A New AS-PCR Method to Detect CSN2(01) Allele, Genotyping at Ca-Sensitive Caseins Loci and Milk Traits Association Studies in Autochthonous Lazio Goats

SIMPLE SUMMARY: Identifying new alleles and mutations at calcium-sensitive casein loci requires continuous updating of genotyping protocols useful for association study. This study reports (1) a new, more efficient, specific PCR-based genotyping protocol to detect the CSN2(01) allele in goats, (2) the genetic characterization at the CSN1S1, CSN2, and CSN1S2 loci in three endangered goat breeds reared in the Lazio Region (Central Italy) and, (3) the association of the genotypes observed in the studied animals with parameters that might affect the milk’s traits. As regards the CSN1S1, CSN2, and CSN1S2 loci, no animals were found to be carriers of the CSN1S1(01), CSN1S1(E), CSN2(01), CSN1S2(D), and CSN1S2(0) alleles; instead, for the CSN1S1 locus, a high frequency of alleles associated to a low (CSN1S1(F)) and high (CSN1S1(A*,B*)) content of the αs1 casein (αs1-Cn) content in milk, with CSN1S1(F)≥ CSN1S1(B*) ≥ CSN1S1(A*) being observed. An association between the different genotypes at the CSN1S1 locus and some milk traits, namely the fat and protein yielded and the fat, protein, solids-not-fat, and casein percentages without an effect on the milk yield, was observed. ABSTRACT: Calcium-sensitive caseins are the main protein component of milk. In the goat, they are encoded by three genes (CSN1S1, CSN2, and CSN1S2) located on chromosome 6. A high number of alleles has been discovered for these genes in the goat species, responsible for changes in the milk’s qualitative and quantitative characteristics. This study aimed to develop an Allele-Specific PCR (AS-PCR), which allowed us to unequivocally detect goat carriers of the CSN2(01) allele. Subsequently, the calcium-sensitive casein loci genotype was investigated in three native goat breeds of the Lazio Region (Bianca Monticellana, Capestrina, and Ciociara Grigia). No individuals were carriers of the CSN1S1(01), CSN1S1(E), CSN2(01), CSN1S2(D), and CSN1S2(0) alleles, while a high frequency of the alleles CSN1S1(F) and CSN1S1(A*,B*) was observed. Association analyses between the different genotypes at the CSN1S1 locus and some milk traits, namely the fat and protein yielded and the fat, protein, solids-not-fat, and casein percentages without an effect on the milk yield, were observed.