Genetic Resources and Crop Evolution

, Volume 59, Issue 4, pp 517–538 | Cite as

Genetic diversity and population structure of Capsicum baccatum genetic resources

  • Elena Albrecht
  • Dapeng Zhang
  • Robert A. Saftner
  • John R. Stommel
Research Article


Capsicum baccatum is one of five domesticated pepper species which, despite its morphological and ecological variability, has been underexploited for germplasm improvement. Utilizing a broad spectrum of domesticated and wild C. baccatum germplasm, we utilize AFLP markers to describe the species’ molecular diversity and population structure in the South American gene pool. Analysis of molecular variance (AMOVA) revealed greater genetic diversity in the wild form of C. baccatum (C. baccatum var. baccatum) than in the domesticated form of the species (C. baccatum var. pendulum). Both Bayesian and distance based clustering analysis, as well as principal coordinates analysis (PCA), concordantly demonstrated admixture/shared ancestry between wild and cultivated C. baccatum botanical varieties. Two principal genetic groups were identified in the domesticated C. baccatum accessions largely based on their geographic distribution in South America. One group was predominated by accessions from the western territories of the species’ distribution (Peru, Colombia, Ecuador, Bolivia, Chile and northwestern Argentina) and the second by accessions from the eastern regions, Paraguay and eastern Argentina). The two genetic groups overlapped in the geographic location of present-day Bolivia. The grouping pattern suggested that C. baccatum was domesticated in multiple sites and that its evolution took two lineages followed by lineage differentiation. The wild accessions most closely related to the cultigens were found in the highlands of Peru and Bolivia, which support the early hypothesis that this region is one of the domestication sites of this species. A Bayesian assignment analysis demonstrated that Brazilian wild forms of C. baccatum were genetically distant to all other accessions and made little to no contribution to the domesticated genepool. Moreover, results of clustering analysis suggested that C. baccatum likely originated from present day Paraguay. Analysis of inter-specific relationships across selected Capsicum species supported independent lineages for the two crossability groups within Capsicum, the baccatum species-complex (including C. baccatum) and the annuum species-complex (including C. annuum, C. chinense and C. frutescens). However, the results did not support taxonomic distinction of C. baccatum var. umbilicatum from C. baccatum var. pendulum. The present study provides new insights into the domestication of C. baccatum. The results will be useful for identifying accessions for crop improvement and guiding the development of in situ and ex situ conservation programs.


AFLP Cluster analysis Domestication Germplasm Pepper Taxonomy 



We thank Joshua Simpson, City University of New York, for assistance with ArcGI. This work was supported by a Cooperative Research and Development Agreement (58-3K95-8-1253) with Keygene Inc. Mention of trade names or commercial products is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the United States Department of Agriculture.


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Copyright information

© Springer Science+Business Media B.V. (outside the USA) 2011

Authors and Affiliations

  • Elena Albrecht
    • 1
  • Dapeng Zhang
    • 2
  • Robert A. Saftner
    • 3
  • John R. Stommel
    • 4
  1. 1.Keygene Inc.RockvilleUSA
  2. 2.Sustainable Perennial Crops Laboratory, Agriculture Research Service, Beltsville Agricultural Research Center, Plant Sciences InstituteUnited States Department of AgricultureBeltsvilleUSA
  3. 3.Food Quality Laboratory, Agriculture Research Service, Beltsville Agricultural Research Center, Plant Sciences InstituteUnited States Department of AgricultureBeltsvilleUSA
  4. 4.Genetic Improvement of Fruits and Vegetables Laboratory, Agriculture Research Service, Beltsville Agricultural Research Center, Plant Sciences InstituteUnited States Department of AgricultureBeltsvilleUSA

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