Genome-wide genotyping of a novel Mexican Chile Pepper collection illuminates the history of landrace differentiation after Capsicum annuum L. domestication

Nathan Taitano, Vivian Bernau, Lev Jardón-Barbolla, Brian Leckie, Michael Mazourek, Kristin Mercer, Leah McHale, Andrew Michel, David Baumler, Michael Kantar, Esther van der Knaap

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


Studies of genetic diversity among phenotypically distinct crop landraces improve our understanding of fruit evolution and genome structure under domestication. Chile peppers (Capsicum spp. L.) are economically valuable and culturally important species, and extensive phenotypic variation among landraces exists in southern Mexico, a center of C. annuum diversity. We collected 103 chile pepper seed accessions from 22 named landraces across 27 locations in southern Mexico. We genotyped these accessions with genotyping by sequencing (GBS), yielding 32,623 filtered single-nucleotide polymorphisms. Afterward, we genotyped 32 additional C. annuum accessions from a global collection for comparison to the Mexican collection. Within the Mexican collection, genetic assignment analyses showed clear genetic differentiation between landraces and clarified the unique nature of the Tusta landrace. Further clustering analyses indicated that the largest fresh-use Chile de Agua and dry-use Costeño landraces were part of separate clades, indicating that these two landraces likely represent distinct populations. The global accessions showed considerable admixture and limited clustering, which may be due to the collapse of use-type divisions outside of Central America. The separation of the Mexican landraces in part by fruit morphology related to use highlights the relevance of this use-type morphological diversity for plant breeders and the utility of fruit development variation for evolutionary biologists.

Original languageEnglish (US)
Pages (from-to)78-92
Number of pages15
JournalEvolutionary Applications
Issue number1
StatePublished - Jan 2019

Bibliographical note

Funding Information:
We would like to acknowledge the Ohio State University Center for Applied Plant Sciences for funding the collection trips, and the OARDC SEEDS grant for funding the GBS library construction and sequencing. We would also like to acknowledge our collaborators Ernesto Gonz?lez Gaona, Esa? Ru?z S?nchez, Luis Latournerie Moreno, Salvador Montes Hernandez, Porfirio L?pez L?pez, Luis Eguiarte Fruns, Jose Carillo, Araceli Aguilar Melendez, and Catarino Perales Segouia for their help in all stages of the project. We also thank Brian Pace and Rachel Capouya, who helped organize and manage the collections. We would also like to thank the many chile growers who graciously allowed us into their homes and shared with us the fruits of their labor. This study is founded upon countless generations of their work.

Publisher Copyright:
© 2018 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd


  • GBS
  • domestication
  • fruit morphology
  • genetic diversity
  • landrace
  • pepper


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