Bootstrap study of genome-enabled prediction reliabilities using haplotype blocks across Nordic Red cattle breeds.

Publisher: American Dairy Science Association Country of Publication: United States NLM ID: 2985126R Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1525-3198 (Electronic) Linking ISSN: 00220302 NLM ISO Abbreviation: J Dairy Sci Subsets: MEDLINE

Publication: Champaign, IL : American Dairy Science Association
Original Publication: Lancaster, Pa. [etc.]

Genetic Variation* ; Genome* ; Haplotypes* ; Polymorphism, Single Nucleotide*; Cattle/*genetics; Animals ; Bayes Theorem ; Breeding ; Female ; Male

This study compared the accuracy of genome-enabled prediction models using individual single nucleotide polymorphisms (SNP) or haplotype blocks as covariates when using either a single breed or a combined population of Nordic Red cattle. The main objective was to compare predictions of breeding values of complex traits using a combined training population with haplotype blocks, with predictions using a single breed as training population and individual SNP as predictors. To compare the prediction reliabilities, bootstrap samples were taken from the test data set. With the bootstrapped samples of prediction reliabilities, we built and graphed confidence ellipses to allow comparisons. Finally, measures of statistical distances were used to calculate the gain in predictive ability. Our analyses are innovative in the context of assessment of predictive models, allowing a better understanding of prediction reliabilities and providing a statistical basis to effectively calibrate whether one prediction scenario is indeed more accurate than another. An ANOVA indicated that use of haplotype blocks produced significant gains mainly when Bayesian mixture models were used but not when Bayesian BLUP was fitted to the data. Furthermore, when haplotype blocks were used to train prediction models in a combined Nordic Red cattle population, we obtained up to a statistically significant 5.5% average gain in prediction accuracy, over predictions using individual SNP and training the model with a single breed.
(Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

Keywords: Nordic Red cattle; bootstrap analysis; haplotype block; multi-breed genomic prediction

Date Created: 20150803 Date Completed: 20160607 Latest Revision: 20181202

20221213

10.3168/jds.2015-9360

26233439