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Stratégies de génotypage pour la sélection génomique chez la poule pondeuse

Abstract : The development of a commercial high density (HD) SNP chip of 600,000 SNPs enabled the implementation of genomic selection in layer and broiler. However, genotyping costs with this tool still remain high for a routine use on the selection candidates. Concurrently, new sequencing technologies (NGS) allow to consider other solutions than SNP chip for genomic selection. One of the main goal of genomic selection is to develop less expensive tools for genotyping or sequencing the selection candidates. Then, from the HD genotypes of a reference population, it is possible with different imputation methods to deduce the HD genotypes of the candidates. Firstly, the aim was to investigate the impact of different factors concerning the development of low density SNPchips or the constitution of the reference population on imputation accuracy. The impact of the use or not of imputation on genomic evaluation was also studied. The results showed that an equidistant methodology, for a SNP density higher than 5K, is suitable to get good imputation accuracy and good genomic evaluation accuracy. For an SNP density higher than 5K, it is also possible to use low density SNP chips without imputation.Low density genotypes were then replaced by genotypes from simulated RAD-Seq methods. Depending on the restriction enzyme used, studies have shown that RAD-Seq methods could be an interesting alternative to low density SNP chips.
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Submitted on : Wednesday, April 7, 2021 - 12:26:09 PM
Last modification on : Thursday, April 8, 2021 - 3:39:36 AM


Version validated by the jury (STAR)


  • HAL Id : tel-02789314, version 2
  • PRODINRA : 495066



Florian Herry. Stratégies de génotypage pour la sélection génomique chez la poule pondeuse. Génétique animale. Agrocampus Ouest, 2019. Français. ⟨NNT : 2019NSARB330⟩. ⟨tel-02789314v2⟩



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