Effects on Production Traits of Haplotypes Among Casein Genes in Norwegian Goats and Evidence for a Site of Preferential Recombination

Abstract

In goat milk the most abundant proteins are the casein genes, CSN1S1, CSN2, CSN1S2, and CSN3. Mutations have been identified within these genes affecting the level of gene expression, and effects on milk production traits have been reported. The aim of this study was to detect polymorphisms (SNPs) in the casein genes of Norwegian goats, resolve haplotype structures within the loci, and assess the effect of these haplotypes on milk production traits. Four hundred thirty-six Norwegian bucks were genotyped for 39 polymorphic sites across the four loci. The numbers of unique haplotypes present in each locus were 10, 6, 4, and 8 for CSN1S1, CSN2, CSN1S2, and CSN3, respectively. The effects of the CSN1S1 haplotypes on protein percentage and fat kilograms were significant, as were the effects of CSN3 haplotypes on fat percentage and protein percentage. A deletion in exon 12 of CSN1S1, unique to the Norwegian goat population, explained the effects of CSN1S1 haplotypes on fat kilograms, but not protein percentage. Investigation of linkage disequilibrium between all possible pairs of SNPs revealed higher levels of linkage disequilbrium for SNP pairs within casein loci than for SNP pairs between casein loci, likely reflecting low levels of intragenic recombination. Further, there was evidence for a site of preferential recombination between CSN2 and CSN1S2. The value of the haplotypes for haplotype-assisted selection (HAS) is discussed.

Extreme frequencies of the αs1-casein “null” variant in milk from Norwegian dairy goats – Implications for milk composition, micellar size and renneting properties

“…These results are in agreement with the previously published results of Hayes et al (2006). Frequencies "strong", "intermediate" and "weak" goats in our study were 17%, 2% and 11%, respectively.…”

“…Such "A-like" variants (Lane 5 in Fig. 1) may correspond to "new" protein variants (encoded by α s1 -casein haplotype 4) recently identified in the Norwegian goat population (Hayes et al 2006;Pellerud 2006). This particular haplotype found at a frequency of 6% and with a positive impact on protein content in the milk was suggested as the "link" between the A variant and the Norwegian "null" variant (referred to as haplotype 1).…”

“…The situation regarding frequencies of α s1 -casein variants in Norwegian caprine milk is strikingly different. In a study by Hayes et al (2006) where 39 SNPs of the 4 casein genes were typed in 436 bucks, the "null" variant, unique to the Norwegian goat population, was found at a very high frequency (0.72). This particular mutation arising from a deletion in exon 12 of the α s1 -casein gene (CSN1S1) and referred to as the D allele (referred to as allele 1 of exon 12 in Hayes et al (2006)) was found to decrease contents of protein and fat of the milk (Ådnøy et al 2003;Dagnachew 2009).…”

Genetic Factors that Regulate Milk Protein and Lipid Composition in Goats

“…However, this methodological strategy has been rarely carried out, probably because of the technical challenge of simultaneously typing such highly polymorphic loci in a fast and reliable way. Casein haplotypes have been characterized in a number of breeds from Italy (Sacchi et al 2005, Caroli et al 2006, Finocchiaro et al 2008, Gigli et al 2008, Norway (Hayes et al 2006, Finocchiaro et al 2008, Berget et al 2010, Germany (Küpper et al 2010), Czech Republic (Sztankóová et al 2009), West Africa ) and India (Rout et al 2010). However, most of these studies just report the variability of the casein cluster in selected populations rather than analysing its impact on milk quality phenotypes.…”

Relationship Between Kappa Casein Genes (CSN3) and Industrial Yield in Holstein Cows in Nariño-Colombia

“…they do not code for any protein. Individuals heterozygously synthesize a protein, one for each allele that they possess, in the homologous chromosomes [32].…”