Genome-Wide Association Study of Conformation and Milk Yield in Mixed-Breed Dairy Goats.

Identification of genetic markers that affect economically important traits is of high value both from a biological point of view (identification of candidate genes) as well as practical benefits for the industry (genomic selection). This study is one of the first to investigate genetic background of economically important traits in dairy goats using the caprine 50k SNP chip. The aim of the project was to perform a genome-wide association study for milk yield and conformation of udder, teat, legs and feet. A total of 4563 goats had conformation and milk yield data, out of which 402 were genotyped with the Illumina Caprine 50K BeadChip. GWAS was performed using the Multi-Locus Mixed Model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8.  Genome-wise significant SNP for milk yield was identified on chromosome 19, with additional chromosome-wise significant SNP on chromosomes 4, 8, 14, 28, 29 . Three genome-wise significant SNP for conformation were identified on chromosome 19, and chromosome-wise SNPs were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 23, 27, 28. The proportion of variance explained by the significant SNPs was between 0.4 to 15.0%. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Due to small sample size, associations with candidate genes should be treated as an indication and certainly require further research to be validated.