Genetic Resources and Crop Evolution

, Volume 61, Issue 4, pp 741–755 | Cite as

Microsatellite based analysis of the genetic structure and diversity of Capsicum chinense in the Neotropics

  • Marissa MosesEmail author
  • Pathmanathan Umaharan
  • Selvadurai Dayanandan
Research Article


Capsicum chinense Jacq., one of the five domesticated species of pepper grown in the New World, is a major contributor to both local and international markets and the economy of the Caribbean islands. The planning and implementation of germplasm conservation and breeding programs for the sustainable use of C. chinense genetic resources are hampered by the poor understanding of the genetic structure and diversity of C. chinense in the region. In the present study, the genetic structure, diversity and relatedness of C. chinense germplasm collections within the Caribbean basin and South America were assessed using nuclear microsatellite markers. C. chinense accessions (102) representing seven geographical regions were genotyped using nine polymorphic nuclear microsatellite markers along with 16 accessions representing four other species of Capsicum. The results revealed that the highest genetic diversity (He = 0.58) was found in the Amazon region supporting the postulated center of diversity of C. chinense as the Amazon basin. The cluster analysis resulted in two distinct genetic clusters corresponding to Upper Amazon and Lower Amazon regions, suggesting two independent domestication events or two putative centers of diversity in these regions respectively. The cluster analysis further revealed that populations in Central America and the Caribbean may have been primarily derived from progenitors from Upper Amazon region and later diverged through geographical isolation. Conservation and germplasm collection programs should therefore target these genetically distinct clusters and satellite populations, towards supporting breeding programs to harness heterosis.


Capsicum sinense Caribbean Dispersion Domestication Genetic diversity Hot pepper Microsatellite Neotropics 



Special thanks are extended to Baharul Choudhury and Shivaprakash Nagaraju for their assistance in this work.


