基于全基因组重测序分析西门塔尔牛遗传多样性与群体结构  

Analysis of Genetic Diversity and Population Structure of Simmental Cattle Based on Whole Genome Resequencing

作　　者：胡鑫 游伟[1,2] 姜富贵 成海建[1,2] 孙志刚 宋恩亮[1,2] HU Xin;YOU Wei;JIANG Fugui;CHENG Haijian;SUN Zhigang;SONG Enliang(Shandong Key Laboratory of Animal Disease Control and Breeding,Institute of Animal Science and Veterinary Medicine,Shandong Academy of Agricultural Sciences,Jinan 250100,China;Key Laboratory of Livestock and Poultry Multi-omics of Ministry of Agriculture and Rural Affairs,Jinan 250100,China;Green Food Agriculture and Animal Husbandry Technology Co.,LTD.,Yantai 265701,China)

机构地区：[1]山东省农业科学院畜牧兽医研究所,山东省畜禽疫病防治与繁育重点实验室,济南250100 [2]农业农村部畜禽生物组学重点实验室,济南250100 [3]格润富德农牧科技股份有限公司,烟台265701

出　　处：《畜牧兽医学报》2025年第3期1189-1202,共14页ACTA VETERINARIA ET ZOOTECHNICA SINICA

基　　金：泰山产业领军人才工程专项经费;烟台市科技计划项目(2023ZDCX024);现代农业(肉牛牦牛)产业技术体系(CARS-37);山东省现代农业产业技术体系牛产业创新团队(SDAIT-09-03);山东省农业科学院创新工程(CXGC2024F10)。

摘　　要：旨在对西门塔尔牛群体遗传多样性和遗传结构进行分析,为配种方案和遗传改良提供理论依据。本研究对149头西门塔尔牛的全基因组进行了重测序,并利用这些基因组数据获取的高质量单核苷酸多态性(single-nucleotide polymorphisms,SNPs)位点,对其遗传结构、连续纯合片段(runs of homozygosity,ROH)以及其亲缘关系和家系构建等方面进行了深入的分析。结果显示,149头西门塔尔牛平均测序深度为5×,质控后共鉴定到1265356个SNPs位点,平均最小等位基因频率为0.067,平均多态信息含量为0.083,平均观察杂合度为0.121,平均期望杂合度为0.157。亲缘关系G矩阵与状态同源(identical by state,IBS)遗传距离矩阵具有相似的结果,大部分个体间的亲缘关系呈中等水平。在149头西门塔尔牛个体中,共检测到70个基因组ROH,且ROH总长度为127627.935 kb,其中有98.57%的ROH是长度介于在1~5 Mb之间。基于ROH计算得到的近交系数为0.0003,提示近亲繁殖程度不高。此外,进化树分析将这149头西门塔尔牛划分成为22个不同的家系分支。综上所述,西门塔尔牛群体表现出相对丰富的多样性和适度的亲缘关系。在少数个体中观察到近亲繁殖,但种群的整体近亲繁殖水平仍然很低。The aim was to analyze the genetic diversity and genetic structure of Simmental cattle populations to provide a theoretical basis for breeding programs and genetic improvement.In this study,149 Simmental cattle were subjected to whole genome resequencing,and genetic structure,runs of homozygosity(ROH),and kinship and lineage construction were analyzed based on high-quality single-nucleotide polymorphisms(SNPs)sites obtained from all the genomic data.The results showed that the average sequencing depth of 149 Simmental cattle was 5×,and a total of 1265356 SNPs loci were identified after quality control,with an average minimum allele frequency of 0.067,an average polymorphic information content of 0.083,an average observed heterozygosity of 0.121,and an average expected heterozygosity of 0.157.The G matrix of kinship and the IBS distance matrix had similar results,and most individuals had medium level of kinship.A total of 70 genomic ROH were detected in 149 Simmental cattle with a total ROH length of 127627.935 kb,of which 98.57%were between 1 to 5 Mb in length.The inbreeding coefficient based on ROH was 0.0003,suggesting a low degree of inbreeding.In addition,evolutionary tree analysis classified these 149 Simmental cattle into 22 different family branches.In summary,the Simmental cattle herd showed relatively rich diversity and moderate relatedness.Inbreeding was observed in a few individuals,but the overall level of inbreeding in the population remained low.

关 键 词：西门塔尔牛 低密度全基因组重测序 群体遗传结构 遗传多样性 亲缘关系 

分 类 号：S823.2[农业科学—畜牧学]