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OA北大核心CSTPCD

[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.