  1. Aguilar-Melendez A, Morrell PL, Roose ML, Kim SC (2009) Genetic diversity and structure in semiwild and domesticated chiles (Capsicum annuum; Solanaceae) from Mexico. Am J Bot 96(6):1190–1202PubMedCrossRefGoogle Scholar
  2. Albrecht E, Zhang D, Saftner RA, Stommel JR (2012) Genetic diversity and population structure of Capsicum baccatum genetic resources. Genet Resour Crop Evol 59(4):517–538CrossRefGoogle Scholar
  3. Baral JB, Bosland PW (2004) Unraveling the species dilemma in Capsicum frutescens and C. chinense (Solanaceae): a multiple evidence approach using morphology, molecular analysis, and sexual compatibility. J Am Soc Hortic Sci 129(6):826–832Google Scholar
  4. Barboza GE, De Bem Bianchetti L (2005) Three new species of Capsicum (Solanaceae) and a key to the wild species from Brazil. Syst Bot 30(4):863–871CrossRefGoogle Scholar
  5. Bosland PW, Coon D, Reeves G (2012) ‘Trinidad Moruga Scorpion’pepper is the world’s hottest measured Chile pepper at more than two million Scoville heat units. HortTechnology 22(4):534–538Google Scholar
  6. Callaghan RT (2011) Patterns of contact between the islands of the Caribbean and the surrounding mainland as a navigation problem. In: Curet A, Hauser M (eds) Islands at the crossroads: migration, seafaring, and interaction in the Caribbean. University Alabama Press, Alabama, pp 59–72Google Scholar
  7. Clement CR (1999) 1492 and the loss of Amazonian crop genetic resources. I. The relation between domestication and human population decline. Econ Bot 53(2):188–202CrossRefGoogle Scholar
  8. Clement CR, de Cristo-Araújo M, d’Eeckenbrugge GC, Pereira AA, Picanço-Rodrigues D (2010) Origin and domestication of native Amazonian crops. Diversity 2(1):72–106CrossRefGoogle Scholar
  9. Cooper B, Gordon M, Ameen I (1993) Hotpepper production guide for Antigua. CARDI, AntiguaGoogle Scholar
  10. Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359–361CrossRefGoogle Scholar
  11. Eshbaugh WH (1993) Peppers: history and exploitation of a serendipitous new crop discovery. In: Janick J, Simon JE (eds) New crops. Wiley, NY, pp 132–139Google Scholar
  12. Frankham R, Briscoe DA, Ballou JD (2002) Introduction to conservation genetics. Cambridge Univ Press, NYCrossRefGoogle Scholar
  13. Geleta LF, Labuschagne MT (2004) Hybrid performance for yield and other characteristics in peppers (Capsicum annuum L.). J Am Sci 142(4):411–419Google Scholar
  14. Gémes Juhász A, Stágel A, Ács S, Zatykó L (2006) Microsatellite markers and automated fragment analysis techniques for efficient and precise hybrid identification and genetic purity testing in pepper (Capsicum annuum L.). Acta Agron Hung 54(2):141–146CrossRefGoogle Scholar
  15. Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. J Hered 86(6):485–486Google Scholar
  16. Hanáček R, Vyhnánek T, Rohrer M, Cieslarová J, Stavělíková H (2009) DNA polymorphism in genetic resources of red pepper using microsatellite markers. Hortic Sci 36(4):127–132Google Scholar
  17. Ibiza VP, Blanca J, Cañizares J, Nuez F (2012) Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region. Genet Resour Crop Evol 59(6):1077–1088CrossRefGoogle Scholar
  18. Ince AG, Karaca M, Onus AN (2010) Polymorphic microsatellite markers transferable across Capsicum species. Plant Mol Biol Rep 28(2):285–291CrossRefGoogle Scholar
  19. Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14):1801–1806PubMedCrossRefGoogle Scholar
  20. Kresovich S, McFerson JR (1992) Assessment and management of plant genetic diversity: considerations of intra-and interspecific variation. Field Crops Res 29(3):185–204CrossRefGoogle Scholar
  21. Lee JM, Nahm SH, Kim YM, Kim BD (2004) Characterization and molecular genetic mapping of microsatellite loci in pepper. Theor Appl Genet 108(4):619–627PubMedCrossRefGoogle Scholar
  22. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128–2129PubMedCrossRefGoogle Scholar
  23. McLeod MJ, Guttman SI, Eshbaugh WH (1982) Early evolution of chili peppers (Capsicum). Econ Bot 36(4):361–368CrossRefGoogle Scholar
  24. Minamiyama Y, Tsuro M, Hirai M (2006) An SSR-based linkage map of Capsicum annuum. Mol Breed 18(2):157–169CrossRefGoogle Scholar
  25. Moses M, Umaharan P (2012) Genetic structure and phylogenetic relationships of Capsicum chinense. J Am Soc Hortic Sci 137(4):250–262Google Scholar
  26. Motamayor JC, Lachenaud P, e Mota JWS, Loor R, Kuhn DN, Brown JS, Schnell RJ (2008) Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L.). PLoS One 3(10):e3311PubMedCentralPubMedCrossRefGoogle Scholar
  27. Nagy I, Polley A, Ganal M (1998) Development and characterization of microsatellite markers in pepper. In: Palloix A, Daunay MC (eds) Proceedings of the Xth EUCARPIA Meet. Genet. and breeding on Capsicum and eggplant, 7–11, September. European Association for Research on Plant Breeding (EUCARPIA), Avignon, France, pp 235–237Google Scholar
