| 王 晨1，马 宁2，郭春和1，袁仁强1，曾检华3，宋德清3，张惠文2，陈瑶生1，刘小红1.基于SNP 芯片分析的蓝塘猪遗传群体结构[J].广东农业科学,2018,45(6):110-115 |
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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 |
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| DOI：10.16768/j.issn.1004-874X.2018.06.018 |
| 中文关键词: 蓝塘猪 SNP 芯片 群体结构 ROH 近交 |
| 英文关键词: Lantang pig SNP chip population structure ROH inbreeding |
| 基金项目: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） |
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| 中文摘要: |
| 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。 |
| 英文摘要: |
| To protect and utilize the germplasm resource of Lantang pig，Illumina CAUPorince 50K 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. |
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