Impact of preselection in genomic evaluations

Ibrahim Jibrila

Research output: Thesisinternal PhD, WU

Abstract

The development of genomic evaluation models over the last two decades has resulted in faster genetic improvement of animals, compared to when only pedigree-based genetic evaluation models were used. In large animal breeding programs, selection of parents of the next generation usually takes place in multiple stages, and the initial stages of this selection are collectively called preselection. Preselection takes place when selection candidates are young, sometimes even before they have records for any breeding goal trait. As the preselected animals grow older, they generally get records for more breeding goal traits, and they are re-evaluated in subsequent evaluations to select the final set of parents of the next generation. Impact of preselection on accuracy and bias of subsequent genomic evaluation of preselected animals is poorly understood. The same applies for the role of genotypes of preculled animals (i.e. animals removed from the breeding program at preselection stage) in subsequent genomic evaluation of their preselected sibs. In this thesis, I used single-step genomic best linear unbiased prediction (ssGBLUP) as the representative genomic evaluation model, and used simulated and real datasets to investigate the impact of i) types and intensities of preselection and ii) genotypes and phenotypes of different groups of animals, on accuracy and bias in ssGBLUP evaluation of preselected animals. I showed that preselection, regardless of its type and intensity, results in some accuracy loss in subsequent ssGBLUP evaluation of preselected animals, compared to a scenario without preselection. I explained that the accuracy loss is mainly due to loss of relatives with records. I also showed that ssGBLUP evaluates preselected animals without preselection bias, regardless of type and intensity of preselection. I further showed that genotypes of preculled animals are only needed in subsequent ssGBLUP evaluation of their genomically preselected sibs if some of their parents are not genotyped. The results of this thesis also showed that if ssGBLUP is used in subsequent evaluation of genomically preselected animals, realized genetic gain is only slightly lower compared to a scenario without preselection. To minimize this loss of genetic gain as a result of genomic preselection, I recommended that commercial animal breeding programs genotype as many young selection candidates as economically possible.

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • Veerkamp, Roel, Promotor
  • Calus, Mario, Promotor
  • ten Napel, Jan, Co-promotor
Award date25 May 2022
Place of PublicationWageningen
Publisher
Print ISBNs9789464471021
DOIs
Publication statusPublished - 25 May 2022

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