Linkage Disequilibrium Estimation of Chinese Beef Simmental Cattle Using High-density SNP Panels

M. Zhu; B. Zhu; Y. H. Wang; Y. Wu; L. Xu; L. P. Guo; Z. R. Yuan; L. P. Zhang; X. Gao; H. J. Gao; S. Z. Xu; J. Y. Li

doi:10.5713/ajas.2012.12721

Asian-Australasian Journal of Animal Sciences (Jun 2013)

Linkage Disequilibrium Estimation of Chinese Beef Simmental Cattle Using High-density SNP Panels

M. Zhu,
B. Zhu,
Y. H. Wang,
Y. Wu,
L. Xu,
L. P. Guo,
Z. R. Yuan,
L. P. Zhang,
X. Gao,
H. J. Gao,
S. Z. Xu,
J. Y. Li

Affiliations

M. Zhu: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
B. Zhu: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
Y. H. Wang: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
Y. Wu: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
L. Xu: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
L. P. Guo: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
Z. R. Yuan: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
L. P. Zhang: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
X. Gao: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
H. J. Gao: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
S. Z. Xu: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
J. Y. Li: Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China

DOI: https://doi.org/10.5713/ajas.2012.12721
Journal volume & issue: Vol. 26, no. 6
pp. 772 – 779

Abstract

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Linkage disequilibrium (LD) plays an important role in genomic selection and mapping quantitative trait loci (QTL). In this study, the pattern of LD and effective population size (Ne) were investigated in Chinese beef Simmental cattle. A total of 640 bulls were genotyped with IlluminaBovinSNP50BeadChip and IlluminaBovinHDBeadChip. We estimated LD for each autosomal chromosome at the distance between two random SNPs of <0 to 25 kb, 25 to 50 kb, 50 to 100 kb, 100 to 500 kb, 0.5 to 1 Mb, 1 to 5 Mb and 5 to 10 Mb. The mean values of r2 were 0.30, 0.16 and 0.08, when the separation between SNPs ranged from 0 to 25 kb to 50 to 100 kb and then to 0.5 to 1 Mb, respectively. The LD estimates decreased as the distance increased in SNP pairs, and increased with the increase of minor allelic frequency (MAF) and with the decrease of sample sizes. Estimates of effective population size for Chinese beef Simmental cattle decreased in the past generations and Ne was 73 at five generations ago.

Published in Asian-Australasian Journal of Animal Sciences

ISSN: 1011-2367 (Print); 1976-5517 (Online)
Publisher: Asian-Australasian Association of Animal Production Societies
Country of publisher: Korea, Republic of
LCC subjects: Agriculture: Animal culture; Science: Physiology: Animal biochemistry
Website: https://www.ajas.info/

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