Genome-wide association study for coat colour and other qualitative morphological traits in indigenous goat breeds of Sindh-Pakistan using 50k SNP bead chip

Abstract

Sindh province harbours the largest number of indigenous goat breeds in Pakistan, and these breeds are distinguished from one another largely on the basis of qualitative morphological traits such as coat colour and pattern, eye colour, hair length, nose shape and horn orientation. The present study was designed to identify genomic regions and candidate genes associated with seven qualitative morphological traits in nine indigenous goat breeds of Sindh, viz. Barri, Bugi-Tori, Chappar, Jattan, Kachan, Kamori, Pateri, Tapri and Thari. Phenotypes were recorded on 395 goats (49 males and 346 females) through standardised photography and a structured proforma, and genomic DNA extracted from jugular blood was genotyped with the Illumina Goat SNP50 BeadChip. Association analysis was performed in PLINK 1.9 using a case-control model for six binary traits and a quantitative model for nose length, fitting breed, sex and correlated traits as covariates, with Benjamini-Hochberg control of the false discovery rate. A total of 38 SNPs reached significance: five for black body coat, four for flowery colour pattern, one for brown eye colour, seven for short hair, nine for Roman nose shape and twelve for upward horn orientation, whereas no SNP was significant for nose length. Two SNPs on chromosomes 1 (IL1RAP) and 9 (PRKN) were shared between black coat and flowery pattern. These markers provide the first genome-wide evidence on the architecture of qualitative morphological traits in Pakistani goats and offer a starting point for marker-assisted selection of breed-defining phenotypes.