Skip to main content
SpringerLink
Log in

Evaluation of Genetic Diversity of Chilli Landraces from North Eastern India Based on Morphology, SSR Markers and the Pun1 Locus

  • Original Paper
  • Published:
Plant Molecular Biology Reporter Aims and scope Submit manuscript

Abstract

The chilli (Capsicum sp.) germplasm found throughout North Eastern (NE) India exhibits wide variability in fruit morphology, pungency, bearing habit and crop duration. As the genetic resources of chilli landraces from this region are not well documented, it is likely that they have hitherto unknown alleles and/or genes for economically important traits. In this study, 53 chilli accessions from different areas of this NE region were evaluated for genetic diversity using various morphological characters and 50 simple sequence repeat markers. It was found that erect and campanulate fruit types are grouped in separate clusters. The number of alleles per locus ranged from 3 to 9 with an average of 5.36. The average polymorphic information content value was 0.52. Percentage variation among populations, within individuals of population and within individuals was found to be 34, 57.9 and 8.05 %, respectively, indicating diversity in the landraces sampled. Allele mining across acyltransferase 3 (AT3) gene in a set of landraces led to identification of new single nucleotide polymorphisms (SNPs). Sequence analysis of the 2,349 bp AT3 region revealed the presence of a total of 79 SNPs and 3 indels. This overview of diversity of chilli landraces from NE India paves the way for conservation and utilisation of germplasm and contributes to the development of systematic breeding strategies.

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

Similar content being viewed by others

References

  • Adetula O (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 

  • Aluru MR, Mazourek M, Landry LG, Curry J, Jahn M, O’Connell MA (2003) Differential expression of fatty acid synthase genes, Acl, Fat and Kas, in Capsicum fruit. J Exp Botany 54:1655–1664

    Article  CAS  Google Scholar 

  • Asati BS, Yadav DS (2004) Diversity of horticultural crops in north eastern region. ENVIS Bull Himal Ecol 12:1–11

    Google Scholar 

  • Barerra LQ, Garcia MC, Giraldo MC, Melgarejo LM (2005) Isozyme characterization of Capsicum accessions from the Amazonian Colombia collection. Revista Colombiana de Biotechnologia 7:59–65

    Google Scholar 

  • Basu SK, De AK (2003) Capsicum: historical and botanical perspectives. In: De AK (ed) The genus Capsicum. Taylor & Francis, London, pp 1–15

    Google Scholar 

  • Bhagowati RR, Changkija S (2009) Genetic variability and traditional practices in Naga king chilli landraces of Nagaland. Asian Agri-Hist 13:171–180

    Google Scholar 

  • Board S (2004) Spice Statistics. Spice Board Cochin, Kerala, p 281

    Google Scholar 

  • Borgohain R, Devi J, Samar N (2005) Intra- and interspecific genetic diversity exploration in chilli (Capsicum spp.) using morphological and randomly applied polymorphic DNA markers. Indian J Agri Sci 75:582–585

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–333

    PubMed  CAS  Google Scholar 

  • Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Evolution 21:550–570

    Article  Google Scholar 

  • Dhaliwal MS (2007) Solanaceous vegetables. In: Handbook of vegetable crops. Kalyani Publishers, Ludhiana, India

  • 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 

  • Gogoi D, Gautam BP (2002) Variability, heritability and genetic advance in chilli (Capsicum spp.). Agric Sci Dig 22:102–104

    Google Scholar 

  • Guinness Book of World Records (2006) Hottest spice. http://www.guinnessworldrecords.com

  • Guzman FA, Ayala H, Azurdia C, Duque MC, de Vicen 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 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Huff DR, Peakall R, Smouse PE (1993) RAPD variation within and among populations of outcrossing buffalograss (Buchloe dactyloides (Nutt.) Engelm). Theor Appl Genet 86:927–934

    Article  CAS  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

    Google Scholar 

  • Ince AG, Karaca M, Onus AN (2010a) CAPS-microsatellites: use of CAPS method to convert non-polymorphic microsatellites into useful markers. Mol Breed 25:491–499

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Indian Horticulture Database (2011) National Horticulture Board. Aristo Printing Press, New Delhi, pp 6–7

    Google Scholar 

  • International Board for Plant Genetic Resources (IBPGR) (1983) Genetic resources of Capsicum, a global plan and action. Rome. 8–10

  • Jung J, Park SW, Liu WY, Kang BC (2010) Discovery of single nucleotide polymorphism in Capsicum and SNP markers for cultivar identification. Euphytica 175:91–107

    Article  CAS  Google Scholar 

  • Kang BC, Nahm SH, Huh JH, Yoo HS, Yu JW (2001) An interspecific (Capsicum annuum × C. chinese) F2 linkage map in pepper using RFLP and AFLP markers. Theor Appl Genet 102:531–539

    Article  CAS  Google Scholar 

  • Kochieva EZ, Ryzhova NN (2003) Molecular AFLP analysis of the genotypes of pepper Capsicum annuum cultivars. Russ J Genet 39:1345–1348

    Article  CAS  Google Scholar 

  • Kwon YS, Lee JM, Yi GB, Yi SI, Kim KM, Soh EH, Bae KM, Park EK, Song IH, Kim BD (2005) Use of SSR markers to complement tests of distinctiveness, uniformity, and stability (DUS) of pepper (Capsicum annuum L.) varieties. Mol Cells 19:428–435

