基于全基因组重测序评估郏县红牛保种群遗传多样性与群体结构
Genetic Diversity and Population Structure Analysis of Jiaxian Red Cattle Based on Whole Genome Sequencing
张岩 1魏稚彤 1虎业浩 1张花菊 2张曼 1付彤 1刘贤 3李志钢 2祁兴磊 4王二耀 5张子敬 5梁栋 1高腾云1
作者信息
- 1. 河南农业大学动物科技学院,郑州 450046
- 2. 平顶山市畜牧技术推广站,平顶山 467000
- 3. 河南省畜牧总站,郑州 450008
- 4. 泌阳县畜牧技术服务中心,泌阳 463700
- 5. 河南省农业科学院畜牧兽医研究所,郑州 450002
- 折叠
摘要
[目的]了解郏县红牛保种群的群体结构和遗传多样性,从而更好地保护和利用郏县红牛遗传资源.[方法]基于全基因组重测序技术,对30头郏县红牛的全基因组单核苷酸多态性(single nucleotide polymorphism,SNP)进行检测,并通过分析群体遗传多样性、群体结构、连续纯合片段(runs of homozygosity,ROH)分布特征和亲缘关系,对郏县红牛保种群的保种效果进行综合评估.[结果]在30头郏县红牛个体中共检测到41 215 797个高质量SNPs位点;郏县红牛群体遗传多样性丰富,最小等位基因频率为0.13±0.13,多态性标记比例为0.58±0.33,期望杂合度为0.192±0.152,观测杂合度为0.191±0.158,核苷酸多样性为0.003±0.001.郏县红牛群体的有效群体含量呈逐代下降趋势,在1 000代前有效群体含量为2 716头,在20代前为143头;郏县红牛个体间的遗传距离介于0.80～0.89之间,平均遗传距离为0.83±0.02.聚类分析显示,30头郏县红牛共分为7个家系,15头公牛可分为5个家系;30头郏县红牛个体中共检测到5 947个ROH,总长度为2.8 Gb,长度为0～0.5 Mb的ROH占比最多(73.08％),2～4 Mb的ROH占比最少(0.40％),基于ROH的平均近交系数为0.19±0.07,15头公牛的平均近交系数为0.15±0.05.[结论]郏县红牛保种群遗传多样性丰富,群体结构没有出现明显分层,整体上保持了较高水平的近交,出现了一定的近交风险,需加强选种选配工作,以确保郏县红牛遗传资源的可持续发展.
Abstract
[Objective]This study was aimed to understand the genetic diversity and population structure of Jiaxian Red cattle conservation population,make a better protection and utilization of the genetic resources of Jiaxian Red cattle.[Method]Based on whole genome sequencing technology,the single nucleotide polymorphism(SNP)of 30 Jiaxian Red cattle were detected,and a comprehensive assessment of the conservation effectiveness in Jiaxian Red cattle conservation population was conducted by analyzing population genetic diversity,population structure,distribution characteristics of runs of homozygosity(ROH),and kinship relationships.[Result]A total of 41 215 797 high-quality SNPs were detected among 30 individuals of Jiaxian Red cattle.The genetic diversity within Jiaxian Red cattle population was extensive,with a minimum allele frequency of 0.13±0.13,polymorphic marker ratio of 0.58±0.33,expected heterozygosity of 0.192±0.152,observed heterozygosity of 0.191±0.158,and nucleotide diversity of 0.003±0.001.The effective population size of Jiaxian Red cattle population showed a decreasing trend over the generations,with an effective population size of 2 716 individuals before 1 000 generations ago,and 143 individuals before 20 generations ago.The genetic distance among individuals of Jiaxian Red cattle ranges from 0.80 to 0.89,with an average genetic distance of 0.83±0.02.Cluster analysis revealed that 30 individuals of Jiaxian Red cattle were divided into a total of 7 families,with 15 bulls being divided into 5 families.A total of 5 947 ROH were detected among 30 individuals of Jiaxian Red cattle,with a cumulative length of 2.8 Gb.The segments ranging from 0 to 0.5 Mb represented the highest proportion at 73.08％,while segments of 2 to 4 Mb represented the lowest proportion at 0.40％.The average inbreeding coefficient based on ROH was 0.19±0.07,and the average inbreeding coefficient of 15 bulls was 0.15±0.05.[Conclusion]The conservation population of Jiaxian Red cattle exhibited rich genetic diversity and no obvious stratification,maintaining higher levels of inbreeding overall.For the emerging risk of inbreeding,it was necessary to strengthen breeding selection and matching efforts to ensure the sustainable development of genetic resource in Jiaxian Red cattle.
关键词
郏县红牛/全基因组重测序/遗传多样性/群体结构Key words
Jiaxian Red cattle/whole genome sequencing/genetic diversity/population structure引用本文复制引用
基金项目
国家自然科学基金青年项目(32202636)
河南省重大科技专项(221100110200)
河南省肉牛产业技术体系(HARS-22-13-T)
现代农业产业技术体系(CARS36)
出版年
2024
国家科技期刊平台
NSTL
万方数据