川中黑山羊基因组近交系数和选择信号分析  

Analyses of Genomic Inbreeding Coefficients and Selection Signals in Chuanzhong Black Goats

作　　者：郭家中[1] 孙学良 向秋楠 肖凤敏 张红平[1] GUO Jiazhong;SUN Xueliang;XIANG Qiunan;XIAO Fengmin;ZHANG Hongping(College of Animal Science and Technology,Sichuan Agricultural University,Chengdu 611130,China)

机构地区：[1]四川农业大学动物科技学院,成都611130

出　　处：《四川农业大学学报》2022年第5期656-663,共8页Journal of Sichuan Agricultural University

基　　金：国家重点研发计划项目(2021YFD1100206,四川省凉山州肉羊提质增效技术集成与示范);四川省科技计划项目(2021YFYZ0003,育种攻关)。

摘　　要：【目的】旨在利用高密度SNPs评估川中黑山羊的近交水平并鉴定选择信号。【方法】基于41个川中黑山羊全基因组重测序数据筛选全基因组SNPs,分析连锁不平衡、估计有效群体大小并检测长纯合片段(runs of homozygosity,ROH)。使用5种方法(F_(ROH)、F_(UNI)、F_(HOM)、F_(VR1)和F_(VR2))估计个体基因组近交系数并进行比较。采用ROH岛、iHH12和XP-EHH 3种方法,鉴定川中黑山羊中正选择基因。【结果】连锁不平衡分析表明,SNPs之间的物理距离为10 bp时r^(2)为0.51,当此距离增加到1000 bp时r^(2)为0.2。在999世代前川中黑山羊有效群体大小为5696只,而13世代前则降低到190只。基于ROH,川中黑山羊群体的近交主要发生在250~500世代(F_(ROH 0.1-0.2 Mb))和100~250世代(F_(ROH 0.2-0.5 Mb))。另外,F_(ROH)与F_(UNI)和F_(HOM)估计值呈现显著正相关,而F_(UNI)与F_(VR1)的相关性最高(r=0.983)。在鉴定的67个正选择基因中,NCAPG和LCORL在川中黑山羊群体中受到强烈的选择,这两个基因中共存在4个错义突变和2个移码突变。【结论】研究结果为川中黑山羊的遗传改良提供了参考,鉴定到的正选择基因可进一步应用于川中黑山羊的标记辅助选择。【Objective】This study aimed to evaluate inbreeding levels and identify selection signals in Chuanzhong Black goats using high-density SNP data.【Method】The whole-genome sequencing data for 41 goats were used to screen genome-wide SNPs,analyze linkage disequilibrium and effective population size and detect runs of homozygosity in Chuanzhong Black goats.Individual genomic inbreeding coefficients were obtained and compared based on five methods(i.e.,F_(ROH),F_(UNI),F_(HOM),F_(VR1),and F_(VR2)).The positively selected genes in Chuanzhong Black goats were identified by using ROH islands,iHH12,and XP-EHH.【Result】The linkage disequilibrium analysis revealed that the genome-wide mean r2 decreased rapidly from 0.51 between SNP pairs at a distance of 10 bp to 0.20 at 1000 bp.The estimated effective population size showed a continuous reduction from 5696 at 999 generations ago to 190 at 13 generations ago in Chuanzhong Black goats.On the basis of identified ROH,the inbreeding levels at current generation were mainly caused by 250-500 generations(F_(ROH 0.1-0.2 Mb))and 100-250 generations(F_(ROH 0.2-0.5 Mb))in Chuanzhong Black goats.In addition,FROH showed significant correlations with F_(UNI) and F_(HOM)(P<0.05),and the highest correlation(r=0.983)was between F_(UNI) and F_(VR1).A total of 67 postively selected genes were detected using ROH islands,iHH12,and XP-EHH.Strikingly,both NCAPG and LCORL genes were under strong selection,in which four missense and two frameshift mutations were present.【Conclusion】The results of this study provide a reference for the genetic improvement of Chuanzhong Black goats.The identified positively selected genes may promote the application of the marker-assisted selection of Chuanzhong Black goats.

关 键 词：山羊 全基因组重测序 基因组近交系数 选择信号 

分 类 号：S827[农业科学—畜牧学]