title: The evaluation of bovine SNP50 beadchip assay performance in Polish red cattle breed.
abstract: According to increasing interest in the use of high density SNP (single nucleotide polymorphism) genotyping assays for genome-wide genetic studies in farm animals, there is a need to assess the usefulness of currently available genomic tools for application in different breeds. The performance of the assays may differ between the breeds because of discrepancies in allele frequencies of the polymorphisms or differences in linkage disequilibrium patterns. In this study we attempted to test the performance of the Bovine SNP50 v2 genotyping assay (Illumina) for population genetic and other applications in the Polish Red cattle breed. We found that 37,977 of the 53,438 autosomal markers included in the assay give high quality genomic information and can be used for different applications concerning this breed. The remaining markers were denoted as "of limited use" or redundant because of their weak performance, deviation from Hardy-Weinberg equilibrium, low minor allele frequency, high linkage disequilibrium with other neighboring markers or location on sex chromosomes.
authors.affiliation: National Research Institute of Animal Production, Laboratory of Genomics, Krakowska 1, 32-083 Balice, Poland. agurgul@izoo.krakow.pl
authors.forename: Artur
authors.initials: A
authors.lastname: Gurgul
authors.forename: Kacper
authors.initials: K
authors.lastname: Zukowski
authors.forename: Klaudia
authors.initials: K
authors.lastname: Pawlina
authors.forename: Tomasz
authors.initials: T
authors.lastname: Zabek
authors.forename: Ewelina
authors.initials: E
authors.lastname: Semik
authors.forename: Monika
authors.initials: M
authors.lastname: Bugno-Poniewierska
mesh_terms: D000483:Alleles; D000818:Animals; D002417:Cattle / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000662:veterinary*; D020641:Polymorphism, Single Nucleotide