Aarhus University Seal / Aarhus Universitets segl

Effect of marker-data editing on the accuracy of genomic prediction

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

  • Vahid Edriss, Danmark
  • Bernt Guldbrandtsen, Danmark
  • Mogens Sandø Lund, Danmark
  • Guosheng Su
Genomic selection is a method to predict breeding values using genome-wide single-nucleotide polymorphism (SNP) markers. High-quality marker data are necessary for genomic selection. The aim of this study was to investigate the effect of marker-editing criteria on the accuracy of genomic predictions in the Nordic Holstein and Jersey populations. Data included 4429 Holstein and 1071 Jersey bulls. In total, 48 222 SNP for Holstein and 44 305 SNP for Jersey were polymorphic. The SNP data were edited based on (i) minor allele frequencies (MAF) with thresholds of no limit, 0.001, 0.01, 0.02, 0.05 and 0.10, (ii) deviations from Hardy–Weinberg proportions (HWP) with thresholds of no limit, chi-squared p-values of 0.001, 0.02, 0.05 and 0.10, and (iii) GenCall (GC) scores with thresholds of 0.15, 0.55, 0.60, 0.65 and 0.70. The marker data sets edited with different criteria were used for genomic prediction of protein yield, fertility and mastitis using a Bayesian variable selection and a GBLUP model. De-regressed EBV were used as response variables. The result showed little difference between prediction accuracies based on marker data sets edited with MAF and deviation from HWP. However, accuracy decreased with more stringent thresholds of GC score. According to the results of this study, it would be appropriate to edit data with restriction of MAF being between 0.01 and 0.02, a p-value of deviation from HWP being 0.05, and keeping all individual SNP genotypes having a GC score over 0.15.
TidsskriftJournal of Animal Breeding and Genetics
Sider (fra-til)128-135
Antal sider8
StatusUdgivet - apr. 2013

Se relationer på Aarhus Universitet Citationsformater

ID: 46033388