engleski

Genomic patterns of homozygosity around casein gene cluster in Italian Holstein cattle

Most of the milk produced in Italy is processed into various types of cheese. Therefore, the insight into the milk processing properties is highly important. Caseins are milk proteins that are considered the most important in the context of cheese production. 54 SNP polymorphisms have been detected in the casein gene cluster on chromosome 6 in Italian Holsteins. With the increasing availability of SNP arrays in livestock species, a lot of genomic information has been generated, enabling a range of genomic analyses, including breeding values, inbreeding, population structure, genome-wide association studies, mapping of positive selection, and others. Runs of Homozygosity and Extended Haplotype Homozygosity are approaches that reveal precise patterns of homozygosity and provide valuable insights into past or ongoing selection events. In this study, 160, 000 Italian Holstein cattle genotyped with a 50k SNP array were used to analyse the casein gene cluster on chromosome 6 for extreme Runs of Homozygosity islands and integrated Haplotype Scores. The results showed that a certain number of animals have high levels of autozygosity on chromosome 6, which is also confirmed for homozygosity at the haplotype level based on high iHS scores. These analyses confirm the effects of selection on certain casein gene variants, although they were not included in the selection scheme. Since the casein gene cluster is important for the Italian Holstein population, the results of the selection signature analysis should be evaluated and hopefully contribute to the selection plans.

Runs of Homozygosity ; Extended Haplotype Homozygosity ; Italian Holstein cattle

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