Multi-environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection

McLeod Louis, Barchi Lorenzo, Tumino Giorgio, Tripodi Pasquale, Salinier Jérémy, Gros Christophe, Boyaci Filiz, Ozalp Ramazan, Borovsky Yelena, Schafleitner Roland, Barchenger Derek, Finkers Richard, Brouwer Matthijs, Stein Nils, Rabanus-Wallace Mark Timothy, Giuliano Giovanni, Voorrips Roeland, Paran Ilan, Lefebvre Véronique. 2023. Multi-environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection. The Plant Journal, 116 (5) : 1508-1528.

Résumé : Investigating crop diversity through genome-wide association studies (GWAS) on core collections helps in deciphering the genetic determinants of complex quantitative traits. Using the G2P-SOL project world collection of 10 038 wild and cultivated Capsicum accessions from 10 major genebanks, we assembled a core collection of 423 accessions representing the known genetic diversity. Since complex traits are often highly dependent upon environmental variables and genotype-by-environment (G × E) interactions, multi-environment GWAS with a 10 195-marker genotypic matrix were conducted on a highly diverse subset of 350 Capsicum annuum accessions, extensively phenotyped in up to six independent trials from five climati-cally differing countries. Environment-specific and multi-environment quantitative trait loci (QTLs) were detected for 23 diverse agronomic traits. We identified 97 candidate genes potentially implicated in 53 of the most robust and high-confidence QTLs for fruit flavor, color, size, and shape traits, and for plant productivity, vigor, and earliness traits. Investigating the genetic architecture of agronomic traits in this way will assist the development of genetic markers and pave the way for marker-assisted selection. The G2P-SOL pepper core collection will be available upon request as a unique and universal resource for further exploitation in future gene discovery and marker-assisted breeding efforts by the pepper community.

Mots-clés Agrovoc : locus des caractères quantitatifs, Capsicum annuum, collection de matériel génétique, caractère agronomique, marqueur génétique, phénotype, banque de gènes, génotype, variation génétique, ressource génétique végétale, gène

Mots-clés libres : Multi-environment trials, Association study, Core collection, Pepper, Capsicum annuum L., Agronomic traits, Candidate genes

Classification Agris : F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : CTS 2 (2019-) - Transitions agroécologiques

Auteurs et affiliations

• McLeod Louis, INRAE (FRA)
• Barchi Lorenzo, Universita di Torino (ITA) - auteur correspondant
• Tumino Giorgio, Wageningen University (NLD)
• Tripodi Pasquale, CREA (ITA)
• Salinier Jérémy, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0001-6352-8513
• Gros Christophe, INRAE (FRA)
• Boyaci Filiz, BATEM (TUR)
• Ozalp Ramazan, BATEM (TUR)
• Borovsky Yelena, ARO (ISR)
• Schafleitner Roland, World Vegetable Center (TWN)
• Barchenger Derek, World Vegetable Center (TWN)
• Finkers Richard, Wageningen University and Research Centre (NLD)
• Brouwer Matthijs, Wageningen University and Research Centre (NLD)
• Stein Nils, Georg-August University of Göttingen (DEU)
• Rabanus-Wallace Mark Timothy, Leibniz Institute of Plant Genetics and Crop Plant Research (DEU)
• Giuliano Giovanni, ENEA (ITA)
• Voorrips Roeland, Wageningen University and Research Centre (NLD)
• Paran Ilan, ARO (ISR)
• Lefebvre Véronique, INRAE (FRA) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/608579/)

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