Casein haplotype diversity in seven dairy goat breeds

Selection, drift, gene flow and breeding have extensively shaped the genomic variability of domestic animals. In goat species, several mutations identified within the casein genes have been shown to affect the level of gene expression of milk production traits. The four casein genes – CSN1S1, CSN2, CSN1S2 and CSN3 – are organized in a cluster of 250 kb located in chromosome 6, and due to tight linkage, their genetic variability is well depicted by haplotypes which are transmitted to the progeny. Thirty single nucleotide polymorphisms (SNPs) located within the casein gene cluster were used to characterize the haplotype variability of six southern Italian goat breeds (Girgentana, Maltese, Rossa Mediterranea, Argentata dell'Etna, Messinese, Capra dell'Aspromonte). A representative sample of the Norwegian dairy goat breed (Norsk melkegeit) has been used as an out-group to obtain a weighted measure of genetic diversity in the metapopulation. A total of 54 haplotypes were detected among the seven breeds: 26, 9, 8 and 11 haplotypes were found at CSN1S1, CSN2, CSN1S2 and CSN3 respectively. The number of haplotypes per breed was 14 (Norwegian), 26 (Messinese), 27 (Rossa Mediterranea and Girgentana) and 31 (Maltese, Argentata dell'Etna and Capra dell'Aspromonte). The Maltese breed showed the highest number of private haplotypes, whereas the Norwegian goat recorded the highest number of shared haplotypes. The linkage disequilibrium analysis showed higher levels of association for the SNP pairs within casein loci than SNP pairs between casein loci, likely reflecting low levels of intra-genic recombination. The highest linkage disequilibrium values were found in CSN1S1 and CSN2 genes in all the breeds, except for Argentata dell'Etna and Rossa Mediterranea. The resolution of the haplotype diversity at the casein cluster can be exploited both for selective and conservative plans.