Skip to main content
SpringerLink
Log in

Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region

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

Abstract

The Capsicum genus is native to tropical America and consists of 27 species, five of which are used as fresh vegetables and spices: Capsicum annuum L., Capsicum chinense Jacq., Capsicum frutescens L., Capsicum baccatum L. and Capsicum pubescens R. et P. The study of the relationships among species of cultivate Capsicum species will be useful for breeding new cultivars or hybrids. This study is focused on the genetic diversity and relationships of these species that were collected in the Andean region. Ten microsatellites and four AFLP combinations were used to characterize 260 Capsicum accessions. The AFLP tree turned out to be informative regarding relationships among species. The data clearly showed the close relationships between C. chinense and C. frutescens. Moreover, C. cardenasii and C. eximium were indistinguishable as a single, morphologically variable species. Our data showed C. baccatum and C. praetermissum to be distinct species that form a compact group. In the present work, AFLP fingerprinting indicated that C. chacoense was placed in the C. baccatum complex and showed C. tovarii as a separate species. In addition, SSR data indicated that there is intraspecific differentiation in the species C. chinense, C. baccatum and C. pubescens, as the PCoA-based clustering showed a clear geographic division related to country. Even though Bolivia is considered to be the nuclear area for these species, we have found similar variability in Ecuador and Peru for several Capsicum species.

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

Similar content being viewed by others

References

  • Aguilar-Melendez A, Morrell PL, Mikeal LR, Seung Chul K (2009) Genetic diversity and structure in semiwild and domesticated chiles (Capsicum annuum; Solanaceae) from Mexico. Am J Bot 96:1190–1202

    Article  PubMed  CAS  Google Scholar 

  • Belkhir K, Borsa P, Chikhi L, Rafaste N, Bonhomme T (1996) Genetix 4.04 Logiciel sours Windous TM pour la genetique des populations. Laboratoire Génome, populations, interactions, Université de Montpellier II, Montpellier. Website http://www.genetix.univ-montp2.fr/genetix/genetix.htm

  • Benham J, Jeung JU, Jasieniuk M, Kanazin V, Blake T (1999) Genographer: a graphical tool for automated AFLP and microsatellite analysis. J Agric Genomics 4:3

    Google Scholar 

  • Blanca JM, Prohens J, Anderson GJ, Zuriaga E, Canizares J, Nuez F (2007) AFLP and DNA sequence variation in an Andean domesticate, pepino (Solanum muricatum, Solanaceae): Implications for evolution and domestication. Am J Bot 94:1219–1229

    Article  PubMed  CAS  Google Scholar 

  • Bornet B, Goraguer F, Joly G, Branchard M (2002) Genetic diversity in European and Argentinian cultivated potatoes (Solanum tuberosum subsp. tuberosum) detected by inter-simple sequence repeats (ISSRs). Genome 45:481–484

    Article  PubMed  CAS  Google Scholar 

  • Bosland PW, Votava EJ (2000) Peppers: vegetable and spice capsicums. CAB International, Wallingford

    Google Scholar 

  • Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Evolution 32:550–570

    Article  Google Scholar 

  • Choong CY (1998) DNA polymorphisms in the study of relationships and evolution in Capsicum. Ph.D. Thesis, University of Reading

  • Crosby KM (2008) Pepper. In: Prohens J, Nuez F, Carena MJ (eds) Vegetables II, 1st edn. Springer, New York, pp 221–248

    Chapter  Google Scholar 

  • De Swart EAM (2007) Potential for breeding sweet pepper adapted to cooler growing conditions. A physiological and genetic analysis of growth traits in Capsicum. Ph.D. Thesis, Wageningen University

  • DeWitt D, Bosland PW (1996) Peppers of the world: an identification guide. Ten Speed Press, Berkeley

    Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  • Eshbaugh WH (1976) Genetic and biochemical systematic studies of chili peppers (Capsicum-Solanaceae). Bull Torrey Bot Club 102:396–403

    Article  Google Scholar 

  • Fery RL, Thies JA (1997) Evaluation of Capsicum chinense Jacq. cultigens for resistance to the southern root-knot nematode. Hortscience 32:923–926

    Google Scholar 

  • Furini A, Wunder J (2004) Analysis of eggplant (Solanum melongena)-related germplasm: morphological and AFLP data contribute to phylogenetic interpretations and germplasm utilization. Theor Appl Genet 108:197–208

    Article  PubMed  CAS  Google Scholar 

  • Geleta LF, Labuschagne MT, Viljoen CD (2005) Genetic variability in pepper (Capsicum annuum L.) estimated by morphological data and Amplified Fragment Length Polymorphism markers. Biodivers Conserv 14:2361–2375

    Article  Google Scholar 

  • Guzman FA, Ayala H, Azurdia C, Duque MC, de Vicente MC (2005) AFLP assessment of genetic diversity of Capsicum genetic resources in Guatemala: home gardens as an option for conservation. Crop Sci 45:363–370

