基于SNP芯片的固原鸡遗传结构与保种效果分析

Analysis of genetic structure and conservation effect of Guyuan chicken based on SNP chip

了解固原鸡的保种效果,为更好地保护和利用固原鸡这一重要地方种质资源提供参考和帮助。从固原鸡群体中随机采集公鸡、母鸡各30只血样,采用“京芯一号”55K芯片技术对固原鸡进行保种分析。结果显示,固原鸡群体有效含量为8.9,多态标记比例为0.828,期望杂合度为0.360,观测杂合度为0.359,说明该群体遗传变异较小,整齐度较高;G矩阵表明该群体中存在近亲交配的趋势;在检测到的1431个长纯合片段(runs of homozygosity,ROH)中,ROH长度在50~100 Mb的个体数量最多,占比达36.67%,该群体平均近交系数为0.11。结合基因组亲缘关系分析和聚类分析结果,现有30只公鸡样本可以划分为10个家系,其中25只母鸡分别划入不同家系,另外5只母鸡和所检测的公鸡亲缘关系系数均小于0.1,亲缘关系都比较远,因此,将它们归入了“其他”分类中。综上所述,该保种固原鸡群体遗传变异较小,选育程度较高,为降低群体的近交增量,后期的保种过程中需考虑亲缘关系再进行配种。

In order to understand the conservation effect of Gujun chicken and provide reference and help for better protection and utilization of Gujun chicken,an important local germplasm resource.Blood samples of 30 roosters and 30 hens were randomly collected from Guyuan chicken population,and the conservation of Guyuan chicken was analyzed by“Jingxin No.1”55K chip techno log y.The results showed that the effective population size was 8.9,the proportion of polymorphic markers was 0.828,the expected heterozygosity was 0.360,and the observed heterozygosity was 0.359,which indicated that the genetic variation of the population was small and the uniformity was high;and the G matrix showed that there was a trend of inbreeding in the population;Among the 1431 runs of homozygosity(ROH),the number of individuals with ROH between 50 Mb and 100 Mb was the largest,accounting for 36.67%,and the average inbreeding coefficient was 0.11.According to the results of genetic relationship analysis and cluster analysis,the 30 roosters were divided into 10 families,of which 25 hens were divided into different families,and the kinship coefficients between the other 5 hens and the tested cocks were all less than 0.1,so they were classified as“others”.To sum up,the genetic variation of the conserved Guyuan chicken population was small and the breeding degree was high,in order to reduce the inbreeding increment of the population,it was necessary to consider the genetic relationship before mating in the later conservation process.