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Favorable conditions for genomic evaluation to outperform classical pedigree evaluation highlighted by a proof-of-concept study in poplar

Pégard Marie, Segura Vincent, Munoz Facundo, Bastien Catherine, Jorge Véronique, Sanchez Leopoldo. 2020. Favorable conditions for genomic evaluation to outperform classical pedigree evaluation highlighted by a proof-of-concept study in poplar. Frontiers in Plant Science, 11:581954, 23 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
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Abstract : Forest trees like poplar are particular in many ways compared to other domesticated species. They have long juvenile phases, ongoing crop-wild gene flow, extensive outcrossing, and slow growth. All these particularities tend to make the conduction of breeding programs and evaluation stages costly both in time and resources. Perennials like trees are therefore good candidates for the implementation of genomic selection (GS) which is a good way to accelerate the breeding process, by unchaining selection from phenotypic evaluation without affecting precision. In this study, we tried to compare GS to pedigree-based traditional evaluation, and evaluated under which conditions genomic evaluation outperforms classical pedigree evaluation. Several conditions were evaluated as the constitution of the training population by cross-validation, the implementation of multi-trait, single trait, additive and non-additive models with different estimation methods (G-BLUP or weighted G-BLUP). Finally, the impact of the marker densification was tested through four marker density sets. The population under study corresponds to a pedigree of 24 parents and 1,011 offspring, structured into 35 full-sib families. Four evaluation batches were planted in the same location and seven traits were evaluated on 1 and 2 years old trees. The quality of prediction was reported by the accuracy, the Spearman rank correlation and prediction bias and tested with a cross-validation and an independent individual test set. Our results show that genomic evaluation performance could be comparable to the already well-optimized pedigree-based evaluation under certain conditions. Genomic evaluation appeared to be advantageous when using an independent test set and a set of less precise phenotypes. Genome-based methods showed advantages over pedigree counterparts when ranking candidates at the within-family levels, for most of the families. Our study also showed that looking at ranking criteria as Spearman rank correlation can reveal benefits to genomic selection hidden by biased predictions.

Mots-clés Agrovoc : Populus nigra, évaluation des ressources forestières, Méthode d'amélioration génétique, Sélection, Choix des variétés, Méthode statistique, Analyse multivariée, Sélection assistée par marqueurs

Mots-clés libres : Genomic selection, Markers, Phenotype, Multi-trait model, Breeding

Classification Agris : F30 - Plant genetics and breeding

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Agence(s) de financement européenne(s) : European Commission

Programme de financement européen : FP7

Projet(s) de financement européen(s) : Novel tree breeding strategies

Auteurs et affiliations

  • Pégard Marie, INRA (FRA)
  • Segura Vincent, INRA (FRA)
  • Munoz Facundo, CIRAD-BIOS-UMR ASTRE (FRA) ORCID: 0000-0002-5061-4241
  • Bastien Catherine, INRA (FRA)
  • Jorge Véronique, INRA (FRA)
  • Sanchez Leopoldo, INRA (FRA) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/596848/)

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