    Article  CAS  Google Scholar 

  • Hanacek P, Vyhnanek T, Rohrer M, Cieslarova J, Stavelikova H (2009) DNA polymorphism in genetic resources of red pepper using microsatellite markers. Horticul Sci 36:127–132

    CAS  Google Scholar 

  • Ibiza VP, Canizares J, Nuez F (2010) EcoTILLING in Capsicum species: searching for new virus resistances. BMC Genomics 11:631

    Article  PubMed  Google Scholar 

  • Ince AG, Karaca M, Onus AN (2010) Genetic relationships within and between Capsicum species. Biochem Genet 48:83–95

    Article  PubMed  CAS  Google Scholar 

  • Langella O (2002) Populations 1.2.28, population genetic software. CNRS Website http://www.bioinformatics.org/~tryphon/populations/

  • Lefebvre V, Goffinet B, Chauvet JC, Caromel B, Signoret P, Brand R, Palloix A (2001) Evaluation of genetic distances between pepper inbred lines for cultivar protection purposes: comparison of AFLP, RAPD and phenotypic data. Theor Appl Genet 102:741–750

    Article  CAS  Google Scholar 

  • Li YC, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21:991–1007

    Article  PubMed  CAS  Google Scholar 

  • Loaiza-Figueroa F, Ritland K, Laborde-Cancino JA, Tanksley SD (1989) Patterns of genetic variation of the genus Capsicum (Solanaceae) in Mexico. Plant Syst Evol 165:159–188

    Article  Google Scholar 

  • Louette D, Charrier A, Berthaud J (1997) In situ conservation of maize in Mexico: genetic diversity and maize seed management in a traditional community. Econ Bot 51:20–38

    Article  Google Scholar 

  • McLeod MJ, Eshbaugh WH, Guttman SI (1979a) A pre-liminary biochemical systematic study of the genus Capsicum-Solanaceae. In: Hawkes JG, Lester RN, Skelding AD (eds) The biology and taxonomy of the Solanaceae. Academic Press, New York, pp 701–714

    Google Scholar 

  • McLeod MJ, Eshbaugh WH, Guttman SI (1979b) Electrophoretic study of Capsicum (Solanaceae)—purple flowered taxa. Bull Torrey Bot Club 106:326–333

    Article  Google Scholar 

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

    Article  Google Scholar 

  • McLeod MJ, Guttman SI, Eshbaugh WH, Rayle RE (1983) An electrophoretic study of evolution in Capsicum (Solanaceae). Evolution 37:562–574

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Moscone EA, Baranyi M, Ebert I, Greilhuber J, Ehrendorfer F, Hunziker AT (2003) Analysis of nuclear DNA content in Capsicum (Solanaceae) by flow cytometry and Feulgen densitometry. Ann Bot 92:21–29

    Article  PubMed  Google Scholar 

  • Moscone EA, Scaldaferro MA, Grabiele M, Cecchini NM, Garcia YS, Jarret R, Davina JR, Ducasse DA, Barboza GE, Ehrendorfer F (2007) The evolution of chili peppers (Capsicum—Solanaceae): a cytogenetic perspective. In: Proceedings of the VIth international Solanaceae conference. Solanaceae VI: Genomics Meets Biodiversity, pp 137–169

  • Nuez F, Gil R, Costa J (1996) El cultivo de pimientos, chiles y ajies. Mundi-Prensa, Madrid

    Google Scholar 

  • Nuez F, Prohens J, Blanca JM (2004) Relationships origin, and diversity of Galapagos tomatoes: implications for the conservation of natural populations. Am J Bot 91:86–99

    Article  PubMed  Google Scholar 

  • Onus AN, Pickersgill B (2004) Unilateral incompatibility in Capsicum (Solanaceae): occurrence and taxonomic distribution. Ann Bot 94:289–295

    Article  PubMed  Google Scholar 

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

    Article  Google Scholar 

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

    Google Scholar 

  • Pickersgill B (1991) Cytogenetics and evolution of Capsicum L. In: Tsuchiya T, Gupta PK (eds) Chromosome engineering in plants: genetics, breeding, evolution. Elsevier, Amsterdam, pp 139–160

    Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Polston JE, Cohen L, Sherwood TA, Ben-Joseph R, Lapidot M (2006) Capsicum species: symptomless hosts and reservoirs of Tomato yellow leaf curl virus. Phytopathology 96:447–452

    Article  PubMed  CAS  Google Scholar 

  • Portis E, Nagy I, Sasvari Z, Stagel 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 172:640–648

    Article  CAS  Google Scholar 

  • R Development Core Team (2007) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Website http://www.r-project.org/

  • Rodriguez JM, Berke T, Engle L, Nienhuis J (1999) Variation among and within Capsicum species revealed by RAPD markers. Theor Appl Genet 99:147–156

