Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/18862
Title: Genomic best linear unbiased prediction using differential evolution
Contributor(s): Al-Mamun, Hawlader A (author); Kwan, Paul H  (author); Clark, Sam A  (author)orcid ; Lee, S H (author); Lee, H K (author); Song, K D (author); Lee, S H (author); Gondro, Cedric  (author)orcid 
Publication Date: 2015
Open Access: Yes
Handle Link: https://hdl.handle.net/1959.11/18862
Open Access Link: http://www.aaabg.org/aaabghome/AAABG21papers/Al-Mamun21145.pdfOpen Access Link
Abstract: In this paper we proposed a method to improve the accuracy of prediction of genomic best linear unbiased prediction (GBLUP). In GBLUP a genomic relationship matrix (GRM) is used to define the variance-covariance relationship between individuals and is calculated from all available genotyped markers. Instead of using all markers to build the GRM, which is then used for trait prediction, we used an evolutionary algorithm (differential evolution - DE) to subset the marker set and identify the markers that best capture the variance-covariance structure between individuals for specific traits. This subset of markers was then used to build a trait relationship matrix (TRM) that replaces the GRM in GBLUP (herein referred to as TBLUP). The predictive ability of TBLUP was compared against GBLUP and a Bayesian method (Bayesian LASSO) using simulated and real data. We found that TBLUP has better predictive ability than GBLUP and Bayesian LASSO in almost all scenarios.
Publication Type: Conference Publication
Conference Name: 21st Conference of the Association for the Advancement of Animal Breeding and Genetics, Lorne, Australia, 28th - 30th September, 2015
Conference Details: 21st Conference of the Association for the Advancement of Animal Breeding and Genetics, Lorne, Australia, 28th - 30th September, 2015
Grant Details: ARC/DP130100542
Source of Publication: Proceedings of the Twenty-first Conference of the Association for the Advancement of Animal Breeding and Genetics, p. 145-148
Publisher: AAABG: Association for the Advancement of Animal Breeding and Genetics
Place of Publication: Bundoora, Australia
Field of Research (FOR): 070201 Animal Breeding
060408 Genomics
080108 Neural, Evolutionary and Fuzzy Computation
Peer Reviewed: Yes
HERDC Category Description: E1 Refereed Scholarly Conference Publication
Other Links: http://www.aaabg.org/aaabghome/proceedings21.php
Series Name: Proceedings of the AAABG ... Conference
Series Number : 21
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