Variations in Casein Genes Are Associated with Milk Protein and Fat Contents in Sarda Goats (Capra hircus), with an Important Role of CSN1S2 for Milk Yield

Extensive goat breeding follows principles of sustainable agriculture, and it can be achieved with local breeds because their genome has been shaped by centuries of interaction with the environment in which goats were raised. The Sarda goat is well adapted to the arid environment of Sardinia (Italy). The aim of the present work was to study the variability of the casein genes, the main proteins of milk. We measured milk traits such as protein, fat, lactose, total solids, and milk yield, and performed association analyses with casein gene variants. The variability of the four casein genes was associated with milk protein, fat, total solids, and milk energy. The main finding was that intronic variants of the CSN1S2 gene (encoding the αs2-casein protein) were associated with milk yield and protein and fat content. This information might be used in selection schemes, and in future investigations aiming to disclose the direct link between genotype and phenotype. This work aimed to assess the variability of casein genes in a population of 153 bucks and 825 lactating does of the Sarda breed, and to perform association analysis between polymorphic sites and milk yield and composition traits. To genotype the casein genes, we chose an SNP panel including 44 SNPs mapping to the four casein genes CSN1S1, CSN2, CSN1S2, and CSN3. Genotyping (made by KASP™ genotyping assay, based on competitive allele-specific PCR) revealed the high variability of the Sarda goat, and haplotype analysis revealed linkage disequilibrium (LD) between CSN1S1 and CSN2 genes, in addition to two LD blocks within the CSN1S2 and two LD blocks within the CSN3 gene, in bucks and does. Association analysis revealed that variability at all four casein genes was associated with milk protein content, total solids, and milk energy. The three Ca-sensitive casein genes were associated with lipid content, and CSN1S2 showed a unique pattern, with intron variants associated with milk yield, in addition to milk pH, NaCl, and SCS (Somatic Cell Score). This ...