Abstract
BackgroundIn crossbreeding programs, various genomic prediction models have been proposed for using phenotypic records of crossbred animals to increase the selection response for crossbred performance in purebred animals. A possible model is a model that assumes identical single nucleotide polymorphism (SNP) effects for the crossbred performance trait across breeds (ASGM). Another model is a genomic model that assumes breed-specific effects of SNP alleles (BSAM) for crossbred performance. The aim of this study was to derive and validate equations for predicting the reliability of estimated genomic breeding values for crossbred performance in both these models. Prediction equations were derived for situations when all (phenotyping and) genotyping data have already been collected, i.e. based on the genetic evaluation model, and for situations when all genotyping data are not yet available, i.e. when designing breeding programs.ResultsWhen all genotyping data are available, prediction equations are based on selection index theory. Without availability of all genotyping data, prediction equations are based on population parameters (e.g., heritability of the traits involved, genetic correlation between purebred and crossbred performance, effective number of chromosome segments). Validation of the equations for predicting the reliability of genomic breeding values without all genotyping data was performed based on simulated data of a two-way crossbreeding program, using either two closely-related breeds, or two unrelated breeds, to produce crossbred animals. The proposed equations can be used for an easy comparison of the reliability of genomic estimated breeding values across many scenarios, especially if all genotyping data are available. We show that BSAM outperforms ASGM for a specific breed, if the effective number of chromosome segments that originate from this breed and are shared by selection candidates of this breed and crossbred reference animals is less than half the effective number of all chromosome segments that are independently segregating in the same animals.ConclusionsThe derived equations can be used to predict the reliability of genomic estimated breeding values for crossbred performance using ASGM or BSAM in many scenarios, and are thus useful to optimize the design of breeding programs. Scenarios can vary in terms of the genetic correlation between purebred and crossbred performances, heritabilities, number of reference animals, or distance between breeds.
Highlights
In crossbreeding programs, various genomic prediction models have been proposed for using phenotypic records of crossbred animals to increase the selection response for crossbred performance in purebred animals
The results of this study showed that the reliabilities of genomic estimated breeding values (EBV) for crossbred performance predicted without availability of genotyping data were of the same order of magnitude as those predicted with availability of genotyping data
Several equations for predicting the reliability of genomic EBV for crossbred performance based on across-breed SNP genotype models (ASGM) or on BSAM were derived for three different scenarios
Summary
Various genomic prediction models have been proposed for using phenotypic records of crossbred animals to increase the selection response for crossbred performance in purebred animals. Assuming only additive gene action, one approach to accommodate this is to model differences between allele substitution SNP effects using a multivariate genomic model that assumes a correlation structure between the effects of SNPs across the purebred and crossbred populations, or equivalently, by assuming a genetic correlation structure across the trait measured in purebred and crossbred populations [9, 10] These multivariate genomic models are referred to hereafter as across-breed SNP genotype models (ASGM), since the estimates of SNP allele substitution effects for the crossbred performance trait are used to predict breeding values for crossbred performance of purebred selection candidates, regardless of their breed of origin [4, 6]. Third, purebred and crossbred animals may be exposed to different environments, leading to genotype by environment interactions Because of these reasons, estimated allele substitution effects at SNPs for the crossbred performance trait may be breed-specific. Results from simulations have shown that BSAM can result in greater accuracy of genomic estimated breeding values (EBV) of purebreds for crossbred performance than ASGM under some conditions [2, 4, 11]
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