Genome-Wide Association Study of Milk Composition in Karachai Goats

Simple Summary The growth rate of dairy goat farming is due to the special qualities of goat milk, which are directly determined by its composition. Goat's milk has a higher concentration of special fatty acids but less protein than cow's milk, which is why high-quality cheeses are made from goat's milk. Therefore, the goal of breeding dairy goats is not only to increase their milk yield but also to improve the quality composition of their milk. Karachai goats are a breed of local selection, the milk of which is widely used in the regions of the North Caucasus for the production of unique cheeses. While a relatively large number of genome studies have been carried out for transboundary goat breeds, such as Saanen goats, there is not yet enough research on local goat breeds. That is why we conducted a genome-wide association study (GWAS) on the milk component traits of Karachai goats. The use of genomic evaluation in the selection of Karachai goats will increase the rate of breeding progress in terms of enhancing milk productivity traits and thereby increase the profitability of their use.Abstract This study is first to perform a genome-wide association study (GWAS) to investigate the milk quality traits in Karachai goats. The objective of the study was to identify candidate genes associated with milk composition traits based on the identification and subsequent analysis of all possible SNPs, both genome-wide (high-confidence) and suggestive (subthreshold significance). To estimate the milk components, 22 traits were determined, including several types of fatty acids. DNA was extracted from ear tissue or blood samples. A total of 167 Karachai goats were genotyped using an Illumina GoatSNP53K BeadChip panel (Illumina Inc., San Diego, CA, USA). Overall, we identified 167 highly significant and subthreshold SNPs associated with the milk components of Karachai goats. A total of 10 SNPs were located within protein-coding genes and 33 SNPs in close proximity to them (+/- 0.2 Mb). The largest number of genome-wide significant SNPs was found on chromosomes 2 and 8 and some of them were associated with several traits. The greatest number of genome-wide significant SNPs was identified for crude protein and lactose (6), and the smallest number-only 1 SNP-for freezing point depression. No SNPs were identified for monounsaturated and polyunsaturated fatty acids. Functional annotation of all 43 SNPs allowed us to identify 66 significant candidate genes on chromosomes 1, 2, 3, 4, 5, 8, 10, 13, 16, 18, 21, 23, 25, 26, and 27. We considered these genes potential DNA markers of the fatty acid composition of Karachai goat milk. Also, we found 12 genes that had a polygenic effect: most of them were simultaneously associated with the dry matter content and fatty acids (METTL, SLC1A 8, PHACTR1, FMO2, ECI1, PGP, ABCA3, AMDHD2). Our results suggest that the genes identified in our study affecting the milk components in Karachai goats differed from those identified in other breeds of dairy goats.