Global range expansion history of pepper ( Capsicum spp.) revealed by over 10,000 genebank accessions - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles Proceedings of the National Academy of Sciences of the United States of America Year : 2021

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

Mark Timothy Rabanus-Wallace
  • Function : Author
Lorenzo Barchi
Salvatore Esposito
Maarten van Zonneveld
  • Function : Author
Andreas Börner
Jérémy Salinier
Arnaud Bovy
  • Function : Author
Filiz Boyaci
Gancho Pasev
Ronny Brandt
  • Function : Author
Axel Himmelbach
Ezio Portis
  • Function : Author
Richard Finkers
Sergio Lanteri
Ilan Paran
Véronique Lefebvre
Giovanni Giuliano
Nils Stein

Abstract

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.

Dates and versions

hal-03414637 , version 1 (04-11-2021)

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Pasquale Tripodi, Mark Timothy Rabanus-Wallace, Lorenzo Barchi, Sandip Kale, Salvatore Esposito, et al.. 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, 2021, 118 (34), pp.e2104315118. ⟨10.1073/pnas.2104315118⟩. ⟨hal-03414637⟩
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