SpringerLink
Log in

Phenotypic, biochemical and genetic diversity of pepper (Capsicum spp.) germplasm reflects selection for cultivar types and spatial distribution

  • Original Article
  • Published:
Plant Biotechnology Reports Aims and scope Submit manuscript

Abstract

Throughout the globe morphological, biochemical and genetic variability exists in chilli and is harnessed to achieve specific breeding objectives. In this study, chilli germplasm was characterized based on horticultural traits, biochemical quantification and simple sequence repeat (SSR) polymorphism for diversity estimation. A total of 36 SSR primers were utilised to study the genetic divergence among 48 genotypes of chilli collected from nine states of India. Among the 36 primers, sixteen amplified null alleles. A total of 41 alleles were detected with average 2.05 alleles per locus. The largest number of alleles (5) were obtained with marker CAMS-234. The polymorphic information content ranged from 0.06 to 0.72 with an average of 0.50. On the basis of SSR analysis, the UPGMA cluster classified 48 genotypes into three groups. There was significant variability in germplasm for all morpho-biochemical traits. Kashi Anmol (100.50 q/ha) expressed the highest yield. Highest vitamin C content at green stage was recorded in IC-561635 (187 mg/100 g) and the greatest capsaicin content (9547.90 µg/g) equivalent to pungency of 171,862.2 Scoville heat units (SHU) was recorded in Bhut Jolokia. Principal component analysis indicates that the first five principal components explain 74.63% per cent of the total variation. Additionally, analysis of molecular variance (AMOVA) showed that 1% of the total genetic variation occurred among the population and 99% genetic variation within the populations, whereas the pairwise Fst specified the moderate genetic variation ranging from 0.002 to 0.020. The present investigation has strengthened the knowledge of genetic worth of this germplasm for application in various genetic improvement programmes.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (France)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig.  4
Fig.  5
Fig. 6
Fig.  7

Similar content being viewed by others

Data availability

The datasets analyzed during the current study are available from the corresponding author on reasonable request.

References

  • Ahmed N, Hou X (2022) Genetic variation and population structure analysis of Leymus chinensis (Trin.) Tzvelev from Eurasian steppes using SSR makers. Genet Res Crop Evol 69:2425–2436

    Article  CAS  Google Scholar 

  • AOAC (1984) Official Methods of Analysis. Association of official analytical chemists 13th edition, Washington D.C. pp 497

  • Aremu CO (2011) Genetic diversity: a review for need and measurements for intraspecies crop improvement. J Microbiol Biotechol Res 1(2):80–85

    Google Scholar 

  • ASTA (1986) Official analytical methods of the American Spice Trade Association, 2nd edn. ASTA, Englewood Chiffs, N. I.

    Google Scholar 

  • Bhattacharya A, Chattopadhyay A, Mazumdar D, Chakravarty A, Pal S (2010) Antioxidant constituents and enzymes activities in chilli peppers. Int J Veg Sci 16(3):201–211

    Article  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 30:137–139

    Google Scholar 

  • Bosland PW, Votava EJ (2003) Peppers: vegetable and spice Capsicum. CAB International, England, p 333

    Google Scholar 

  • Costa FRD, Pereira TNS, Vitoria AP, De Campos KP, Rodrigues R, Da Silva DH, Pereira MG (2006) Genetic diversity among Capsicum accessions using RAPD markers. Crop Breed Appl Biotechnol 6:18–23

    Article  Google Scholar 

  • Dan M (2012) The red-hot chilli cook book: fabulously fiery recipes for chilli fans, published by Ryland Peters and small 20–21 Jockey’s fields London WCIR 4 BW and 519 Broadway, New York

  • Dewitt D (1999) The Chile Pepper Encyclopedia. New Work, William Marrow

    Google Scholar 

  • Dhaliwal MS, Yadav A, **dal SK (2014) Molecular characterization and diversity analysis in chilli pepper using simple sequence repeats (SSR) markers. African J Biotechnol 13(31):3137–3143

    Article  CAS  Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12(1):13–15

    Google Scholar 

  • Farhad M, Hasanuzzaman M, Biswas BK, Arifuzzaman M, Islam MM (2010) Genetic divergence in chilli (Capsicum annuum L.). Bangladesh Res Pub J 3(3):1045–1051

    Google Scholar 

  • Fonseca RM, Lopes R, Barros SW, Lopes MTG, Ferreira FM (2008) Morphological characterization and genetic diversity of Capsicum chinensis Jacq accessions along the upper Rio-Negro-Amazonas. Crop Breed Appl Biotechnol 8:187–194

