Linkage disequilibrium over short physical genomic distances measured using medium density snp beadchip in native goat breeds of Kerala

Abstract

The extent of linkage disequilibrium (LD) at genome wide level is crucial in determining the effectiveness of genomics tools in livestock breeding. The present population genomic study was conducted in native goat breeds of Kerala namely; Attapady Black goats (n=24) and Malabari goats (n=24) to characterise extent of LD within 40kbp marker interval using genome wide single nucleotide polymorphism (SNP) marker data obtained by SNP50 BeadChip genotyping. Extent of LD between bi allelic markers was measured using correlation coefficient (r2). Mean r2 between adjacent SNP pairs across all autosomes within 40Kbp marker interval was low (Attapady Black: 0.1336; Malabari: 0.1284). The LD varied across autosomes in native goats. It was the highest for SNP pairs on Capra hircus autosome 6 (CHI 6) and the lowest for SNP pairs harboured in CHI 28 in Attapady Black goats and for SNP pairs in CHI 29 in Malabari goats. The low LD estimates indicate the genetically diverse nature of native goats. Current results also imply that denser SNP beadchip array with inter marker interval of below 40kbp would be desirable for effective genome wide association study (GWAS) and genomic selection in native goats.

Keywords

• linkage disequilibrium
• goat
• snp beadchip