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

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Abstract

The identification of the breed of origin of cattle derived productshas recently assumed particular relevance since theincreasing interest in marketing mono-breed labelled cheeseand beef. These products are usually sold at a higher price creatingfinancial incentives to substituting them with lower valueproducts coming from undifferentiated or common breeds orcrossbred animals. Frauds can damage these valuable niche markets that, indirectly, may help to preserve genetic diversitythrough the economic incentive on raising local breeds, derivedby the high value products, that are usually less productive. DNAanalysis can help to identify fraudulent behaviour as we alreadydemonstrated for Parmigiano Reggiano cheese produced fromonly Reggiana cattle milk. In this study we used IlluminaBovineSNP50 BeadChip genotyping data from different cattlebreeds to identify single nucleotide polymorphisms (SNPs) thatcould be useful for breed authentication of dairy and beef products.The dataset was made of genotyping data obtained from thechip v.1 or v.2 analysed on 749 Italian Brown, 2093 ItalianFriesian, 479 Italian Simmental, 410 Marchigiana, 71 Cinisaraand 72 Modicana cattle. About 51,000 SNPs were retained for furtheranalyses after filtering according to a few parameters(Hardy-Weinberg equilibrium ≥0.0001; call rate ≥0.90). A quitehigh number of SNPs presented fixed alleles in one breed thathad minor allele frequency (MAF) >0.30-0.40 in the other breeds.This was true for all breed combinations. These SNPs were indicatedas highly informative for authentication purposes. Usingthe selected panel of SNPs, Principal Component Analysis (PCA)was able to discriminate investigated breeds. These results mayrepresent a starting point to develop targeted DNA based tests forauthentication of mono-breed cattle products.
Original languageEnglish
Pages64-65
Number of pages2
Publication statusPublished - 2013

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