基于简化基因组测序评估陇南山羊群体遗传多样性和群体结构  

Evaluation of Genetic Diversity and Population Structure of Longnan Goats Using SLAF-seq

作　　者：马克岩 刘占经 白雅琴 马友记[1] Ma Keyan;Liu Zhanjing;Bai Yaqin;Ma Youji(College of Animal Science and Technology,Gansu Agricultural University,Lanzhou,730070,Gansu;Animal Disease Control and Prevention Center of Tianzhu Tibetan Autonomous County,Wuwei,733200,Gansu;Animal Husbandry Technology Extension Station of Gansu Province,Lanzhou,730030,Gansu)

机构地区：[1]甘肃农业大学动物科学技术学院,甘肃兰州730070 [2]天祝县动物疫病预防控制中心,甘肃武威733200 [3]甘肃省畜牧技术推广总站,甘肃兰州730030

出　　处：《中国畜禽种业》2024年第4期8-17,共10页The Chinese Livestock and Poultry Breeding

基　　金：农业农村部政府购买服务合同项目(19221204);中央财政农业产业发展资金项目“甘肃省羊遗传资源普查”(CFCAD2023-019);甘肃省2022年农业种质资源普查项目(GSCQ-2022-03)。

摘　　要：该试验旨在利用简化基因组测序(specific-locus amplified fragment sequencing, SLAF-seq)分析陇南山羊群体遗传多样和群体结构,为陇南山羊后续保种计划的制订提供依据。该研究对50只陇南山羊(公、母各25只)进行全基因组SNP检测;计算观测杂合度(Ho)、期望杂合度(He)、多态信息含量(PIC)、香浓维纳指数(SHI)、基因多样性指数(Nei)及次要等位基因频率(MAF)等6个指标进行遗传多样性评估。结果表明,50只陇南山羊共检测到655514个SNPs位点。陇南山羊的Ho、 He、 PIC、 SHI、 Nei及MAF指标值分别为0.193、0.286、 0.236、 0.449、 0.290、 0.200,说明该群体遗传多样性较低。陇南山羊群体LD值较低,衰退速度较快,说明该群体并未受到过强烈的人工选择压力。此外,PCA与系统发育树结果均表明陇南山羊群体内部出现分化,可分为2个大的亚群。陇南山羊群体平均IBS遗传距离为0.7391,结合亲缘关系G矩阵热图,表明陇南山羊群体大部分个体亲缘关系较远。50只陇南山羊个体共检测到47206个ROH,平均ROH长度37.86 Mb,基于ROH的近交系数FROH范围为0.0535~0.2574,平均FROH值为0.1472,说明陇南山羊群体存在近交风险。可见,陇南山羊内部存在分化,可分为2个大的亚群,陇南山羊群体遗传多样性较低,部分个体间存在较大的近交风险,可能需要采取保种措施保护陇南山羊遗传资源。This study aims to analyze the genetic diversity and population structure of Longnan goats using specific-locus amplified fragment sequencing(SLAF-seq).The findings of this research will provide a basis for the formulation of conservation plans for the Longnan goats.This study performed whole-genome SNP genotyping on a total of 50 Longnan goats,consisting of 25 males and 25 females,to investigate their genetic diversity.Six genetic diversity indices,including observed heterozygosity(Ho),expected heterozygosity(He),polymorphic information content(PIC),Shannon-Weaver index(SHI),Nei's genetic diversity index(Nei),and minor allele frequency(MAF),were calculated for evaluation.The results showed that a total of 655514 SNPs were detected in the 50 Longnan goats.The values of Ho,He,PIC,SHI,Nei,and MAF for the Longnan goat population were 0.193,0.286,0.236,0.449,0.290,and 0.200,respectively,indicating a relatively low level of genetic diversity in the population.The LD values within the Longnan goat population were low,and the decay rate was rapid,suggesting that the population has not been subjected to strong artificial selection pressure.Furthermore,both PCA and phylogenetic tree analysis consistently indicated the occurrence of population differentiation within the Longnan goat population,separating it into two major subgroups.The average IBS genetic distance within the Longnan goat population was 0.7391,and the kinship relationship G matrix heatmap indicated that most individuals within the population have relatively distant kinship.A total of 47206 ROH were detected in the 50 Longnan goats,with an average ROH length of 37.86 Mb.The FROH based on ROH ranged from 0.0535 to 0.2574,with an average FROH value of 0.1472,indicating the presence of inbreeding risk in the Longnan goat population.In summary,the Longnan goat population had a relatively low level of genetic diversity,and there is a significant risk of inbreeding among some individuals.Additionally,the population showed evidence of differentiation,which can be d

关 键 词：陇南山羊 简化基因组测序 种质资源 遗传多样性 连续纯合片段 

分 类 号：S813.9[农业科学—畜牧学]