Skip to main content
SpringerLink
Log in

Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers

  • Research Article
  • Published:
Physiology and Molecular Biology of Plants Aims and scope Submit manuscript

Abstract

A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24 %) detected a total of 76 alleles (average, 3.04; range, 2–5). The average polymorphic information content (PIC) was 0.69 (range, 0.29–0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44–0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin.

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

  • Adetula OA (2006) Genetic diversity of Capsicum using random amplified polymorphic DNAs. Afr J Biotech 5:120–122

    CAS  Google Scholar 

  • Aktas H, Abak K, Sensoy S (2009) Genetic diversity in some Turkish pepper (Capsicum annuum L.) genotypes revealed by AFLP analyses. Afr J Biotech 8:4378–4386

    CAS  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 59:517–538

    Article  Google Scholar 

  • Bosland PW, Baral JB (2007) ‘Bhut Jolokia’—the world’s hottest known chile pepper is a putative naturally occurring inter specific hybrid. HortSci 42:222–224

    CAS  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    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 4:359–361

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  PubMed  CAS  Google Scholar 

  • FAOSTAT (2011) http://faostat.fao.org/default.aspx

  • Gepts P (2004) Crop domestication as a long-term selection experiment. Plant Breed Rev 24:1–44

    Google Scholar 

  • Ince AG, Karaca M, Onus AN (2009) Development and utilization of diagnostic DAMD-PCR markers for Capsicum accessions. Genet Resour Crop Evol 56:211–221

    Article  CAS  Google Scholar 

  • Jaccard P (1908) Nouvellesrecherchessur la distribution florale. Bull Soc Vaud Sci Natur 44:223–270

    Google Scholar 

  • Jha TB, Dafadar A, Ghorai A (2012) New genetic resource in Capsicum L. from Eastern Himalayas. Plant Genet Resour 10:141–144

    Article  Google Scholar 

  • Keatinge JDH, Ledesma DR, Keatinge FJD, Hughes JDA (2012) Projecting annual air temperature changes to 2025 and beyond: implications for vegetable production worldwide. The J Agricultural Science. doi:10.1017/S0021859612000913

  • Kumar S, Kumar R, Singh J (2006a) Cayenne/American pepper (Capsicum species). In: Peter KV (ed) Handbook of herbs and spices. Woodhead, Cambridge, pp 299–312

    Chapter  Google Scholar 

  • Kumar S, Kumar S, Singh M, Singh AK, Rai M (2006b) Identification of host plant resistance to pepper leaf curl virus in chilli (Capsicum species). Sci Hortic 110:359–361

    Article  CAS  Google Scholar 

  • Kumar S, Singh V, Singh M, Rai S, Kumar S, Rai SK, Rai M (2007) Genetics and validation of fertility restoration associated RAPD markers in pepper (Capsicum annuum L.). Sci Hortic 111:197–202

    Article  CAS  Google Scholar 

  • Kumar R, Kumar S, Dwivedi N, Kumar S, Rai A, Singh M, Yadav DS, Rai M (2009) Validation of SCAR markers, diversity analysis of male sterile cytoplasms (S-) and isolation of an alloplasmic S-cytoplasm in Capsicum. Sci Hortic 120:167–172

    Article  CAS  Google Scholar 

  • Kumar S, Kumar R, Kumar S, Singh AK, Singh M, Rai AB, Rai M (2011) Incidence of leaf curl disease on Capsicum germplasm under field conditions. Indian J Agric Sci 80:187–189

    Google Scholar 

  • Lefebvre V, Palloix A, Max R (1993) Nuclear RFLP between pepper cultivars (Capsicum annuum L.). Euphytica 71:189–199

    Article  Google Scholar 

  • Mantel NA (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    PubMed  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 

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

    Article  PubMed  CAS  Google Scholar 

  • Ortiz RF, De la Flor D, Alvarado G, Crossa J (2010) Classifying vegetable genetic resources-A case study with domesticated Capsicum spp. Sci Hortic 126:186–191

