全基因组重测序解析秦川牛保种群遗传多样性和遗传结构

Analysis of genetic diversity and genetic structure of Qinchuan cattle conservation population using whole-genome resequencing

在畜禽资源保护中,群体遗传多样性和遗传结构是决定保种效果的重要因素。本研究采用全基因组重测序技术检测100头秦川牛(30头公牛、70头母牛)的基因组变异,通过分析群体遗传多样性、连续纯合片段(runs of homozygosity,ROH)分布特征、亲缘关系和家系结构,对秦川牛的保种效果进行了综合评估。结果显示,100头秦川牛共检测到20,968,017个高质量SNPs位点,平均最小等位基因频率为0.191±0.124,平均多态信息含量为0.279±0.131,平均观察杂合度为0.275±0.131,平均期望杂合度为0.279±0.131,表明秦川保种群遗传多样性较为丰富。秦川牛保种群体平均状态同源(identity by state,IBS)遗传距离为0.243±0.020,其中公牛为0.242±0.021,亲缘关系G矩阵结果与IBS距离矩阵结果一致,均显示秦川牛保种群部分个体间亲缘关系较近。100头秦川牛个体共检测到8258个基因组ROH,ROH总长度为9.64 GB,平均ROH长度为1.167±1.203 Mb,69.35%的ROH是长度为0.5~1 Mb的短ROH。个体平均ROH总长度为96.40 Mb。基于ROH的平均近交系数为0.039±0.039,其中30头秦川公牛的平均近交系数为0.044±0.035,表明部分公牛个体存在一定程度的近交积累。进化树结果显示,秦川牛保种群所测个体可分为8个家系,包括7个含公牛家系和1个不含公牛家系。本研究表明,秦川牛保种群的遗传多样性较为丰富,未出现较大程度近交积累,但部分个体间存在近交风险,应强化选配以确保秦川牛资源的可持续发展。

In the conservation of livestock and poultry resources,population genetic diversity and genetic structure of the conservation population are important factors affecting the effectiveness of conservation.In this study,whole-genome resequencing technology was used to detect genomic variation in 100 Qinchuan cattle(30 bulls and 70 cows).By analyzing population genetic diversity,runs of homozygosity(ROH)distribution features,kinship relationships,and family structure,the conservation effectiveness of Qinchuan cattle was comprehensively evaluated.The results showed that a total of 20,968,017 high-quality SNPs were detected in 100 Qinchuan cattle,the average minimum allele frequency was 0.191±0.124,the average polymorphic information content was 0.279±0.131,and the average observed heterozygosity was 0.275±0.131,the average expected heterozygosity is 0.279±0.131,indicating that the genetic diversity of the Qinchuan cattle conservation population is relatively rich.The average identity by state(IBS)distance of the Qinchuan conservation population was 0.243±0.020,with a value of 0.242±0.021 for the bulls.The results of the kinship G-matrix were consistent with the results of the IBS distance matrix,both showing that some individuals in the conservation population had close kinship.A total of 8258 genomic ROH were detected in 100 Qinchuan cattle,with a total length of 9.64 GB.The average length of ROH fragments was 1.167±1.203 Mb,69.35%of the ROH were short ROH with a length of 0.5~1 Mb,and the average total length of ROH per individual was 96.40 Mb.The average inbreeding coefficient based on ROH was 0.039±0.039,with a value of 0.044±0.035 for the bulls,indicating that some bulls had a certain degree of inbreeding accumulation.The results of the phylogenetic tree combined with kinship analysis showed that the individuals in the Qinchuan cattle conservation population could be divided into eight families,including seven families with bulls and one family without bulls.This study demonstrated that the genetic diversity of the Qinchuan conservation population is relatively rich,with no significant inbreeding accumulation,but there is a risk of inbreeding among some individuals.Therefore,it is necessary to strengthen selection and mating to ensure the sustainable development of Qinchuan cattle resources.