Sharma Aditi, Lim Dajeong, Chai Han-Ha, Choi Bong-Hwan, Cho Yongmin
Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, Wanju 55365, Korea.
Genomics Inform. 2016 Dec;14(4):230-233. doi: 10.5808/GI.2016.14.4.230. Epub 2016 Dec 31.
Linkage disequilibrium (LD) is the non-random association between the loci and it could give us a preliminary insight into the genetic history of the population. In the present study LD patterns and effective population size (Ne) of three Korean cattle breeds along with Chinese, Japanese and Mongolian cattle were compared using the bovine Illumina SNP50 panel. The effective population size (Ne) is the number of breeding individuals in a population and is particularly important as it determines the rate at which genetic variation is lost. The genotype data in our study comprised a total of 129 samples, varying from 4 to 39 samples. After quality control there were ~29,000 single nucleotide polymorphisms (SNPs) for which r value was calculated. Average distance between SNP pairs was 1.14 Mb across all breeds. Average r between adjacent SNP pairs ranged between was 0.1 for Yanbian to 0.3 for Qinchuan. Effective population size of the breeds based on r varied from 16 in Hainan to 226 in Yanbian. Amongst the Korean native breeds effective population size of Brindle Hanwoo was the least with Ne = 59 and Brown Hanwoo was the highest with Ne = 83. The effective population size of the Korean cattle breeds has been decreasing alarmingly over the past generations. We suggest appropriate measures to be taken to prevent these local breeds in their native tracts.
连锁不平衡（LD）是基因座之间的非随机关联，它能让我们初步了解种群的遗传历史。在本研究中，使用牛Illumina SNP50芯片比较了三个韩国牛品种以及中国牛、日本牛和蒙古牛的连锁不平衡模式和有效种群大小（Ne）。有效种群大小（Ne）是种群中繁殖个体的数量，由于它决定了遗传变异丢失的速率，所以尤为重要。我们研究中的基因型数据总共包含129个样本，样本数量从4个到39个不等。经过质量控制后，计算了约29,000个单核苷酸多态性（SNP）的r值。所有品种中SNP对之间的平均距离为1.14 Mb。相邻SNP对之间的平均r值范围从延边牛的0.1到秦川牛的0.3。基于r值计算的各品种有效种群大小从海南牛的16到延边牛的226不等。在韩国本土品种中，斑纹韩牛的有效种群大小最小，Ne = 59，棕色韩牛的有效种群大小最大，Ne = 83。在过去几代中，韩国牛品种的有效种群大小一直在惊人地下降。我们建议采取适当措施来保护这些本土地区的本地品种。
