Skip to main content

Advertisement

SpringerLink
Log in

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

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • 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):1190–1202

    Article  CAS  PubMed  Google Scholar 

  • 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):517–538

    Article  Google Scholar 

  • 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):826–832

    Google Scholar 

  • 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):863–871

    Article  Google Scholar 

  • 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):534–538

    Google Scholar 

  • 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 59–72

    Google Scholar 

  • 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):188–202

    Article  Google Scholar 

  • 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):72–106

    Article  Google Scholar 

  • Cooper B, Gordon M, Ameen I (1993) Hotpepper production guide for Antigua. CARDI, Antigua

    Google Scholar 

  • 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):359–361

    Article  Google Scholar 

  • Eshbaugh WH (1993) Peppers: history and exploitation of a serendipitous new crop discovery. In: Janick J, Simon JE (eds) New crops. Wiley, NY, pp 132–139

    Google Scholar 

  • Frankham R, Briscoe DA, Ballou JD (2002) Introduction to conservation genetics. Cambridge Univ Press, NY

    Book  Google Scholar 

  • Geleta LF, Labuschagne MT (2004) Hybrid performance for yield and other characteristics in peppers (Capsicum annuum L.). J Am Sci 142(4):411–419

    Google Scholar 

  • 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):141–146

    Article  Google Scholar 

  • Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. J Hered 86(6):485–486

    Google Scholar 

  • 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):127–132

    Google Scholar 

  • 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):1077–1088

    Article  Google Scholar 

  • Ince AG, Karaca M, Onus AN (2010) Polymorphic microsatellite markers transferable across Capsicum species. Plant Mol Biol Rep 28(2):285–291

    Article  CAS  Google Scholar 

  • 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):1801–1806

    Article  CAS  PubMed  Google Scholar 

  • Kresovich S, McFerson JR (1992) Assessment and management of plant genetic diversity: considerations of intra-and interspecific variation. Field Crops Res 29(3):185–204

    Article  Google Scholar 

  • Lee JM, Nahm SH, Kim YM, Kim BD (2004) Characterization and molecular genetic mapping of microsatellite loci in pepper. Theor Appl Genet 108(4):619–627

    Article  CAS  PubMed  Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128–2129

    Article  CAS  PubMed  Google Scholar 

  • McLeod MJ, Guttman SI, Eshbaugh WH (1982) Early evolution of chili peppers (Capsicum). Econ Bot 36(4):361–368

    Article  Google Scholar 

  • Minamiyama Y, Tsuro M, Hirai M (2006) An SSR-based linkage map of Capsicum annuum. Mol Breed 18(2):157–169

    Article  CAS  Google Scholar 

  • Moses M, Umaharan P (2012) Genetic structure and phylogenetic relationships of Capsicum chinense. J Am Soc Hortic Sci 137(4):250–262

    Google Scholar 

  • 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):e3311

    Article  PubMed Central  PubMed  Google Scholar 

  • 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 235–237

  • 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):668–688

    Article  CAS  PubMed  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci 70(12):3321–3323

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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):231–241

    Article  Google Scholar 

  • 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):67–76

    Google Scholar 

  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6(1):288–295

    Article  Google Scholar 

  • Pickersgill B (1971) Relationships between weedy and cultivated forms in some species of chili peppers (genus Capsicum). Evolution 25(4):683–691

    Article  Google Scholar 

  • Pickersgill B (1988) The genus Capsicum: a multidisciplinary approach to the taxonomy of cultivated and wild plants. Biol Zentralbl 107(4):381–389

    Google Scholar 

  • Pickersgill B (1997) Genetic resources and breeding of Capsicum spp. Euphytica 96(1):129–133

    Article  Google Scholar 

  • Pickersgill B (2007) Domestication of plants in the Americas: insights from Mendelian and molecular genetics. Ann Bot 100(5):925–940

    Article  PubMed Central  PubMed  Google Scholar 

  • 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):640–648

    Article  CAS  Google Scholar 

  • 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):259–269

    Article  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959

    CAS  PubMed Central  PubMed  Google Scholar 

  • Reid B (2007) Popular myths about Caribbean history. Archaeology Centre. The Department of History, Faculty of Humanities, University of the West Indies, Trinidad

  • Rouse I (1992) The Tainos. Rise and decline of the people who greeted Columbus. Yale University Press, New Haven

    Google Scholar 

  • Sanwen H, Baoxi Z, Milbourne D, Cardle L, Guimei Y, Jiazhen G (2001) Development of pepper SSR markers from sequence databases. Euphytica 117(2):163–167

    Article  Google Scholar 

  • Soulé M (1986) Conservation biology: the science of scarcity and diversity. Sinauer, Massachusetts

    Google Scholar 

  • 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):819–831

    Article  CAS  PubMed  Google Scholar 

  • Tewksbury JJ, Nabhan GP (2001) Seed dispersal. Directed deterrence by capsaicin in chilies. Nature 412(6845):403–404

    Article  CAS  PubMed  Google Scholar 

  • 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):e47676

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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):639–647

    Article  Google Scholar 

  • 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 Tobago

  • 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):113–130

    Article  CAS  PubMed  Google Scholar 

  • 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):1470–1479

    Article  CAS  Google Scholar 

Download references

Acknowledgments

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

Author information

Authors and Affiliations

  1. Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago, West Indies

    Marissa Moses

  2. Cocoa Research Centre, The University of the West Indies, St. Augustine, Trinidad and Tobago, West Indies

    Pathmanathan Umaharan

  3. Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St W, Montreal, QC, H4B 1R6, Canada

    Selvadurai Dayanandan

  4. Québec Centre for Biodiversity Science, W6-19, 1205 Dr. Penfield Avenue, Montreal, QC, Canada

    Selvadurai Dayanandan

Authors
  1. Marissa Moses
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pathmanathan Umaharan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Selvadurai Dayanandan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Marissa Moses.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Moses, M., Umaharan, P. & Dayanandan, S. Microsatellite based analysis of the genetic structure and diversity of Capsicum chinense in the Neotropics. Genet Resour Crop Evol 61, 741–755 (2014). https://doi.org/10.1007/s10722-013-0069-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-013-0069-y

Keywords

Search

Navigation