Analysis of Illumina BovineSNP50 BeadChip data in different Italian cattle breeds to identify useful markers for breed authentication of dairy and beef products

Abstract

The identification of the breed of origin of cattle derived products has recently assumed particular relevance since the increasing interest in marketing mono-breed labelled cheese and beef. These products are usually sold at a higher price creating financial incentives to substituting them with lower value products coming from undifferentiated or common breeds or crossbred animals. Frauds can damage these valuable niche markets that, indirectly, may help to preserve genetic diversity through the economic incentive on raising local breeds, derived by the high value products, that are usually less productive. DNA analysis can help to identify fraudulent behaviour as we already demonstrated for Parmigiano Reggiano cheese produced from only Reggiana cattle milk. In this study we used Illumina BovineSNP50 BeadChip genotyping data from different cattle breeds to identify single nucleotide polymorphisms (SNPs) that could be useful for breed authentication of dairy and beef products. The dataset was made of genotyping data obtained from the chip v.1 or v.2 analysed on 749 Italian Brown, 2093 Italian Friesian, 479 Italian Simmental, 410 Marchigiana, 71 Cinisara and 72 Modicana cattle. About 51,000 SNPs were retained for further analyses after filtering according to a few parameters (Hardy-Weinberg equilibrium ≥0.0001; call rate ≥0.90). A quite high number of SNPs presented fixed alleles in one breed that had minor allele frequency (MAF) >0.30-0.40 in the other breeds. This was true for all breed combinations. These SNPs were indicated as highly informative for authentication purposes. Using the selected panel of SNPs, Principal Component Analysis (PCA) was able to discriminate investigated breeds. These results may represent a starting point to develop targeted DNA based tests for authentication of mono-breed cattle products.