1. Whole genome study of linkage disequilibrium in Sahiwal cattle
- Author
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Adeela Ajmal, Waqas Ahmad Khan, Khalid Javed, Talat Naseer Pasha, Tad S. Sonstegard, Huson J. Heather, Hamid Mustafa, Kim Euisoo, Asad Ali, Nisar Ahmad, and J.J. Kim
- Subjects
molecular marker ,0301 basic medicine ,Genetics ,Sahiwal cattle ,Linkage disequilibrium ,Single-nucleotide polymorphism ,minor allele frequency ,Biology ,Quantitative trait locus ,Breeding value, linkage disequilibrium, minor allele frequency, molecular marker ,Genome ,Minor allele frequency ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,Molecular marker ,Animal Science and Zoology ,Allele frequency ,Breeding value ,linkage disequilibrium - Abstract
The linkage disequilibrium (LD) is an important tool to study quantitative trait locus (QTL) mapping and genetic selection. In this study, we identified the extent of linkage disequilibrium (LD) in Sahiwal (n = 14) cattle using the bovine high density single-nucleotide polymorphisms (SNPs) BeadChip. After data filtering, 500,968 SNPs comprising 2518.1 Mb of the genome, were used for the LD estimation. The minior allele frequency (MAF) was 0.21 in a substantial proportion of SNPs and mean distance between adjacent markers was 4.77 ± 2.83 kb. The overall mean LD between adjacent markers was 0.18 (r 2 ) and 0.55 (|D'|), respectively. The LD (r 2 ) values reduced with the increase in distance between adjacent markers from 1 kb (0.35) to 100 kb (0.12) and |D'| specified distinct decay of the LD. Chromosomes 1, 27, 28 and 29 presented the LD at some distance between markers. The extent of LD was higher, except these four chromosomes, for markers separated by 20 kb. At < 3 kb distance, the upper value of the linkage disequilibrium (LD) was observed at 0.30. High level of the linkage disequilibrium (LD) between markers was observed at high minor allele frequency (MAF) threshold (0.15), at the short distance between markers. The results of this study revealed that the Bovine high density SNPs BeadChip will be informative for the estimation of breeding value in Sahiwal cattle. Keywords: Breeding value, linkage disequilibrium, minor allele frequency, molecular marker
- Published
- 2018