Abstract
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.
Highlights
The casein cluster is a genomic region of particular interest in dairy ruminants
The distribution of the allelic frequencies was markedly different between the Norwegian sample and the Italian breeds: in particular 20 of 30 single nucleotide polymorphisms (SNPs) in NOR had a frequency of the minor allele (MAF) below 20 %, whereas a maximum of 7 of 30 SNPs reported the same frequency threshold among the Italian breeds (ASP)
A sizable number (13) of SNPs were in Hardy–Weinberg disequilibrium in GIR (Table 1), while a maximum of three SNPs were in HW disequilibrium in the other Italian breeds, and there were none in NOR
Summary
The casein cluster is a genomic region of particular interest in dairy ruminants. In goat species, the genetic variability of caseins arises from several mutations that have been shown to affect gene expression level; the quantitative alleles modify the amount of single caseins in individual milk and, the technological and nutritional properties of goat milk (Marletta et al, 2007). South Italy preserves a rich heritage of dairy goat breeds: some of them originate from the Far and Middle East (Porter, 1996); others are derived from indigenous goats or were locally developed through different crossbreeding strategies. All these breeds have low population sizes; some of them are threatened by extinction and genetic erosion. The resolution of the haplotype diversity at the casein cluster can be exploited
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