    Article  CAS  Google Scholar 

  • Ryzhova NN, Kochieva EZ (2004) Analysis of microsatellite loci of the chloroplast genome in the genus Capsicum (pepper). Russian J Genet 40:892–896

    Article  CAS  Google Scholar 

  • Sifres A, Blanca J, Nuez F (2010) Pattern of genetic variability of Solanum habrochaites in its natural area of distribution. Genet Resour Crop Evol. doi:10.1007/s10722-010-9578-0

  • Spooner DM, McLean K, Ramsay G, Waugh R, Bryan GJ (2005) A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping. Proc Natl Acad Sci USA 102:14694–14699

    Article  PubMed  CAS  Google Scholar 

  • Sudre CP, Goncalves LSA, Rodrigues R, do Amaral AT, Riva-Souza EM, Bento CD (2010) Genetic variability in domesticated Capsicum spp. as assessed by morphological and agronomic data in mixed statistical analysis. Genet Mol Res 9:283–294

    Article  PubMed  CAS  Google Scholar 

  • Tam SM, Lefebvre V, Palloix A, Sage-Palloix AM, Mhiri C, Grandbastien MA (2009) LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers. Theor Appl Genet 119:973–989

    Article  PubMed  CAS  Google Scholar 

  • Tong N, Bosland PW (1999) Capsicum tovarii, a new member of the Capsicum baccatum complex. Euphytica 109:71–77

    Article  Google Scholar 

  • Toquica SP, Rodriguez F, Martinez E, Duque MC, Tohme J (2003) Molecular characterization by AFLPs of Capsicum germplasm from the Amazon Department in Colombia, characterization by AFLPs of Capsicum. Genet Resour Crop Evol 50:639–647

    Article  Google Scholar 

  • Walsh BM, Hoot SB (2001) Phylogenetic relationships of Capsicum (Solanaceae) using DNA sequences from two noncoding regions: the chloroplast atpB-rbcL spacer region and nuclear waxy introns. Int J Plant Sci 162:1409–1418

    Article  CAS  Google Scholar 

  • Yoon JB, Yang DC, Do JW, Park HG (2006) Overcoming two post-fertilization genetic barriers in interspecific hybridization between Capsicum annuum and Capsicum baccatum for introgression of anthracnose resistance. Breeding Sci 56:31–38

    Article  CAS  Google Scholar 

  • Zewdie Y, Bosland PW (2000) Capsaicinoid inheritance in an interspecific hybridization of Capsicum annuum × C. chinense. J Am Soc Hortic Sci 125:448–453

    CAS  Google Scholar 

  • Zijlstra S, Purimahu AC, Lindhout P (1991) Pollen tube growth in interspecific crosses between Capsicum species. HortScience 26:585–586

    Google Scholar 

  • Zuriaga E, Blanca J, Nuez F (2009a) Classification and phylogenetic relationships in Solanum section Lycopersicon based on AFLP and two nuclear gene sequences. Genet Resour Crop Evol 56:663–678

    Article  CAS  Google Scholar 

  • Zuriaga E, Blanca JM, Cordero L, Sifres A, Blas-Cerdan WG, Morales R, Nuez F (2009b) Genetic and bioclimatic variation in Solanum pimpinellifolium. Genet Resour Crop Evol 56:39–51

    Article  Google Scholar 

Download references

Acknowledgments

VPI is the recipient of an FPU fellowship of the Ministerio de Educación y Ciencia. We want to recognize the invaluable task carried out by the Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV, Spain), the Universidad Nacional de Loja (UNL, Ecuador), the Universidad Nacional de Piura (UNP, Peru), the Universidad Nacional Agraria La Molina (UNAM, Peru), the Universidad Nacional de Trujillo (UNT, Peru), the Universidad Nacional Pedro Ruiz Gallo (UNPRG, Peru), the Universidad Mayor de San Simón (UMSS, Bolivia), the United States Department of Agriculture (USDA, USA), the Center for Genetic Resources (CGN, The Netherlands) and the Radboud University of Nijmegen (RUN, The Netherlands), which provided important accessions. The help of Joshua Bergen in improving the English of this manuscript is gratefully acknowledged.

Author information

Authors and Affiliations

  1. Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia, 8E CPI, Camino de Vera s/n, 46022, Valencia, Spain

    Vicente P. Ibiza, José Blanca, Joaquín Cañizares & Fernando Nuez

Authors
  1. Vicente P. Ibiza
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. José Blanca
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Joaquín Cañizares
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Fernando Nuez
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Fernando Nuez.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ibiza, V.P., Blanca, J., Cañizares, J. et al. Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region. Genet Resour Crop Evol 59, 1077–1088 (2012). https://doi.org/10.1007/s10722-011-9744-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-011-9744-z

Keywords

Search

Navigation