Selecting breed informative genetic markers from high density assays

Samantha Wilkinson, P. Wiener, A. Archibald, A. Law, R.D. Schnabel, S.D. McKay, J. Taylor, Rob Ogden

Research output: Contribution to conferenceAbstract


Genetic markers can be used to identify and verify the origin of individuals. Motivation for the inference of ancestry ranges from conservation genetics to food authentication. High density assays featuring Single Nucleotide Polymorphism (SNP) markers can be exploited to create a reduced panel containing the most informative markers for these purposes. The objective of this study was to determine how many markers from the BovineSNP50 BeadChip are required to verify the origin of purebred individuals in European cattle breeds. The data consisted of individual genotypes of known ancestry sampled from 16 cattle breeds and genotyped for 40,483 markers. Breeds of interest were beef, dairy and traditional British breeds. Several SNP selection methods were implemented to determine marker informativeness. Individual assignment analysis was performed using the ranked informative markers. Stringency levels were applied by log-likelihood ratio to assess the confidence of the assignment test. The power of assignment success varied markedly between the selection methods and between breeds. Certain breeds required fewer markers (95% assignment success. The power of assignment success will depend on the levels of genetic heterogeneity between breeds and the pool of samples considered. It was found that a substantially reduced set of SNP markers can be taken from the BovineSNP50 assay to effectively assign individuals to breed of origin. Thus, with effective exploration of available high density genetic markers, a diagnostic panel of highly informative markers can be produced.
Original languageUndefined/Unknown
Pagesabstract W456
Publication statusPublished - 2011
EventPlant & Animal Genomes XIX Conference - San Diego, United States
Duration: 15 Jan 201119 Jan 2011


ConferencePlant & Animal Genomes XIX Conference
Country/TerritoryUnited States
CitySan Diego

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