Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding.
2020
Tamisier, Lucie | Szadkowski, Marion | Nemouchi, Ghislaine | Lefebvre, Véronique | Szadkowski, Emmanuel | Duboscq, Renaud | Santoni, Sylvain | Gautier, Sarah | Sauvage, Christopher | Palloix, Alain | Moury, Benoît | Unité de Pathologie Végétale (PV) ; Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Génétique et Amélioration des Fruits et Légumes (GAFL) ; 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 SupAgro ; 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) | Biologie et Amélioration des Plantes department and Sustainable Management of Crop Health (SMaCH) metaprogramme of INRA; Région Provence-Alpes-Côte d’Azur; NR PRC project ArchiV (2019-2022)
International audience
Mostrar más [+] Menos [-]Inglés. In this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping-by-sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome-wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.
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