Abstract

BackgroundIn crossbreeding programs, genomic selection offers the opportunity to make efficient use of information on crossbred (CB) individuals in the selection of purebred (PB) candidates. In such programs, reference populations often contain genotyped PB animals, although the breeding objective is usually more focused on CB performance. The question is what would be the benefit of including a larger proportion of CB individuals in the reference population.MethodsIn a deterministic simulation study, we evaluated the benefit of including various proportions of CB animals in a reference population for genomic selection of PB animals in a crossbreeding program. We used a pig breeding scheme with selection for a moderately heritable trait and a size of 6000 for the reference population.ResultsApplying genomic selection to improve the performance of CB individuals, with a genetic correlation between PB and CB performance (rPC) of 0.7, selection accuracy of PB candidates increased from 0.49 to 0.52 if the reference population consisted of PB individuals, it increased to 0.55 if the reference population consisted of the same number of CB individuals, and to 0.60 if the size of the CB reference population was twice that of the reference population for each PB line. The advantage of using CB rather than PB individuals increased linearly with the proportion of CB individuals in the reference population. This advantage disappeared quickly if rPC was higher or if the breeding objective put some emphasis on PB performance. The benefit of adding CB individuals to an existing PB reference population was limited for high rPC.ConclusionsUsing CB rather than PB individuals in a reference population for genomic selection can provide substantial advantages, but only when correlations between PB and CB performances are not high and PB performance is not part of the breeding objective.

Highlights

  • In crossbreeding programs, genomic selection offers the opportunity to make efficient use of information on crossbred (CB) individuals in the selection of purebred (PB) candidates

  • Reference population structure For the base scenario, where rPC = 0.7 and the breeding objective aimed at improving CB performance, the index accuracy based on PB phenotypic information alone was 0.45

  • The relative increase in index accuracy due to genomic selection was 7.3% (0.491 vs. 0.526) if the reference population included PB animals and was 12.8% (0.491 vs 0.554) if a CB reference population of equal size was used

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Summary

Introduction

Genomic selection offers the opportunity to make efficient use of information on crossbred (CB) individuals in the selection of purebred (PB) candidates In such programs, reference populations often contain genotyped PB animals, the breeding objective is usually more focused on CB performance. PB and CB performances can be considered as two genetically correlated traits; the correlation between PB and CB performances (rPC) is affected by the extent of nonadditive genetic effects ( dominance) and the genetic distance between lines or breeds crossed. This correlation often reflects genotype by environment interactions due to nucleus PB and commercial CB animals being exposed to different environments. Bijma and van Arendonk [3] showed that extensive use of sib information on CB individuals can lead to increased rates of inbreeding

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