Genome wide association analysis for twinning ability in Jabal Akhdar Omani goats

The objective of the current study was to identify SNPs associated with twinning ability in Jabal Akhdar Omani female goats. 72 Jabal Akhdar Omani female goats were genotyped for the current study using the Illumina GoatSNP50 BeadChip, which contains 53,347 SNPs. After genotypic data filtration, the number of SNPs remaining for analysis was 46,035 SNPs from 29 autosomes. Genome Wide Association Analysis (GWAS) of twinning ability was performed using the GenABEL package in R software. A multiple testing correction approach (simpleM) was used to adjust for multiple testing of SNPs. Later, BioMart-Ensamble was used to look for candidate genes within 100 kb upstream and downstream of the significant SNPs. Eight SNPs associated significantly at a chromosome wide threshold with litter size. Out of these, three SNPs were found in the intronic region of genes AK8 on chromosome 11, PLXDC2 on chromosome 13 and ABCC8 on chromosome 15. Moreover, two SNPs were found in the downstream region of genes EML5 on chromosome 10 and SBDS on chromosome 25. While the remaining 3 SNPs were found in the intergenic regions of genes CLCN3 on chromosome 8, OPTC on chromosome 16 and CLEC19A on chromosome 25. Previous studies have shown that some of these genes are involved in reproductive performance which merits further sequence variation analysis in them with relation to twinning ability in Jabal Akhdar goats.