业科学》2018年第6期110-115,174,共7页Guangdong Agricultural Sciences

基　　金：国家科技基础性工作专项(2014FY120800);广东省扬帆计划项目(2014YT02H042);广东省生猪产业创新团队建设项目(2017LM1137);广东省科技计划项目(2014B020202001)

摘　　要：为了保护和利用蓝塘猪种质资源,采用Illumina CAUPorince 50K SNP芯片对139头蓝塘猪进行遗传群体结构分析。结果显示,SNP芯片基因型分型的平均检出率高达98.24%,表明该芯片适合应用于中国地方猪。蓝塘猪的平均遗传距离值为0.3326±0.0339,主成分分析和G矩阵结果表明部分种猪之间亲缘关系较近。139头蓝塘猪种猪可以分成5个家系,分别为家系A、B、C、D和E,其中家系A、B、C和D均有种公猪。蓝塘猪的Y染色体共有两种单倍型,其中家系A和B属于单倍型A,家系C和D属于单倍型B。在蓝塘猪中共检测到1 680个ROH片段,10~20 Mb长度的ROH数量最多、占44.52%,平均每个蓝塘猪的ROH数量为12.09(±5.90)个,平均总长度为246.90(±170.93)Mb。通过SNP芯片,从遗传水平反映了一个蓝塘猪种群的群体结构,为地方猪种的保种、开发与利用提供了有力工具。To protect and utilize the germplasm resource of Lantang pig,Illumina CAUPorince 50 K SNP chip was used to analyze the population structure of 139 Lantang pigs. The results showed the average call rate of all the pigs was 98.24%,suggesting the SNP Chip was very suitable for Chinese indigenous pig breeds. The average genetic distance was 0.3326±0.0339,and furthermore,both PCA and G matrix revealed some Lantang pigs shared close genetic relationship. These Lantang pigs could be divided into five families,assigned as family A,B,C,D and E,separately,but only family A,B,C and D had stock boars. Two kinds of haplotypes were found on Y chromosome among Lantang pigs,all the individuals of family A and B belonged to haplotype A while family C and D belonged to haplotype B. A total of 1 680 ROHs were detected in Lantang pigs,the amount of ROH with 10～20 Mb size had the highest frequency which reached 44.52%. The average number of ROH per pig was 12.09±5.90,and the average total length of ROH for each pig was 246.90（±170.93）Mb. These results revealed a real population structure of a Lantang pig population in genetic level using the SNP chip,which provided a robust tool for the conversation,development and utilization of indigenous pig breeds.

关 键 词：蓝塘猪 SNP芯片 群体结构 ROH 近交 

分 类 号：S813.9[农业科学—畜牧学]