Genetics. Published Articles Ahead of Print: July 18, 2006, Copyright © 2006
doi:10.1534/genetics.106.058966


A more recent version of this article appeared on September 1, 2006.

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Effects on production traits of haplotypes among casein genes in Norwegian goats and evidence for a site of preferential recombination

Ben Hayes 1*

1 Norwegian University of Life Sciences

* To whom correspondence should be addressed. E-mail: ben.hayes{at}dpi.vic.gov.au.

Submitted on April 5, 2006
Revised on July 2, 2006
Accepted on 2 July 2006


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 and thirty six Norwegian bucks were genotyped for 39 polymorphic sites across the four loci. The number of unique haplotypes present in each locus was 10, 6, 4 and 8 for CSN1S1, CSN2, CSN1S2 and CSN3 respectively. The effects of the CSN1S1 haplotypes on protein % and fat kilograms were significant, as were the effects of CSN3 haplotypes on fat % and protein %. 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 %. Investigation of linkage disequilibrium between all possible pairs of SNPs revealed higher levels of linkage disequilbrium for SNP pairs within casein loci than SNP pairs between casein loci, likely reflecting low levels of intra-genic 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.

Key Words: casein genes, haplotypes, preferential recombination