1. Phenomic Selection: A new and efficient alternative to genomic selection
- Author
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Pauline Robert, Charlotte Brault, Renaud Rincent, Vincent Segura, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Géno-vigne® (UMT Géno-vigne®), Institut Français de la Vigne et du Vin (IFV)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), fond CASDAR,C-2020-5, ANRT, grant number 2018/0577, ANRT, grant number 2019/0060, ANR-19-ECOM-0006,SelGenVit,Sélection génomique au service de l'amélioration de la vigne pour la diversification et le déploiement de variétés résistantes à forts potentiel œnologique(2019), and ANR-10-BTBR-0003,BREEDWHEAT,Développer de nouvelles variétés de blé pour une agriculture durable(2010)
- Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics ,Hyperspectral imaging ,[SDV]Life Sciences [q-bio] ,Genomic selection (GS) ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Plant breeding ,Phenomic selection (PS) ,Genomic-like omics-based (GLOB) selection ,Near-infrared spectroscopy (NIRS) - Abstract
Recently, it has been proposed to switch molecular markers to near-infrared (NIR) spectra for inferring relationships between individuals and further performing phenomic selection (PS), analogous to genomic selection (GS). The PS concept is similar to genomic-like omics-based (GLOB) selection, in which molecular markers are replaced by endophenotypes, such as metabolites or transcript levels, except that the phenomic information obtained for instance by near-infrared spectroscopy (NIRS) has usually a much lower cost than other omics. Though NIRS has been routinely used in breeding for several decades, especially to deal with end-product quality traits, its use to predict other traits of interest and further make selections is new. Since the seminal paper on PS, several publications have advocated the use of spectral acquisition (including NIRS and hyperspectral imaging) in plant breeding towards PS, potentially providing a scope of what is possible. In the present chapter, we first come back to the concept of PS as originally proposed and provide a classification of selected papers related to the use of phenomics in breeding. We further provide a review of the selected literature concerning the type of technology used, the preprocessing of the spectra, and the statistical modeling to make predictions. We discuss the factors that likely affect the efficiency of PS and compare it to GS in terms of predictive ability. Finally, we propose several prospects for future work and application of PS in the context of plant breeding.
- Published
- 2022