Linkage disequilibrium and effective population size in Indian goat breeds

Abstract

Genomic linkage disequilibrium (LD) is an important population diversity measure and an indicator determining the efficacy of genomic applications. The present population genomic study was carried out to comprehensively characterise the extent and pattern of LD in the two divergent Indian goat breeds namely, Attappady Black and Malabari goats reared under small holder production system. The LD was estimated using genome-wide single nucleotide polymorphism (SNP) marker data obtained by Illumina SNP50 goat BeadChip genotyping. The LD between adjacent SNPs across all autosomes measured as correlation coefficient (r2) in the studied population was low and mean ± standard deviation of LD were 0.0657 ± 0.0921 and 0.0661 ± 0.0911 for Attappady Black and Malabari goats, respectively. The LD varied significantly (p < 0.0001) among chromosomes, interaction between chromosome and breed and among marker intervals. The LD (r2) of 0.2 and 0.3 were extended up to 20 kb and 10 kb marker intervals, respectively. Based on the genomic data, Ne was estimated as 512.8198 in Malabari and 371.2220 in Attappady Black goats at 17 generations back. The weak LD observed in Indian goat breeds indicates increased diversity of these Indian goat breeds and also implies that denser SNP panel might be more beneficial for genomic applications.