Linkage Disequilibrium Analysis Across 126 Goat Breeds of the Adaptmap Consortium

The knowledge of linkage disequilibrium (LD) between markers in livestock is an important piece of information to understand the genomic structure and selection background of a breed, and is useful for association and genomic selection studies. In this work, we explored pairwise-LD of 3,197 goat animals from 126 breeds distributed worldwide using 46,654 filtered autosomal SNPs. LD test was performed using Plink 1.9 with low stringency in term of number of SNPs analyzed and distances (10,000 SNPs and 10Mb respectively) but considering R2 values≥0.8. Analyzing the whole dataset, 704 SNPs are in pairwise LD with at least one SNP. Chromosomes 1, 6 and 18 contain the highest number of high-LD SNPs, while chromosomes 9, 28 and 29 contain a minor number of high-LD SNPs. The analyses breed by breed with more than 9 animals, demonstrate a wide difference in term of number of SNPs in LD, from the lowest level in breeds located in Turkey and Egypt (Barki, Kilis, Nubian, Oasis, and Saidi <1,000 SNPs) to the highest level in breeds located in Ireland and the Netherlands (Bilberry and Landrace >30,000 SNPs). The analyses breed by breed showed that chromosomes 1, 2 and 6 are those with the highest number of SNPs in LD for the highest percentage of breeds. These observations provide insight into different genomic architecture of goats worldwide and suggest that chromosomes 1, 6 and 18 are major chromosomes for further investigations using GWAS and population genomic approaches, and to investigate genes within this high LD regions.