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      63 A comparison of clustering methods for cross-validation of genomic predictors when training on phenotypes or deregressed Estimated Breeding Values


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          The objective of the study was to evaluate the impact of clustering methods for cross-validation on the accuracy of prediction of molecular breeding values (MBV) in Red Angus cattle (n = 9,763) and in simulation. Individuals were clustered using seven methods [k-means, k-medoids, principal component analysis on the numerator relationship matrix (A) and identical-by-state genomic matrix (G) as data and covariance matrices, and random] and two response variables [deregressed Estimated Breeding Values (DEBV) and adjusted phenotypes]. Genotypes were imputed to a 50K reference panel. Using cross-validation and a Bayes C model, MBV were estimated for traits including birth weight (BWT), marbling (MARB), rib-eye area (REA), and yearling weight (YWT) for DEBV and BWT, YWT, and ultrasonically measured intramuscular fat percentage and rib eye area for adjusted phenotypes. A bivariate animal model was used to estimate prediction accuracies calculated using the genetic correlation between estimated MBV and the associated response variable. To quantify the difference between true and estimated accuracies, a simulation mimicking a cattle population was replicated five times. The same clustering methods were used as with the Red Angus data with the addition of forward validation and two genotyping methods (random selection and selection of the top 25% of animals). Predicted accuracies were estimated similarly and true accuracies were estimated using the residual correlation of a bivariate model using MBV and true breeding values (TBV). The Rand index was used to quantify the similarity between clustering methods, showing relationship-based clusters were clearly different from random clusters. In simulation, random genotyping led to higher estimated accuracies than selection of top individuals; however, estimated accuracies over predicted true accuracies with random genotyping but under predicted true accuracies with the selection of top individuals. When forward validation was evaluated within simulation, results suggested DEBV led to less biased estimates of MBV accuracy.

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          Author and article information

          J Anim Sci
          J. Anim. Sci
          Journal of Animal Science
          Oxford University Press (US )
          July 2019
          29 July 2019
          : 97
          : Suppl 2 , ASAS Midwestern Section and ADSA® Midwest Branch
          : 34-35
          University of Nebraska - Lincoln
          PMC6666610 PMC6666610 6666610 skz122.064
          © The Author(s) 2019. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

          This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model ( https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

          Page count
          Pages: 2
          Oral Presentations
          Genetics, Genomics & Bioinformatics I

          beef cattle,cross validation,genomic prediction
          beef cattle, cross validation, genomic prediction


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