摘要
旨在深入了解武雪山羊的群体结构,探究种群内部的遗传变异与分化和种群间的遗传差异及地理分布特征,为该品种的种质资源利用与开发提供重要依据。本研究采集18只武雪山羊(WXG)、9只湘东黑山羊(XDB)、9只合川白山羊(HCW)、9只大足黑山羊(DZB)、11只马关无角山羊(MGG)以及10只云岭山羊(YLG)的耳组织样本,用于全基因组重测序,平均测序深度约为10×。本研究基于全基因组数据分别利用GCTA、Plink、Admixture、Vcftools及PopLDdecay软件对6个群体进行了主成分分析、系统发育分析、群体遗传结构分析、杂合度分析、群体分化分析以及连锁不平衡分析。主成分分析的结果显示,武雪山羊与湘东黑山羊被聚为同一大类,表明这两个山羊品种遗传背景相似。系统进化分析的结果显示,武雪山羊与其他品种山羊群体单独聚为一支,在进化树上与湘东黑山羊的遗传距离较近。群体遗传结构分析的结果显示,当CV值最小时(K=3),武雪山羊与湘东黑山羊具有相同的遗传组分,说明两个群体间遗传分化指数程度较小,遗传背景相似。杂合度分析的结果显示,武雪山羊的核苷酸多态性(π)较低,观测杂合度(Ho)最低,且低于期望杂合度(He);ROH(runs of homozygosity)分析显示,武雪山羊的ROH数量和长度也明显高于其他品种,且基因组近交系数(F_(ROH))明显高于其他5个群体,这表明武雪山羊在基因组水平上存在明显的纯合片段积累和遗传多样性降低的现象。连锁不平衡分析的结果显示,武雪山羊表现出最高程度的连锁不平衡,进一步证实了该群体较低的遗传多样性。总之,这项研究系统解析了武雪山羊的遗传特性和群体结构,发现武雪山羊与湘东黑山羊遗传背景相似,其群体的遗传多样性较低,且存在一定的近交趋势,结果提示在后续的保种工作中需重点关注群体规模的扩大和近交系数的控制。这些发现不仅为深入了解其遗传背景提供了科学依据,同时为该品种的遗传资源保护与合理开发利用提供了重要理论参考。
This study aimed to provide an in-depth understanding of its population structure,which can explore the genetic variation and differentiation within populations and genetic differences between populations as well as geographic distribution characteristics,and provide an important basis for germplasm resource utilization and development of this breed.Ear tissues of 18 Wuxue goats(WXG),9 Xiangdong Black goats(XDB),9 Hechuan White goats(HCW),9 Dazu Black goats(DZB),11 Maguan Poll goat(MGG),and 10 Yunling goats(YLG)were collected and used for whole genome resequencing,with an average sequencing depth of about 10×.In this study,principal component analysis,phylogenetic analysis,population genetic structure analysis,heterozygosity analysis,population differentiation analysis,and linkage disequilibrium analysis were performed on 6 populations based on genome-wide data using GCTA,Plink,Admixture,Vcftools,and PopLDdecay software,respectively.The results of principal component analysis showed that Wuxue goats and Xiangdong Black goats were clustered into the same category,indicating that these two goat breeds have similar genetic backgrounds.In the phylogenetic analysis,Wuxue goats and other breeds of goat populations could be clustered into a single cluster,and were genetically closer to Xiangdong Black goats in the evolutionary tree.The results of the analysis of the genetic structure of the population showed that when the CV value was the smallest(K=3),Wuxue goats and Xiangdong Black goats had the same genetic components,indicating that the degree of genetic differentiation index between the two populations was small and the genetic backgrounds were similar.The results of heterozygosity analysis showed that Wuxue goats had lower nucleotide polymorphism(π),the lowest observed heterozygosity(Ho)and lower than the expected heterozygosity(He);ROH(runs of homozygosity)analyses showed that the number and length of ROHs in Wuxue goats were also significantly higher than those in other breeds,and the genomic inbreeding coefficient(F_(ROH))was significantly higher than that of the other 5 populations,which suggests that there was a significant accumulation of purity fragments and a decrease in genetic diversity at the genomic level in Wuxue goats.The results of linkage disequilibrium analyses showed that Wuxue goats exhibited the highest degree of linkage disequilibrium,which further illustrated the low genetic diversity of the population.In conclusion,this study systematically analysed the genetic characteristics and population structure of the Wuxue goat,and found that the genetic background of Wuxue goats is similar to that of Xiangdong Black goats,and that the genetic diversity of their populations is low and there is a certain tendency of inbreeding,which suggests that we should pay attention to the expansion of the population size and the control of the inbreeding coefficient in the subsequent work of breeding conservation.These findings not only provide a scientific basis for the in-depth understanding of the genetic background,but also provide an important theoretical reference for the conservation and rational development and utilization of genetic resources of this breed.
作者
任千姿
张佰忠
王真勍
王向林
龚颖
胡仁科
浦亚斌
苏鹏
李业芳
马月辉
李昊帮
蒋琳
REN Qianzi;ZHANG Baizhong;WANG Zhenqing;WANG Xianglin;GONG Ying;HU Renke;PU Yabin;SU Peng;LI Yefang;MA Yuehui;LI Haobang;JIANG Lin(Institute of Animal Science,Chinese Academy of Agricultural Sciences,Beijing 100193,China;Hunan Institute of Animal and Veterinary Science,Changsha 410131,China;Animal Husbandry and Aquatic Products Affairs Center of Xiangxi Autonomous Prefecture,Jishou 416000,China)
出处
《畜牧兽医学报》
北大核心
2025年第8期3787-3801,共15页
ACTA VETERINARIA ET ZOOTECHNICA SINICA
基金
国家重点研发项目(2022YFD1300204,2022YFF1000104-3)。
关键词
全基因组重测序
遗传多样性
群体进化
武雪山羊
群体结构
whole genome resequencing
genetic diversity
population evolution
Wuxue goat
population structure
