利用全基因组连锁不平衡估计中国荷斯坦牛有效群体大小

有效群体大小是群体遗传学研究的一个重要内容,有助于我们更清楚地了解群体的遗传变异、进化和复杂性状的遗传机制等。随着高密度SNP标记的出现,越来越多的研究利用SNP标记间连锁不平衡估计有效群体大小。文章采集北京地区中国荷斯坦牛2 093个样本,并利用牛SNP芯片(Illumina BovineSNP50,含5 4001 SNPs)进行基因型测定,估计不同世代中国荷斯坦牛的有效群体大小。质量控制标准设定为SNP检出率0.95,最小等位基因频率>0.05,样本检出率0.95,哈代温伯格平衡检验显著性水平P<0.0001。经过质量控制,共1 968个样本和38 796个SNPs用于连锁不平衡分析。文章选取SNP间距0.1、0.2、0.5、1、2、5、10、15(Mb),估计中国荷斯坦牛在4世代之前有效群体大小。结果表明,中国荷斯坦牛的有效群体呈逐代下降趋势,至4世代前,中国荷斯坦牛平均有效群体为45头左右。

Chinese Holstein Cattle effective population size estimated from whole genome linkage disequilibrium

Effective populations size (Ne) is an important population parameter that helps to explain genetic variation, population evolution and understanding of the genetic architecture underlying complex traits. With the availability of high-dense SNP panels, more and more researches focus on estimating of Ne using linkage disequilibrium (LD) between SNPs. In this study, we estimated the effective population size from 2093 Chinese Holstein Cattle genotyped with Illumina BovineSNP50 BeadChip. After removal of individual with call rate lt; 95%, SNPs with call rate lt; 95%, minor allele frequency lt; 5% and Hardy-Weinberg Equilibrium test with Plt;0.0001, 1 968 individuals with 38 796 SNPs were remained. Eight kinds of SNP pairs with the distances 0.1, 0.2, 0.5, 1, 2, 5, 10, and 15 Mb were respectively chosen to estimate the effective population size of Chinese Holstein cattle from 4 generations ago. It is demonstrated from the results of this study that the effective population size of Chinese Holstein is decreased in the past generations, and the corresponding effective population size at ~4 generations ago is only around 45.