  28. Nagy I, Stágel A, Sasvári Z, Röder M, Ganal M (2007) Development, characterization, and transferability to other Solanaceae of microsatellite markers in pepper (Capsicum annuum L.). Genome 50(7):668–688PubMedCrossRefGoogle Scholar
  29. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci 70(12):3321–3323PubMedCentralPubMedCrossRefGoogle Scholar
  30. Oyama K, Pacheco-Olvera A, González-Rodríguez A, Hernández-Verdugo S, Rocha-Ramírez V (2012) Genetic diversity and structure of pepper (Capsicum annuum L.) from Northwestern Mexico analyzed by microsatellite markers. Crop Sci 52(1):231–241CrossRefGoogle Scholar
  31. Patel AS, Sasidharan N, Vala AG (2011) Genetic relation in Capsicum annuum L. cultivars through microsatellite markers: SSR and ISSR. Electron J Plant Breed 2(1):67–76Google Scholar
  32. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6(1):288–295CrossRefGoogle Scholar
  33. Pickersgill B (1971) Relationships between weedy and cultivated forms in some species of chili peppers (genus Capsicum). Evolution 25(4):683–691CrossRefGoogle Scholar
  34. Pickersgill B (1988) The genus Capsicum: a multidisciplinary approach to the taxonomy of cultivated and wild plants. Biol Zentralbl 107(4):381–389Google Scholar
  35. Pickersgill B (1997) Genetic resources and breeding of Capsicum spp. Euphytica 96(1):129–133CrossRefGoogle Scholar
  36. Pickersgill B (2007) Domestication of plants in the Americas: insights from Mendelian and molecular genetics. Ann Bot 100(5):925–940PubMedCentralPubMedCrossRefGoogle Scholar
  37. Portis E, Nagy I, Sasvári Z, Stágel A, Barchi L, Lanteri S (2007) The design of Capsicum spp. SSR assays via analysis of in silico DNA sequence, and their potential utility for genetic mapping. Plant Sci 172(3):640–648CrossRefGoogle Scholar
  38. Pozzobon MT, Schifino-Wittmann MT, De Bem Bianchetti L (2006) Chromosome numbers in wild and semidomesticated Brazilian Capsicum L. (Solanaceae) species: do x = 12 and x = 13 represent two evolutionary lines? Bot J Linn Soc 151(2):259–269CrossRefGoogle Scholar
  39. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959PubMedCentralPubMedGoogle Scholar
  40. Reid B (2007) Popular myths about Caribbean history. Archaeology Centre. The Department of History, Faculty of Humanities, University of the West Indies, TrinidadGoogle Scholar
  41. Rouse I (1992) The Tainos. Rise and decline of the people who greeted Columbus. Yale University Press, New HavenGoogle Scholar
  42. Sanwen H, Baoxi Z, Milbourne D, Cardle L, Guimei Y, Jiazhen G (2001) Development of pepper SSR markers from sequence databases. Euphytica 117(2):163–167CrossRefGoogle Scholar
  43. Soulé M (1986) Conservation biology: the science of scarcity and diversity. Sinauer, MassachusettsGoogle Scholar
  44. Tam SM, Mhiri C, Vogelaar A, Kerkveld M, Pearce SR, Grandbastien MA (2005) Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor Appl Genet 110(5):819–831PubMedCrossRefGoogle Scholar
  45. Tewksbury JJ, Nabhan GP (2001) Seed dispersal. Directed deterrence by capsaicin in chilies. Nature 412(6845):403–404PubMedCrossRefGoogle Scholar
  46. Thomas E, van Zonneveld M, Loo J, Hodgkin T, Galluzzi G, van Etten J (2012) Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in Pleistocene Refugia followed by human-influenced dispersal. PLoS One 7(10):e47676PubMedCentralPubMedCrossRefGoogle Scholar
  47. Toquica S, Rodríguez F, Martínez E, Cristina Duque M, Tohme J (2003) Molecular characterization by AFLPs of Capsicum germplasm from the Amazon department in Colombia. Genet Resour Crop Evol 50(6):639–647CrossRefGoogle Scholar
  48. Umaharan P, Adams H, Moses M (2004) 4.5 Caribbean hotpepper germplasm management. In: Caribbean Agricultural Research and Development Institute (ed) Proceedings of the Caribbean Hotpepper workshop - Charting the way forward, 26–28 November, 2003. Port of Spain, Trinidad and TobagoGoogle Scholar
  49. Yi G, Lee JM, Lee S, Choi D, Kim BD (2006) Exploitation of pepper EST–SSRs and an SSR-based linkage map. Theor Appl Genet 114(1):113–130PubMedCrossRefGoogle Scholar
  50. Yumnam JS, Tyagi W, Pandey A, Meetei NT, Rai M (2012) Evaluation of genetic diversity of Chilli landraces from North Eastern India Based on morphology, SSR markers and the Pun1 locus. Plant Mol Biol Rep 30(6):1470–1479CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Marissa Moses
    • 1
    Email author
  • Pathmanathan Umaharan
    • 2
  • Selvadurai Dayanandan
    • 3
    • 4
  1. 1.Faculty of Science and TechnologyThe University of the West IndiesSt. AugustineTrinidad and Tobago, West Indies
  2. 2.Cocoa Research CentreThe University of the West IndiesSt. AugustineTrinidad and Tobago, West Indies
  3. 3.Department of Biology, Centre for Structural and Functional GenomicsConcordia UniversityMontrealCanada
  4. 4.Québec Centre for Biodiversity ScienceMontrealCanada

Personalised recommendations