Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions

Tripodi Pasquale, Rabanus-Wallace Mark Timothy, Barchi Lorenzo, Kale Sandip, Esposito Salvatore, Acquadro Alberto, Schafleitner Roland, Van Zonneveld Maarten, Prohens Jaime, Diez Maria José, Börner Andreas, Salinier Jérémy, Caromel Bernard, Bovy Arnaud, Boyaci Filiz, Pasev Gancho, Brandt Ronny, Himmelbach Axel, Portis Ezio, Finkers Richard, Lanteri Sergio, Paran Ilan, Lefebvre Véronique, Giuliano Giovanni, Stein Nils. 2021. Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions. Proceedings of the National Academy of Sciences of the United States of America, 118 (34):e2104315118, 9 p.

Url - jeu de données - Entrepôt autre : https://www.ebi.ac.uk/ena/browser/view/PRJEB45375?show=reads / Url - autres données associées : https://github.com/mtrw/ReMIXTURE

Quartile : Outlier, Sujet : MULTIDISCIPLINARY SCIENCES

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Economie-gestion; Psychologie-éthologie-ergonomie

Résumé : Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker–trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper (Capsicum spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed Capsicum annuum to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method ReMIXTURE—using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions—was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.

Mots-clés Agrovoc : Capsicum annuum, banque de gènes, amélioration des plantes, phylogénie, marqueur génétique, variation génétique, locus des caractères quantitatifs, hybridation interspécifique, séquence nucléotidique, phytogénétique, génétique des populations

Mots-clés géographiques Agrovoc : Afrique

Mots-clés libres : Genebank, Pepper, Population genomics, Routes of diversification, GWAS

Agences de financement européennes : European Commission

Programme de financement européen : H2020

Projets sur financement : (EU) Linking genetic resources, genomes, and phenotypes of Solanaceous crops

Auteurs et affiliations

• Tripodi Pasquale, CREA (ITA) - auteur correspondant
• Rabanus-Wallace Mark Timothy, Leibniz Institute of Plant Genetics and Crop Plant Research (DEU)
• Barchi Lorenzo, Universita di Torino (ITA)
• Kale Sandip, Leibniz Institute of Plant Genetics and Crop Plant Research (DEU)
• Esposito Salvatore, CREA (ITA)
• Acquadro Alberto, Universita di Torino (ITA)
• Schafleitner Roland, World Vegetable Center (TWN)
• Van Zonneveld Maarten, World Vegetable Center (TWN)
• Prohens Jaime, UPV (ESP)
• Diez Maria José, UPV (ESP)
• Börner Andreas, Leibniz Institute of Plant Genetics and Crop Plant Research (DEU)
• Salinier Jérémy, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0001-6352-8513
• Caromel Bernard, INRAE (FRA)
• Bovy Arnaud, Wageningen University and Research Centre (NLD)
• Boyaci Filiz, BATEM (TUR)
• Pasev Gancho, Maritsa Vegetable Crops Research Institute (BGR)
• Brandt Ronny, Leibniz Institute of Plant Genetics and Crop Plant Research (DEU)
• Himmelbach Axel, Leibniz Institute of Plant Genetics and Crop Plant Research (DEU)
• Portis Ezio, Universita di Torino (ITA)
• Finkers Richard, Wageningen University and Research Centre (NLD)
• Lanteri Sergio, Universita di Torino (ITA)
• Paran Ilan, ARO (ISR)
• Lefebvre Véronique, INRAE (FRA)
• Giuliano Giovanni, Italian National Agency for New Technologies, Energy, and Sustainable Economic Development (ITA)
• Stein Nils, Georg-August University of Göttingen (DEU) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/608122/)

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