The effect of selection on casein genetic polymorphisms and haplotypes in Italian Holstein cattle

Milk protein genes are known to be highly polymorphic. Several studies have shown the influence of milk proteins genetic variants and casein haplotypes on milk nutritional and technological properties. From 1990, the analysis of caseins polymorphism gained new attention due to the concern about possible negative effects of CSN2*A1 on human health. As a consequence, the CSN2*A2 variant gained interest and milk produced by with A2A2 β-casein cows is now available in different countries. Aim of the present paper was to analyse how casein variants’ and haplotypes’ frequencies changed in the Italian Holstein breed, due to the health ‘claims’ about CSN2*A2, and the possible effects on milk technological properties. Data were compared also with Italian Jersey cattle. A total of 223,655 Holstein and of 622 Jersey were genotyped using Illumina beadchips and data of 62 SNP in the casein cluster were analysed to reconstruct casein genotypes and haplotypes. The results demonstrate that although the selection towards β-casein A2 is not so effective in Italy, an increase of the frequency of this allele to the disadvantage of A1 and B alleles, included in the most favourable genotypes and haplotypes for cheese making, is occurring and should not be forced. Indeed, although a selection for the favourable κ-casein B allele, and against the unfavourable E allele, is occurring and is limiting the general loss of haplotypes associated with good technological properties, the sharp decrease of the favourable B-B and I-B β- κ-haplotypes, is an alert of the risk of losing useful biodiversity.Highlights After the concern about the β-caseinA1 variant on human health, a selection favoring the A2 allele was carried out in different countries. In Italy milk is mostly destined to cheese-making and even without a direct selection for theβ-casein A2 caseins allelic frequencies are changing. Genotyping data should be used to monitor and maybe contrast the reduction of variants associated with milk favorable technological properties.