Comparison of molecular breeding values based on within- and across-breed training in beef cattle

Stephen D Kachman, Matthew L. Spangler, Gary L. Bennett, Kathryn J. Hanford, Larry A. Kuehn, Warren M. Snelling, R. Mark Thallman, Mahdi Saatchi, Dorian J. Garrick, Robert D. Schnabel, Jeremy F. Taylor, E. John Pollak

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

Background: Although the efficacy of genomic predictors based on within-breed training looks promising, it is necessary to develop and evaluate across-breed predictors for the technology to be fully applied in the beef industry. The efficacies of genomic predictors trained in one breed and utilized to predict genetic merit in differing breeds based on simulation studies have been reported, as have the efficacies of predictors trained using data from multiple breeds to predict the genetic merit of purebreds. However, comparable studies using beef cattle field data have not been reported. Methods. Molecular breeding values for weaning and yearling weight were derived and evaluated using a database containing BovineSNP50 genotypes for 7294 animals from 13 breeds in the training set and 2277 animals from seven breeds (Angus, Red Angus, Hereford, Charolais, Gelbvieh, Limousin, and Simmental) in the evaluation set. Six single-breed and four across-breed genomic predictors were trained using pooled data from purebred animals. Molecular breeding values were evaluated using field data, including genotypes for 2227 animals and phenotypic records of animals born in 2008 or later. Accuracies of molecular breeding values were estimated based on the genetic correlation between the molecular breeding value and trait phenotype. Results: With one exception, the estimated genetic correlations of within-breed molecular breeding values with trait phenotype were greater than 0.28 when evaluated in the breed used for training. Most estimated genetic correlations for the across-breed trained molecular breeding values were moderate (> 0.30). When molecular breeding values were evaluated in breeds that were not in the training set, estimated genetic correlations clustered around zero. Conclusions: Even for closely related breeds, within- or across-breed trained molecular breeding values have limited prediction accuracy for breeds that were not in the training set. For breeds in the training set, across- and within-breed trained molecular breeding values had similar accuracies. The benefit of adding data from other breeds to a within-breed training population is the ability to produce molecular breeding values that are more robust across breeds and these can be utilized until enough training data has been accumulated to allow for a within-breed training set.

Original languageEnglish (US)
Article number30
JournalGenetics Selection Evolution
Volume45
Issue number1
DOIs
StatePublished - Aug 20 2013

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DNA Shuffling
breeding value
beef cattle
breeding
breeds
animal
genomics
phenotype
genetic correlation
genotype
Genotype
comparison
Phenotype
weaning
genetic merit
Weaning
purebreds
animals
Industry

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Animal Science and Zoology
  • Genetics

Cite this

Kachman, S. D., Spangler, M. L., Bennett, G. L., Hanford, K. J., Kuehn, L. A., Snelling, W. M., ... Pollak, E. J. (2013). Comparison of molecular breeding values based on within- and across-breed training in beef cattle. Genetics Selection Evolution, 45(1), [30]. https://doi.org/10.1186/1297-9686-45-30

Comparison of molecular breeding values based on within- and across-breed training in beef cattle. / Kachman, Stephen D; Spangler, Matthew L.; Bennett, Gary L.; Hanford, Kathryn J.; Kuehn, Larry A.; Snelling, Warren M.; Thallman, R. Mark; Saatchi, Mahdi; Garrick, Dorian J.; Schnabel, Robert D.; Taylor, Jeremy F.; Pollak, E. John.

In: Genetics Selection Evolution, Vol. 45, No. 1, 30, 20.08.2013.

Research output: Contribution to journalArticle

Kachman, SD, Spangler, ML, Bennett, GL, Hanford, KJ, Kuehn, LA, Snelling, WM, Thallman, RM, Saatchi, M, Garrick, DJ, Schnabel, RD, Taylor, JF & Pollak, EJ 2013, 'Comparison of molecular breeding values based on within- and across-breed training in beef cattle', Genetics Selection Evolution, vol. 45, no. 1, 30. https://doi.org/10.1186/1297-9686-45-30
Kachman, Stephen D ; Spangler, Matthew L. ; Bennett, Gary L. ; Hanford, Kathryn J. ; Kuehn, Larry A. ; Snelling, Warren M. ; Thallman, R. Mark ; Saatchi, Mahdi ; Garrick, Dorian J. ; Schnabel, Robert D. ; Taylor, Jeremy F. ; Pollak, E. John. / Comparison of molecular breeding values based on within- and across-breed training in beef cattle. In: Genetics Selection Evolution. 2013 ; Vol. 45, No. 1.
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