    Google Scholar 

  • Lang Y, Yanagawa S, Sasanuma T, Sasakuma T (2006) A gene encoding a putative acyl-transferase involved in pungency of Capsicum. Breed Sci 56:55–62

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Mantel N (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 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acid Res 8:4321–4325

    Article  PubMed  CAS  Google Scholar 

  • Paran I, Aftergoot E, Shifriss C (1998) Variation in Capsicum annuum revealed by RAPD and AFLP markers. Euphytica 99:167–173

    Article  CAS  Google Scholar 

  • Patel AS, Sasidharan N, Vala AG, Kumar V (2011) Genetic relation in Capsicum annum [L.] cultivars through microsatellite markers: SSR and ISSR. J Plant Breed 2:67–76

    Google Scholar 

  • Pickersgill B, Heiser CB, McNeill J (1979) Numerical taxonomic studies on variation and domestication in some species of Capsicum. In: Hawkes JG, Lester RN, Skelding AD (eds) The biology and taxonomy of Solanaceae. Linnean Society Symposium 7. Academic, London, pp 678–700

    Google Scholar 

  • Prasad BCN, Kumar V, Gururaj HB, Parimalan R, Giridhar P, Ravishankar GA (2006) Characterization of capsaicin synthase and identification of its gene (csy1) for pungency factor capsaicin in pepper (Capsicum sp.). PNAS 103:13315–13320

    Article  PubMed  Google Scholar 

  • Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100

    Article  PubMed  CAS  Google Scholar 

  • Rodrigues KF, Tam HK (2010) Molecular markers for Capsicum frutescens varieties cultivated in Borneo. J Plant Breed Crop Sci 2:165–167

    CAS  Google Scholar 

  • Rossetto M, Weaver PK, Dixon KW (1995) Use of RAPD analysis in devising conservation strategies for the rare and endangered Grevillea scapigera (Proteaceae). Mol Ecol 4:321–329

    Article  PubMed  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 

  • Sitthiwong K, Matsui T, Sukprakarn S, Okuda N, Kosugi Y (2005) Classification of pepper (Capsicum annum L.) accessions by RAPD analysis. Biotechnology 4:305–309

    Article  CAS  Google Scholar 

  • Stewart C, Kang BC, Liu K, Mazourek M, Moore SL, Yoo EY, Kim BD, Paran I, Jahn MM (2005) The Pun1 gene for pungency in pepper encodes a putative acyltransferase. Plant J 42:675–688

    Article  PubMed  CAS  Google Scholar 

  • Thresh JC (1876) Isolation of capsaicin. The Pharmaceutical Journal and Transactions 6:941–947

    Google Scholar 

  • Thul ST, Lal RK, Shasany AK, Darokar MP, Gupta AK, Gupta MM, Verma RK, Khanuja SPS (2009) Estimation of phenotypic divergence in a collection of Capsicum species for yield-related traits. Euphytica 168:189–196

    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. Genet Resour Crop Evol 50:639–647

    Article  Google Scholar 

  • Tsaballa A, Pasentsis K, Tsaftaris AS (2011a) Τhe role of a gibberellin 20-oxidase gene in fruit development in pepper (Capsicum annuum). Plant Mol Biol Rep. doi:10.1007/s11105-011-0364-8

  • Tsaballa A, Pasentsis K, Darzentas N, Tsaftaris A (2011b) Multiple evidence for the role of an ovate-like gene in determining fruit shape in pepper. BMC Plant Biol 11:46

    Article  PubMed  CAS  Google Scholar 

  • 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 114:113–130

    Article  PubMed  CAS  Google Scholar 

  • Yu JK, Paik H, Choi JP, Han J-H, Choe JK, Hur CG (2010) Functional domain marker (FDM): an in silico demonstration in Solanaceae using simple sequence repeats (SSRs). Plant Mol Biol Rep 28:352–356

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported in part by the Intramural Research Project (IRP), Central Agricultural University (CAU), Imphal, India to WT. JSY was supported by a student fellowship from CAU. The authors would like to thank Dr. V.K. Khanna for sharing the seeds of ‘type species’ of Capsicum obtained from IVRI, Varanasi. The authors would also like to thank M.Sc. students of CPGS who helped in collecting landraces from different districts of NE India.

Author information

Authors and Affiliations

  1. School of Crop Improvement, College of Post Graduate Studies, Central Agricultural University, Umroi Road, Umiam, Meghalaya, India, 793103

    Julia S. Yumnam, Wricha Tyagi, N. Tombisana Meetei & Mayank Rai

  2. Division of Crop Improvement, Indian Council of Agricultural Research Complex for North Eastern Hill Region, Umroi Road, Umiam, Meghalaya, India, 793103

    Avinash Pandey

Authors
  1. Julia S. Yumnam
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wricha Tyagi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Avinash Pandey
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. N. Tombisana Meetei
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mayank Rai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Wricha Tyagi.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Table 1

List of chilli genotypes with geographical distribution used in the current study (XLS 22 kb)

Supplementary Table 2

List of edited morphological descriptors used in the current study (XLS 25 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yumnam, J.S., Tyagi, W., Pandey, A. et al. 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, 1470–1479 (2012). https://doi.org/10.1007/s11105-012-0466-y

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11105-012-0466-y

Keywords

Search

Navigation