Using loci with identified dominance effects to improve the prediction of heterosis

E.N. Amuzu-Aweh, P. Bijma, H. Bovenhuis, D.J. de Koning

Research output: Chapter in Book/Report/Conference proceedingAbstract


The availability of high-density single nucleotide polymorphism (SNP) panels creates opportunities for the genomic prediction of heterosis, which would increase the efficiency of commercial crossbreeding programs. In a previous study, the genome-wide average squared difference in allele frequency (SDAF) between parental pure-lines was used to predict heterosis in egg number and egg weight. This assumed that all SNPs had an equal contribution to heterosis. Heterosis was predicted with an accuracy of ~0.5, and results suggested that dominance plays a major role in heterosis. Therefore, in this study our aim was to identify SNPs with dominance effects and to specifically use these SNPs to calculate a weighted SDAF for predicting heterosis. We hypothesised that predicting heterosis with an emphasis on SNPs with dominance effects would increase the accuracy of prediction. We used 60k SNP genotypes from 3,427 sires, allele frequencies from 9 pure-lines, and egg production records from 16 crosses between those lines, representing ~210,000 crossbred hens. We calculated genotype probabilities for the crossbred offspring of each sire and from that derived additive and dominance coefficients. We estimated additive and dominance effects of all SNPs by regressing offspring performance on their additive and dominance coefficients. Next, using the reciprocal of the variance of the estimated dominance effects, we calculated a weighted SDAF and used that as a predictor of heterosis. Preliminary results indicate that dominance effects are more important for egg number than for egg weight: we identified 37 SNPs for egg number and 5 SNPs for egg weight that had significant dominance effects (10% false discovery rate). Results will reveal whether weighing SNPs by their estimated dominance effects can improve the prediction of heterosis.
Original languageEnglish
Title of host publicationBook of Abstracts of the 66th Annual Meeting of the European Federation of Animal Science
Place of PublicationWageningen
PublisherWageningen Academic Publishers
ISBN (Print)9789086862696
Publication statusPublished - 2015
EventEAAP - 66th Annual Meeting 2015 - Warsaw, Poland
Duration: 31 Aug 20154 Sep 2015


ConferenceEAAP - 66th Annual Meeting 2015


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