Whole genome study of linkage disequilibrium in Sahiwal cattle

H Mustafa,A Ali,T.N Pasha,H.J Heather,T.S Sonstegard,A Ajmal,W.A Khan,K Eui-Soo,K Javed,J.J Kim,N Ahmad

doi:10.4314/sajas.v48i2.16

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

Highlights

Sahiwal is an important dairy breed of Pakistan, belonging to Bos indicus
Genetic selection identifies the linkage disequilibrium (LD) between adjacent markers and reveal that chromosome segments will affect the whole population and genes responsible for traits expression (QTL) since the markers are in LD
The |D'| was observed unchanged at different minior allele frequency (MAF) threshold for the adjacent marker (< 10 kb) and at the threshold of MAF increased, the |D'| was lower as reported in the study of different cattle breeds (Bohmanova et al, 2010)

Summary

Introduction

Sahiwal is an important dairy breed of Pakistan, belonging to Bos indicus. This breed is well known in the world for dairy traits and is present in twenty-nine countries (FAO, 2007). Silva et al (2010) genotyped Gyr breed with 54,000 SNPs and found LD (0.21) between adjacent markers.The authors of different studies identified that Bos indicus breeds have a higher percentage of low alleles frequency and a lower level of LD than Bos taurus breeds (McKay et al, 2007; Sargolzaei et al, 2008; Kim & Brian et al, 2009; Espigolan et al, 2013).

Results

Conclusion