    Article  Google Scholar 

  • Oyama K, Verdugo SH, Sanchez C, Rodrıguez AG, Pena PS, Tiznado JAG, Casas A (2006) Genetic structure of wild and domesticated populations of Capsicum annuum (Solanaceae) from northwestern Mexico analyzed by RAPDs. Genet Resour Crop Evol 53:553–562

    Article  Google Scholar 

  • Pacheco-Olvera A, Hernández-Verdugo S, Rocha-Ramírez V, González-Rodríguez A, Oyama K (2012) Genetic diversity and structure of pepper (Capsicum annuum L.) from Northwestern Mexico analyzed by microsatellite markers. Crop Sci 52:231–241

    Article  Google Scholar 

  • Pandey J (2006) Characterization of Capsicum germplasm, inbreds and CMS based crosses with special reference to oleoresin and capsaicin contents. Ph.D. Thesis, Udai Pratap Autonomous College, Varanasi, India

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

    Article  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Pritchard JK, Wen W (2003) Documentation for STRUCTURE software: Version 2. Available from http://pritch.bsd.uchicago.edu

  • Purkayastha J, Alam SI, Gogoi HK, Singh L, Veer V (2012) Molecular characterization of ‘Bhut Jolokia’ the hottest chilli. J Bioscience 37:757–768

    Article  CAS  Google Scholar 

  • Rai VP (2010) Genetic and molecular analyses of pepper leaf curl resistance in chilli (Capsicum annuum L.). Ph.D. Thesis, Banaras Hindu University, Varanasi, India

  • Rohlf FJ (1998) On applications of geometric morphometrics to studies of ontogeny and phylogeny. System Bio 47:147–158

    Article  CAS  Google Scholar 

  • Sanatombi K, Sen-Mandi S, Sharma GJ (2010) DNA profiling of Capsicum landraces of Manipur. Sci Hortic 124:405–408

    Article  CAS  Google Scholar 

  • Sneath PHA, Sokal RR (1973) Numerical taxonomy. Freeman, San Francisco, CA, USA

    Google Scholar 

  • Stágel A, Gyurjan I, Sasvari Z, Lanteri S, Ganal M, Nagy I (2009) Patterns of molecular evolution of microsatellite loci in pepper (Capsicum spp.) revealed by allele sequencing. Plant System Evol 281:251–254

    Article  Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers: their characteristics, development and application to plant breeding and genetics. Trends Biotech 23:48–55

    Article  CAS  Google Scholar 

Download references

Acknowledgments

Financial support provided by Indian Council of Agricultural Research (ICAR), New Delhi, India is gratefully acknowledged. The authors also wish to thank AVRDC–The World Vegetable Canter, Taiwan for several germplasm lines used in this study.

Author information

Authors and Affiliations

  1. Department of Genetics & Plant Breeding, Banaras Hindu University, Varanasi, 221005, India

    Ved Prakash Rai, Sheo Pratap Singh & Rajneesh Paliwal

  2. Indian Institute of Vegetable Research, Varanasi, 221305, India

    Rajesh Kumar, Ashutosh Rai, Major Singh & Awadesh Bahadur Rai

  3. Department of Genetics & Plant Breeding, Jawaharlal Nehru Krishi Vishwavidyalaya, Jabalpur, 482004, India

    Sanjay Kumar

  4. AVRDC—The World Vegetable Center, P.O. Box 42, Shanhua, Tainan, 74199, Taiwan

    Sanjeet Kumar

Authors
  1. Ved Prakash Rai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rajesh Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sanjay Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ashutosh Rai
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sanjeet Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Major Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Sheo Pratap Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Awadesh Bahadur Rai
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Rajneesh Paliwal
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sanjeet Kumar.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

DOCX 17 kb

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rai, V.P., Kumar, R., Kumar, S. et al. Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers. Physiol Mol Biol Plants 19, 575–586 (2013). https://doi.org/10.1007/s12298-013-0185-3

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12298-013-0185-3

Keywords

Search

Navigation