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 < 95%, SNPs with call rate < 95%, minor allele frequency < 5% and Hardy-Weinberg Equilibrium test with P<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 correspond-ing effective population size at ~4 generations ago is only around 45.
NI Gui-Yan, ZHANG Zhe, JIANG Li, MA Pei-Pei, ZHANG Qin, DING Xing-Dong
. Chinese Holstein Cattle effective population size estimated from whole genome linkage disequilibrium[J]. Hereditas(Beijing), 2012
, 34(1)
: 50
-58
.
DOI: 10.3724/SP.J.1005.2012.00050
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