[논문]Demographic Trends in Korean Native Cattle Explained Using Bovine SNP50 Beadchip

Sharma, Aditi; Lim, Dajeong; Chai, Han-Ha; Choi, Bong-Hwan; Cho, Yongmin

doi:10.5808/gi.2016.14.4.230

Demographic Trends in Korean Native Cattle Explained Using Bovine SNP50 Beadchip 원문보기

Genomics & informatics, v.14 no.4, 2016년, pp.230 - 233

Sharma, Aditi (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA) , Lim, Dajeong (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA) , Chai, Han-Ha (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA) , Choi, Bong-Hwan (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA) , Cho, Yongmin (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA)

Abstract ▼ AI-Helper

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 $r^2$ value was calculated. Average distance between SNP pairs was 1.14 Mb across all breeds. Average $r^2$ between adjacent SNP pairs ranged between was 0.1 for Yanbian to 0.3 for Qinchuan. Effective population size of the breeds based on $r^2$ 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.

주제어

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가설 설정

is the average linkage disequilibrium across all distances and Hs is the heterozygosity. Hs was used as a measure of genetic diversity.

제안 방법

Korean cattle are known to have migrated from North China and Mongolia and from Korea to Japan. Considering this fact we conducted this study to understand the LD patterns and the effective population size of the Korean breeds along with Chinese, Mongolian (MG), and Japanese breeds. It is already known that due to various reasons about 16% of the cattle breeds are already extinct and 30% face the risk of extinction.

대상 데이터

Final dataset consisted of a total of 28,708 SNPs. A total of 129 samples were analyzed in the study. SNeP program [9] was used to calculate pairwise LD and Ne.
01). Final dataset consisted of a total of 28,708 SNPs. A total of 129 samples were analyzed in the study.
1. Linkage disequilibrium plotted as a correlation between r² and genetic distance between single nucleotide polymorphisms in the 9 cattle breeds used in this study.
org [6]. There were a total of 129 samples from the 9 Asian breeds in the study (Table 1).
Blood samples were collected from BH, BNH, and JB. Twenty (n = 20) animals were sampled from each Korean breed. Genotype data of Korean cattle was merged with genotype data from six other Asian breeds that included YB, Luxi (LX), Hainan (HN), Qinchuan (QC), Wagyu (WAG), and MG cattle.

이론/모형

Population structure was studied using Fst and principal component analysis (PCA) as implemented in adegent R package [11]. Genetic distances among the pair of populations were calculated using “WC84” method implemented in Hierfstat [12].

참고문헌 (19)

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