Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle

Lu, Duc, Sargolzaei, Mehdi, Kelly, Matthew, Li, Changxi, Vander Voort, Gordon, Wang, Zhiquan, Plastow, Graham, Moore, Stephen and Miller, Stephen P. (2012) Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle. Frontiers in Genetics, 3 AUG: 152.1-152.10. doi:10.3389/fgene.2012.00152

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Author Lu, Duc
Sargolzaei, Mehdi
Kelly, Matthew
Li, Changxi
Vander Voort, Gordon
Wang, Zhiquan
Plastow, Graham
Moore, Stephen
Miller, Stephen P.
Title Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle
Journal name Frontiers in Genetics   Check publisher's open access policy
ISSN 1664-8021
Publication date 2012-08-14
Sub-type Article (original research)
DOI 10.3389/fgene.2012.00152
Open Access Status DOI
Volume 3
Issue AUG
Start page 152.1
End page 152.10
Total pages 10
Place of publication Lausanne, Switzerland
Publisher Frontiers Research Foundation
Language eng
Formatted 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.
Keyword Beef cattle
Linkage disequilibrium
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Article # 152. Published in Specialty Section of Frontiers in Genetics: Frontiers in Livestock Genomics.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2013 Collection
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Created: Wed, 03 Oct 2012, 19:16:03 EST by Matthew John Kelly on behalf of Qld Alliance for Agriculture and Food Innovation