    Article  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 

  • Ghosh A, Pugalendhi L (2012) Studies on the improvement of chilli (Capsicum annuum L.) cv. Co 4 for quality characters through hybridization. Elec J Plant Breed 3(2):811–817

    Google Scholar 

  • Gilbert JE, Lewis RV, Wilkinson MJ, Caligari PDF (1999) Develo** an appropriate strategy to assess genetic variability in plant germplasm collection. Theor Appl Genet 98:1125–1131

    Article  CAS  Google Scholar 

  • Harvell KP, Bosland PW (1997) The environment produces a significant effect on pungency of chiles (Capsicum annuum L.). Hort Sci 32:1292

    Google Scholar 

  • Hasanuzzaman M, Golam F (2011) Selection of parents in chilli (Capsicum annuum L.). Int J Sus Crop Prod 6(1):63–75

    Google Scholar 

  • IPGRI (1999) Isolated from a size-fractionated genomic library of Brassica napus L. (Rapeseed). Theor Appl Genet 91:206–211

    Google Scholar 

  • Janaki M, Naidu LN, Ramana CV, Rao MP (2016) Genetic divergence among chilli (Capsicum annuum L.) genotypes based on quantitative and qualitative traits. Int J Sci Nat 7(1):181–189

    CAS  Google Scholar 

  • Karad SR, Raikar GR, Navale PA (2002) Genetic divergence in chilli. J Maharashtra Agric Univ 27(2):143–145

    Google Scholar 

  • Khodadabi M, Fotokian MH, Miransari M (2011) Genetic diversity of wheat genotypes based on cluster and principal component analysis for breeding strategies. Aust J Crop Sci 5(1):17–24

    Google Scholar 

  • Kumar B, Lal G, Ruchi M, Upadhyay A (2009) Genetic variability, diversity and association of quantitative traits with grain yield in bread wheat (Triticum aestivum L.). Asian J Agri Sci 1(1):4–6

    Google Scholar 

  • Kumar BMD, Kantti A, Mallikarjunaiah H (2010) Genetic divergence in chilli accessions. Electronic J Plant Breeding 1(5):1363–1366

    Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Lannes SD, Finger FL, Schuelter AR, Casali VWD (2007) Growth and quality of Brazilian accessions of Capsicum chinense fruits. Sci Hortic 112:266–270

    Article  Google Scholar 

  • Laurentin H (2009) Data analysis for molecular characterization of plant genetic resources. Genet Res Crop Evol 56:277–292

    Article  CAS  Google Scholar 

  • Mahalanobis PC (1936) On the generalized distance in statistics. Proc Nat Inst Sci Indi 2:49–55

    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 

  • Nahak SC, Nandi A, Sahu GS, Tripathy P, Das S, Mohanty A, Pradhan SR (2018) Assessment of genetic diversity in different chilli (Capsicum annuum L.) genotypes. Int J Curr Microbiol Appl Sci 7(9):634–639

    Article  Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of Restriction endonucleases. Proc Natl Acad Sci USA 79:5269–5273

    Article  Google Scholar 

  • Paran I, Knaap EV (2007) Genetic and molecular regulation of fruit and plant domestication traits in tomato and pepper. J Exp Bot 58(14):3841–3852

    Article  CAS  PubMed  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. population genetic software for teaching and research- an update. Bioinformatics 28:2537–2539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Perry L, Dickau R, Zarrillo S, Holst I, Pearsall DM, Piperno DR, Berman MJ, Cooke RG, Rademaker K, Ranere AJ, Rademaker K, Ranere AJ, Raymond JS, Sandweiss DH, Scaramelli F, Tarble K, Zeidler JA (2007) Starch fossils and the domestication and dispersal of chilli pepper (Capsicum spp. L.). Americas Science 315:986–998

    CAS  PubMed  Google Scholar 

  • Pradhan K, Nandi A, Das A, Sahu, Senapati N (2018) Quantification of capsaicin and ascorbic acid content in twenty-four Indian genotypes of chilli (Capsicum annuum L.) by HPTLC and Volumetric method. Int J Pure Appl Bioscience 6(1):1322–1327

    Article  Google Scholar 

  • Pritchard JK, Stephens M (2000) Inference of population structure using multilocus genotype data. Genetics 155(945–59):56

    Google Scholar 

  • Rao CR (1952) Advanced statistical methods in biometrical research. Wiley, New York

    Google Scholar 

  • Rohlf FJ (1997) NTSYS-PC 2.1: numerical taxonomy and multivariate analysis system. Setauket Newyork Exeter software

    Google Scholar 

  • Rymbai H, Sharma RR, Srivastav M (2011) Bio-colorants and its implications in health and food industry—a review. Int J Pharm Tech Res 3:2228–2244

