Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/22099
Title: Prediction of heterosis using genome-wide SNP-marker data: application to egg production traits in white Leghorn crosses
Contributor(s): Amuzu-Aweh, E N (author); Bijma, P (author); Kinghorn, Brian  (author); Vereijken, A (author); Visscher, J (author); van Arendonk, JAM (author); Bovenhuis, H (author)
Publication Date: 2013
Open Access: Yes
DOI: 10.1038/hdy.2013.77Open Access Link
Handle Link: https://hdl.handle.net/1959.11/22099
Abstract: Prediction of heterosis has a long history with mixed success, partly due to low numbers of genetic markers and/or small data sets. We investigated the prediction of heterosis for egg number, egg weight and survival days in domestic white Leghorns, using ~400 000 individuals from 47 crosses and allele frequencies on ~53 000 genome-wide single nucleotide polymorphisms (SNPs). When heterosis is due to dominance, and dominance effects are independent of allele frequencies, heterosis is proportional to the squared difference in allele frequency (SDAF) between parental pure lines (not necessarily homozygous). Under these assumptions, a linear model including regression on SDAF partitions crossbred phenotypes into pure-line values and heterosis, even without pure-line phenotypes. We therefore used models where phenotypes of crossbreds were regressed on the SDAF between parental lines. Accuracy of prediction was determined using leave-one-out crossvalidation. SDAF predicted heterosis for egg number and weight with an accuracy of ~0.5, but did not predict heterosis for survival days. Heterosis predictions allowed preselection of pure lines before field-testing, saving ~50% of field-testing cost with only 4% loss in heterosis. Accuracies from cross-validation were lower than from the model-fit, suggesting that accuracies previously reported in literature are overestimated. Cross-validation also indicated that dominance cannot fully explain heterosis. Nevertheless, the dominance model had considerable accuracy, clearly greater than that of a general/specific combining ability model. This work also showed that heterosis can be modelled even when pure-line phenotypes are unavailable. We concluded that SDAF is a useful predictor of heterosis in commercial layer breeding.
Publication Type: Journal Article
Source of Publication: Heredity, 111(6), p. 530-538
Publisher: Nature Publishing Group
Place of Publication: United Kingdom
ISSN: 1365-2540
0018-067X
Fields of Research (FoR) 2008: 060412 Quantitative Genetics (incl. Disease and Trait Mapping Genetics)
Fields of Research (FoR) 2020: 310506 Gene mapping
Socio-Economic Objective (SEO) 2008: 830309 Poultry
Socio-Economic Objective (SEO) 2020: 100411 Poultry
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
Appears in Collections:Journal Article

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