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Use of the canonical discriminant analysis to select SNP markers for bovine breed assignment and traceability purposes

Dimauro, Corrado and Cellesi, Massimo and Steri, Roberto and Gaspa, Giustino and Sorbolini, Silvia and Stella, Alessandra and Macciotta, Nicolò Pietro Paolo (2013) Use of the canonical discriminant analysis to select SNP markers for bovine breed assignment and traceability purposes. Animal Genetics, Vol. 44 (4), p. 377-382. eISSN 1365-2052. Article.

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DOI: 10.1111/age.12021

Abstract

Several market research studies have shown that consumers are primarily concerned with the provenance of the food they eat. Among the available identification methods, only DNA-based techniques appear able to completely prevent frauds. In this study, a new method to discriminate among different bovine breeds and assign new individuals to groups was developed. Bulls of three cattle breeds farmed in Italy – Holstein, Brown, and Simmental – were genotyped using the 50K SNP Illumina BeadChip. Multivariate canonical discriminant analysis was used to discriminate among breeds, and discriminant analysis (DA) was used to assign new observations. This method was able to completely identify the three groups at chromosome level. Moreover, a genome-wide analysis developed using 340 linearly independent SNPs yielded a significant separation among groups. Using the reduced set of markers, the DA was able to assign 30 independent individuals to the proper breed. Finally, a set of 48 high discriminant SNPs was selected and used to develop a new run of the analysis. Again, the procedure was able to significantly identify the three breeds and to correctly assign new observations. These results suggest that an assay with the selected 48 SNP could be used to routinely track monobreed products.

Item Type:Article
ID Code:9146
Status:Published
Refereed:Yes
Uncontrolled Keywords:Allocation method, livestock products, multivariate analysis
Subjects:Area 07 - Scienze agrarie e veterinarie > AGR/17 Zootecnica generale e miglioramento genetico
Area 07 - Scienze agrarie e veterinarie > AGR/19 Zootecnica speciale
Divisions:001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Agraria
Publisher:Blackwell / Wiley
eISSN:1365-2052
Copyright Holders:© 2013 The Authors, Animal Genetics, © 2013 Stichting International Foundation for Animal Genetics
Deposited On:04 Jul 2013 13:02

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