Casein haplotype diversity in seven dairy goat breeds
2019
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.
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