    CAS  Google Scholar 

  • Salvador MH (2002) Genetic resources of chilli (Capsicum annuum L.) in Mexico. In: Proceedings of the 16th International Pepper Conference, Tampico, Tamaulipas, Mexico. pp 10–12

  • Sharmin A, Hoque ME, Haque MdM, Khatun F (2018) Molecular diversity analysis of some chilli (Capsicum spp.) genotypes using SSR markers. Amer J Plant Sci 9:368–379

    Article  CAS  Google Scholar 

  • Singh RK, Sharma RK, Singh AK, Singh VP, Singh NK, Tiwari SP, Mohapatra T (2004) Suitability of mapped sequence tagged microsatellite site markers for establishing distinctness, uniformity and stability in aromatic rice. Euphytica 135:135–143

    Article  CAS  Google Scholar 

  • Srinivas B, Thomas B, Gogineni S (2013) Genetic divergence for yield and its component traits in chilli (Capsicum frutescens L.) accessions of Kerala. Int J Sci Res 4:2319–7064

    Google Scholar 

  • Tanksley SD (1984) High rates of cross pollination in chilli pepper. Hort Sci 4:580–582

    Google Scholar 

  • Wang J, Yao J, Li W (2008) Construction of a molecular map for melon (Cucumis melo L.) based on SRAP. Front Agric China 2(4):451–455

    Article  Google Scholar 

  • Ye-yun X, Zhan Z, Yi-** X, Long- ** Y (2005) Identification and purity test of super hybrid rice with SSR molecular markers. Rice Sci 12(1):7–12

    Google Scholar 

  • Yuzbapyoglu E, Ozcan S, Acik L (2006) Analysis of genetic relationships among Turkish cultivars and breeding lines of lens culinatis mestile using RAPD markers. Genet Res Crop Evol 53:507–514

    Article  Google Scholar 

  • Zehra SB (2014) Msc. thesis submitted to Division of Vegetable Science, SKUAST-Kashmir, Shalimar Srinagar

  • Zitter TA, Hopkins DL, Thomas CE (1996) Compendium of Cucurbit Diseases. APS Press, St. Paul, p 87

    Google Scholar 

Download references

Acknowledgements

This work was supported by grant provided by all India coordinated research project on vegetable crops (AICRP-VC), research grant (Division of vegetable science SKUAST-K) and  this research was funded by a National Research Foundation of Korea (NRF) grant funded by the Ministry of Education (2019R1A6A1A11052070).

Author information

Authors and Affiliations

  1. Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K, India

    Sayed Azrah Indrabi, Ajaz Malik & Khursheed Hussain

  2. Division of Vegetable Science and Floriculture, ICAR-Central Institute of Temperate Horticulture, Srinagar, J&K, India

    Geetika Malik

  3. Department of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Wadura, J&K, India

    Asif Shikari

  4. Plant Biotechnology, ICAR-Central Institute of Temperate Horticulture, Srinagar, J&K, India

    Javid Iqbal Mir

  5. National Agrobiodiversity Center, RDA, Jeonju, 54875, Republic of Korea

    Ji Eun Park

  6. Vietnam National University, Ho Chi Minh City, 70000, Vietnam

    Anh Tuan Le

  7. Faculty of Biology and Biotechnology, University of Science, Ho Chi Minh City, 70000, Vietnam

    Anh Tuan Le

  8. Phenomics Laboratory, Division of Plant Resources and Environment, Jeju National University, Jeju-si, Republic of Korea

    Sheikh Mansoor

  9. Transcriptomics Laboratory (K-Lab) Division of Plant Biotechnology, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K, India

    Khalid Z. Masoodi

Authors
  1. Sayed Azrah Indrabi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ajaz Malik
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Geetika Malik
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Khursheed Hussain
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Asif Shikari
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Javid Iqbal Mir
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ji Eun Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Anh Tuan Le
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Sheikh Mansoor
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Khalid Z. Masoodi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Ajaz Malik, Sheikh Mansoor or Khalid Z. Masoodi.

Ethics declarations

Conflicts of interest

The authors declare no conflict of interest.

Ethics approval

Not applicable.

Consent to participate

Not applicable.

Consent for publication

Not applicable.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Indrabi, S.A., Malik, A., Malik, G. et al. Phenotypic, biochemical and genetic diversity of pepper (Capsicum spp.) germplasm reflects selection for cultivar types and spatial distribution. Plant Biotechnol Rep 18, 341–360 (2024). https://doi.org/10.1007/s11816-024-00904-6

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11816-024-00904-6

Keywords

Search

Navigation