摘要
【目的】试验旨在对肃南牦牛进行群体遗传结构、选择信号分析和连续纯合片段(ROH)检测,挖掘肃南牦牛的种质特性相关基因。【方法】选择肃南牦牛、巴州牦牛、斯布牦牛、九龙牦牛和天祝白牦牛5个牦牛品种共计48头牦牛进行全基因组重测序,采用基因组变异检测流程(GATK)获得高质量的单核苷酸多态性(SNP)标记进行下游分析;对5个牦牛品种的基因型数据进行主成分分析、祖先成分分析和系统进化树分析以确定其群体结构;对5个牦牛群体进行ROH检测以及近交系数计算;采用综合单倍型评分(iHS)方法筛选共有高频ROH区域内受选择位点。【结果】5个牦牛品种共鉴定出15092883个SNPs,主要分布于内含子区域。亲缘关系计算结果显示,所有个体均不存在三代以内亲缘关系,满足后续分析要求。主成分分析表明,5个牦牛品种可以显著地分为5个类群,其中肃南牦牛群体内遗传变异较小。群体结构分析显示,肃南牦牛包含其他4种牦牛祖先成分,其中天祝白牦牛祖先成分所占的比例最大。ROH分析显示,5个牦牛品种共检测到8426个ROHs片段,其中高频ROH区域421个。相比于其他4个牦牛品种,肃南牦牛的ROH片段总长度和数目最多,具有较高的连锁程度,其近交系数远大于其他牦牛群体。在肃南牦牛高频ROH区域上注释得到465个候选基因,主要富集到与机体发育、大脑形态形成、脂肪氧化相关的通路,包括胚胎骨骼系统形态发生、前后模式规范、甲状腺发育通路和Hippo通路,其中与胚胎发育及组织分化过程相关的基因有同源框A3(HOXA3)、HOXA5、HOXD3,与肉品质相关的基因有花生四烯酸12B(ALOX12B)、ALOX15B、ALOXE3,与中脑发育相关的基因为成纤维细胞生长因子8(FGF8)。在7号染色体1个高频ROH区域中(Chr7:12661870-13045935)鉴定到3个共享基因(核内不均一性核糖核蛋白K(HNRNPK)、驱动蛋白27(KIF27)、G激酶锚定蛋白1(GKAP1))与牦牛共有的高原适应性有关。对共有高频ROH区域内的位点进行iHS分析,鉴定到的受选择基因主要与抗病性、内质网分泌蛋白加工及细胞周期调节相关,包括N-α乙酰转移酶25(NAA25)、内质网分子伴侣29(ERP29)、跨膜蛋白16(TMEM116)、TRAF型锌指结构域蛋白1(TRAFD1)、HECT结构域E3泛素连接酶4(HECTD4)基因。【结论】本研究从全基因组水平系统评估肃南牦牛的遗传多样性和遗传背景,鉴定了肃南牦牛ROH区域内与表型相关的基因,并重点挖掘了与其他牦牛品种共享高频ROH区域内的受选择基因,为肃南牦牛种质资源开发、利用提供了重要理论依据。
【Objective】The analysis of population genetic structure,selection signal analysis and ROH detection were performed to Sunan yak to explore the genes related to the germplasm characteristics of Sunan yak.【Method】A total of 48 yaks were collected from Sunan yak,Bazhou yak,Sibu yak,Jiulong yak and Tianzhu White yak for genome resequencing.Genome Analysis Toolkit(GATK)mutation detection process was used to obtain high-quality single nucleotide polymorphism(SNP)for downstream analysis.Principal component analysis,ancestral component analysis and phylogenetic tree analysis were used to determine the population structure of 5 yak breeds.ROH detection and inbreeding coefficient calculation of 5 yak populations were carried out.A comprehensive haplotype score(iHS)was used to screen selected sites in shared high-frequency ROH regions.【Result】By analyzing the SNPs identified from 5 yak breeds,a total of 15092883 SNPs were identified.The identified SNPs were mainly distributed in the intron regions.The results of kinship calculation showed that all individuals did not have kinship within 3 generations,which met the requirements of subsequent analysis.Principal component analysis showed that the 5 yak breeds could be significantly divided into 5 groups,and the genetic variation within the Sunan yak group was small.The population structure showed that Sunan yak contained other 4 yak ancestors,among which Tianzhu White yak accounted for the largest proportion.ROH analysis showed that a total of 8426 ROH fragments were detected in 5 yak breeds,of which 421 were in high-frequency ROH regions.Compared with the other 4 yak breeds,Sunan yak had the largest total length and number of ROH regions and had a higher degree of linkage,and its inbreeding coefficient was much larger than that of other yak populations.465 candidate genes were annotated on the high-frequency ROH region of Sunan yak,mainly enriched in pathways related to body development,brain morphogenesis,and fat oxidation,including embryonic skeletal system morphogenesis,anterior and posterior pattern specification,thyroid development pathways and Hippo path.Among them,genes related to embryonic development and tissue differentiation(homeobox A3(HOXA3),HOXA5,HOXD3),meat quality(arachidonic acid 12 B(ALOX12 B),ALOX15 B,ALOXE3),and midbrain development(fibroblast growth factor 8(FGF8))were identified.In addition,3 shared genes(heterogeneous nuclear ribonucleoprotein K(HNRNPK),kinesin family member 27(KIF27),G kinase anchor protein 1(GKAP1))were identified in a high-frequency ROH region on chromosome 7(Chr7:12661870-13045935),which were related to the plateau adaptation shared by yak.The iHS analysis of loci within the shared high-frequency ROH region identified selected genes that were mainly associated with disease resistance,endoplasmic reticulum-secreted protein processing,and cell cycle regulation,including N-alpha-acetyltransferase 25(NAA25),endoplasmic reticulum protein 29(ERP29),transmembrane protein16(TMEM116),TRAF-type zinc finger domain containing 1(TRAFD1)and HECT domain E3 ubiquitin protein ligase 4(HECTD4)genes.【Conclusion】This study systematically investigated the genetic diversity and identified candidate genes related to traits of Sunan yak at the genome-wide level,providing an important theoretical basis for the development and utilization of Sunan yak germplasm resources.
作者
鲍麒
包鹏甲
马晓明
吴晓云
孟光耀
褚敏
曹红梅
郎建英
安玉峰
梁春年
阎萍
BAO Qi;BAO Pengjia;MA Xiaoming;WU Xiaoyun;MENG Guangyao;CHU Min;CAO Hongmei;LANG Jianying;AN Yufeng;LIANG Chunnian;YAN Ping(Lanzhou Institute of Husbandry and Pharmaceutical Sciences,Chinese Academy ofAgricultural Sciences,Lanzhou 730050,China;Key Laboratory of Animal Geneticsand Breeding on Tibetan Plateau,Ministry of Agriculture and Rural Affairs,Lanzhou 730050,China;Key Laboratory of Gansu for Yak Breeding Engineering,Lanzhou 730050,China;Animal Husbandry and Veterinary Service Center of Sunan County,Sunan 734400,China)
出处
《中国畜牧兽医》
CAS
北大核心
2022年第8期2992-3005,共14页
China Animal Husbandry & Veterinary Medicine
基金
国家重点研发计划(2021YFD1600200)
现代农业(肉牛牦牛)产业技术体系建设专项资金(CARS-37)
中国农业科学院创新工程项目(25-LZIHPS-01)
科技援青合作专项(2020-QY-212)
甘肃省科技计划资助(20JR5RA580)。
