Assessment of linkage disequilibrium and haplotype block structure in indigenous cattle populations of Tamil Nadu, India usingwhole genome sequence data

MENDUGULLA TEJASWI SINDHU  RATNAM; ALAGAPPAN  GOPINATHAN; K THILAK PON  JAWAHAR; P  AZHAHIANAMBI; S  VANI; K G  TIRUMURUGAAN; S M K  KARTHICKEYAN

doi:10.56093/ijans.v94.i1.135196

Authors

MENDUGULLA TEJASWI SINDHU RATNAM Tamil Nadu Veterinary and Animal Sciences University, Tamil Nadu 600 007 India
ALAGAPPAN GOPINATHAN Tamil Nadu Veterinary and Animal Sciences University, Tamil Nadu 600 007 India
K THILAK PON JAWAHAR Livestock Farm Complex, Madhav Milk Colony, Chennai
P AZHAHIANAMBI Translational Research Platform for Veterinary Biologicals, Madhavaram Milk Colony, Chennai
S VANI Tamil Nadu Veterinary and Animal Sciences University, Tamil Nadu 600 007 India
K G TIRUMURUGAAN Tamil Nadu Veterinary and Animal Sciences University, Tamil Nadu 600 007 India
S M K KARTHICKEYAN Tamil Nadu Veterinary and Animal Sciences University, Tamil Nadu 600 007 India

https://doi.org/10.56093/ijans.v94.i1.135196

Keywords:

Haplotype, Indigenous cattle breeds, Linkage disequilibrium, WGS data

Abstract

Understanding the nature of linkage disequilibrium (LD) between molecular markers reflects the degree of non-random association between their alleles, which is essential for genome-wide association studies. The main objective of this study was to assess the chromosome-wise linkage disequilibrium and haplotype block structure in indigenous cattle breeds of Tamil Nadu, India. A total of 79 animals belonging to five indigenous cattle breeds were considered as single indigenous cattle population and three samples per breed were sequenced using Illumina NovaSeq^TM 6000 and Illumina HiSeq 2500. The LD parameter (r²) was estimated for a total of 62,095,778 pair- wise SNPs for all autosomes. The chromosome-wise number of SNP pairs, mean r²±standard deviation and median r² values were 2,141,234, 0.484±0.246 and 0.493, respectively. Chromosome-wise mean r² of different distance bins were calculated and it showed the maximum r² value of 0.839 at 31-70 kb distance for Chromosome 11 and minimum r² value of zero for Chromosome 7, 11, 15, 20 and 29, respectively at a distance 71-100 kb. This study also revealed a total of 413, 277 haplotype blocks which covered 2.34% of the autosomal genome. There was a total of 1,589,118 SNPs distributed within the haplotype blocks, covering a total length of 53.62 mb. The results of the study suggest the need for breed-specific reference populations for indigenous cattle breeds, which have a greater density of molecular markers of economic significance and thereby to identify breed-specific haplotypes in future.

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