Do stronger measures of genomic connectedness enhance prediction accuracies across management units?

Haipeng Yu, Matthew L. Spangler, Ronald M. Lewis, Gota Morota

Research output: Contribution to journalArticle

Abstract

Genetic connectedness assesses the extent to which estimated breeding values can be fairly compared across management units. Ranking of individuals across units based on best linear unbiased prediction (BLUP) is reliable when there is a sufficient level of connectedness due to a better disentangling of genetic signal from noise. Connectedness arises from genetic relationships among individuals. Although a recent study showed that genomic relatedness strengthens the estimates of connectedness across management units compared with that of pedigree, the relationship between connectedness measures and prediction accuracies only has been explored to a limited extent. In this study, we examined whether increased measures of connectedness led to higher prediction accuracies evaluated by a cross-validation (CV) based on computer simulations. We applied prediction error variance of the difference, coefficient of determination (CD), and BLUP-type prediction models to data simulated under various scenarios. We found that a greater extent of connectedness enhanced accuracy of whole-genome prediction. The impact of genomics was more marked when large numbers of markers were used to infer connectedness and evaluate prediction accuracy. Connectedness across units increased with the proportion of connecting individuals and this increase was associated with improved accuracy of prediction. The use of genomic information resulted in increased estimates of connectedness and improved prediction accuracies compared with those of pedigree-based models when there were enough markers to capture variation due to QTL signals.

Original languageEnglish (US)
Pages (from-to)4490-4500
Number of pages11
JournalJournal of animal science
Volume96
Issue number11
DOIs
StatePublished - Nov 21 2018

Fingerprint

Pedigree
genomics
prediction
Genomics
Computer Simulation
Breeding
Genome
pedigree
breeding value
computer simulation
genetic relationships
quantitative trait loci
genome

Keywords

  • Genomic connectedness
  • Genomic prediction
  • Relatedness

ASJC Scopus subject areas

  • Food Science
  • Animal Science and Zoology
  • Genetics

Cite this

Do stronger measures of genomic connectedness enhance prediction accuracies across management units? / Yu, Haipeng; Spangler, Matthew L.; Lewis, Ronald M.; Morota, Gota.

In: Journal of animal science, Vol. 96, No. 11, 21.11.2018, p. 4490-4500.

Research output: Contribution to journalArticle

Yu, Haipeng ; Spangler, Matthew L. ; Lewis, Ronald M. ; Morota, Gota. / Do stronger measures of genomic connectedness enhance prediction accuracies across management units?. In: Journal of animal science. 2018 ; Vol. 96, No. 11. pp. 4490-4500.
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