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

doi:10.3724/SP.J.1005.2012.00050

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HEREDITAS ›› 2012, Vol. 34 ›› Issue (1): 50-58.doi: 10.3724/SP.J.1005.2012.00050

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

NI Gui-Yan, ZHANG Zhe, JIANG Li, MA Pei-Pei, ZHANG Qin, DING Xing-Dong

Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China

Received:2011-03-23 Revised:2011-04-27 Online:2012-01-20 Published:2012-01-25

Abstract

Abstract: 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.

Key words: Chinese Holstein Cattle, effective population, linkage disequilibrium

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, 2012, 34(1): 50-58.

References

[1] Reich DE, Lander ES. On the allelic spectrum of human disease. Trends Genet, 2001, 17(9): 502-510.
[2] Falconer DS, CMackay TFC. Introduction to Quantitative Genetics. Harlow: Addison Wesley Longman, 1996.
[3] Wright S. Size of population and breeding structure in relation to evolution. Science, 1938, 87(2263): 430-431.
[4] Sorensen AC, Sørensen MK, Berg P. Inbreeding in Danish dairy cattle breeds. J Dairy Sci, 2005, 88(5): 1865-1872.
[5] Tenesa A, Navarro P, Hayes BJ, Duffy DL, Clarke GM, Goddard ME, Visscher PM. Recent human effective population size estimated from linkage disequilibrium. Genome Res, 2007, 17(4): 520-526.
[6] Hayes BJ, Visscher PM, McPartlan HC, Goddard ME. Novel multilocus measure of linkage disequilibrium to es-timate past effective population size. Genome Res, 2003, 13(4): 635-643.
[7] Kim ES, Kirkpatrick BW. Linkage disequilibrium in the North American Holstein population. Anim Genet, 2009, 40(3): 279-288.
[8] Sargolzaei M, Schenkel FS, Jansen GB, Schaeffer LR. Extent of linkage disequilibrium in Holstein cattle in North America. J Dairy Sci, 2008, 91(5): 2016-2117.
[9] Qanbari S, Pimentel ECG, Tetens J, Thaller G, Lichtner P, Sharifi AR, Simianer H. The pattern of linkage disequilibrium in German Holstein cattle. Anim Genet, 2010, 41(4): 346-356.
[10] Sved JA. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor Popul Biol, 1971, 2(2): 125-141.
[11] Hill WG. Linkage disequilibrium among multiple neutral alleles produced by mutation in finite population. Theor Popul Biol, 1975, 8(2): 117-126.
[12] McVean GAT. A genealogical interpretation of linkage disequilibrium. Genetics, 2002, 162(2): 987-991.
[13] Weir BS, Hill WG. Effect of mating structure on variation in linkage disequilibrium. Genetics, 1980, 95(2): 477-488.
[14] Lewontin RC. The interaction of selection and linkage. I. General considerations; Heterotic models. Genetics, 1964, 49(1): 49-67.
[15] Hill WG. Estimation of linkage disequilibrium in randomly mating populations. Heredity, 1974, 33(2): 229-239.
[16] Zhao H, Nettleton D, Dekkers JCM. Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nu-cleotide polymorphisms. Genet Res, 2007, 89(1): 1-6.
[17] Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinfor-matics, 2005, 21(2): 263-265.
[18] Farnir F, Coppieters W, Arranz JJ, Berzi P, Cambisano N, Grisart B, Karim L, Marcq F, Moreau L, Mni M, Nezer C, Simon P, Vanmanshoven P, Wagenaar D, Georges M. Extensive genome-wide linkage disequilibrium in cattle. Genome Res, 2000, 10(2): 220-227.
[19] de Roos APW, Hayes BJ, Spelman RJ, Goddard ME. Linkage disequilibrium and persistence of phase in Hol-stein-Friesian, Jersey and Angus cattle. Genetics, 2008, 179(3): 1503-1512.
[20] Mueller JC, Lõhmussaar E, Mägi R, Remm M, Bettecken T, Lichtner P, Biskup S, Illig T, Pfeufer A, Luedemann J, Schreiber S, Pramstaller P, Pichler I, Romeo G, Gaddi A, Testa A, Wichmann HE, Metspalu A, Meitinger T. Linkage disequilibrium patterns and tagSNP transferability among European populations. Am J Hum Genet, 2005, 76(3): 387-398.
[21] Smith EM, Wang X, Littrell J, Eckert J, Cole R, Kissebah AH, Olivier M. Comparison of linkage disequilibrium patterns between the HapMap CEPH samples and a family-based cohort of Northern European descent. Genomics, 2006, 88(4): 407-414.
[22] Khatkar MS, Nicholas FW, Collins AR, Zenger KR, Cavanagh JAL, Barris W, Schnabel RD, Taylor JF, Raadsma HW. Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics, 20

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

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