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. 2012 Aug 14:3:152.
doi: 10.3389/fgene.2012.00152. eCollection 2012.

Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle

Duc Lu  1 , Mehdi Sargolzaei, Matthew Kelly, Changxi Li, Gordon Vander Voort, Zhiquan Wang, Graham Plastow, Stephen Moore, Stephen P Miller
Affiliations

Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle

Duc Lu et al. Front Genet. .

Abstract

Linkage disequilibrium (LD) and the persistence of its phase across populations are important for genomic selection as well as fine scale mapping of quantitative trait loci (QTL). However, knowledge of LD in beef cattle, as well as the persistence of LD phase between crossbreds (C) and purebreds, is limited. The objective of this study was to understand the patterns of LD in Angus (AN), Charolais (CH), and C beef cattle based on 31,073, 32,088, and 33,286 SNP in each population, respectively. Amount of LD decreased rapidly from 0.29 to 0.23 to 0.19 in AN, 0.22 to 0.16 to 0.12 in CH, 0.21 to 0.15 to 0.11 in C, when the distance range between markers changed from 0-30 kb to 30-70 kb and then to 70-100 kb, respectively. Breeds and chromosomes had significant effects (P < 0.001) on LD decay. There was significant interaction between breeds and chromosomes (P < 0.001). Correlations of LD phase were high between C and AN (0.84), C and CH (0.81), as well as between AN and CH (0.77) for distances less than or equal to 70 kb. These dropped when the distance increased. Estimated effective population sizes for AN and CH were 207 and 285, respectively, for 10 generations ago. Given a useful LD of at least 0.3 between pairs of SNPs, the LD phase between any pair of the three breed groups was highly persistent. The current SNP density would allow the capture of approximately 49% of useful LD between SNP and marker QTL in AN, and 38% in CH. A higher density SNP panel or redesign of the current panel is needed to achieve more of useful LD for the purpose of genomic selection beef cattle.

Keywords: beef cattle; linkage disequilibrium.

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Figures

Figure 1
Figure 1
Breed composition (%) of the crossbred animals genotyped. AN, Angus; SM, Simental; PI, Piedmontese; CH, Charolais; Others, 15 other breeds.
Figure 2
Figure 2
Average LD over genomic distance for Angus, Charolais, and Crossbred.
Figure 3
Figure 3
Trend lines of average LD over genomic distance on chromosomes 5 and 29 in Angus and Charolais.
Figure 4
Figure 4
Estimated Ne for Angus and Charolais over time.
Figure 5
Figure 5
Correlation of r between Angus and Charolais over past generations.
See this image and copyright information in PMC

References

    1. Abecasis G. R., Noguchi E., Heinzmann A., Traherne J. A., Bhattacharyya S., Leaves N. I., Anderson G. G., Zhang Y., Lench N. J., Carey A., Cardon L. R., Moffatt M. F., Cookson W. O. (2001). Extent and distribution of linkage disequilibrium in three genomic regions. Am. J. Hum. Genet. 68, 191–197 10.1086/316944 - DOI - PMC - PubMed
    1. Affymetrix Inc. (2011). Data sheet. Available online at http://media.affymetrix.com/support/technical/datasheets/axiom_gw_bos1_a... [Accessed April 25, 2012].
    1. American Angus Association. (2012). Genetic trend – EPD by birth year. Available online at http://www.angus.org/Nce/GeneticTrends.aspx [Accessed April 25, 2012].
    1. Bohmanova J., Sargolzaei M., Schenkel F. S. (2010). Characteristics of linkage disequilibrium in North American Holsteins. BMC Genomics 11, 421 10.1186/1471-2164-11-421 - DOI - PMC - PubMed
    1. Casas E., Shackelford S. D., Keele J. W., Stone R. T., Kappes S. M., Koohmaraie M. (2000). Quantitative trait loci affecting growth and carcass composition of cattle segregating alternate forms of myostatin. J. Anim. Sci. 78, 560–569 - PubMed