Skip to main content
SpringerLink
Log in

Identification of novel SNPs in Pun1 locus for pungency in Capsicum species

  • Original Article
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Background

Capsaicin and its analogues known as capsaicinoids are the principal sources of pungency in Capsicum spp. In this study, characterization of North-West Himalayan chilli germplasm and commercial landraces of different Indian states known for different pungency-color combinations was done based on capsaicin concentration. Moreover, molecular variation in pungency among high, medium and mild/not pungent Capsicum spp., especially those adapted to North-West Himalayas were elucidated.

Methods and results

Forty-nine genotypes of chilli comprising breeding lines of Kashmiri origin, commercial landraces of Southern Indian origin and one of the world’s hottest chilli Bhut Jolokia from Nagaland state of India were used as an experimental material. Wide variation in capsaicin content was observed among the genotypes, wherein, Bhut Jolokia (Capsicum chinense) expressed the highest capsaicin content (10,500.75 µg/g). Further, molecular analysis of PunI gene was done for discovering SNPs responsible for variations in pungency. In the non-pungent Nishat-1 (Capsicum annuum var. grossum), the 650 bp DNA fragment was not amplified due to 2.5 kb deletion spanning the putative promoter and first exon of AT3. The amplified DNA product for high and medium pungent was sequencing. Sequence alignment among revealed SNPs which were further observed responsible for variations in amino acid sequence and protein structure.

Conclusion

The observed variation in protein structure might be responsible for high capsaicin production in one genotype as compared to the other and hence the protein conformation determines its interaction with the substrate.

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

  1. Perry L, Dickau R, Zarrillo S, Holst I, Pearsall DM, Piperno DR, Berman MJ, Cooke RG, Rademaker K, Ranere AJ, RademakerK RAJ, Raymond JS, Sandweiss DH, Scaramelli F, Tarble K, Zeidler JA (2007) Starch fossils and the domestication and dispersal of chilli pepper (Capsicum spp. L) in the Americas. Science 315:986–988

    Article  CAS  PubMed  Google Scholar 

  2. 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

  3. Purseglove JW (1977) Tropical crops. Dicotyledon—2. Longman. Green & Co. Publisher, London, pp 524–530

    Google Scholar 

  4. Jordth SE, Julius D (2002) Molecular basis for species specific sensitivity to ‘Hot’ chilli peppers. Cell 11:421–430

    Article  Google Scholar 

  5. Stewart C, Mazourek M, Stellari GM, Connell MO, Jahn M (2007) Genetic control of pungency in C. chinense via the PUN1 locus. J Exp Bot 58:979–991

    Article  CAS  PubMed  Google Scholar 

  6. Suzuki T, Fujiwake H, Iwai K (1980) Intracellular localization of capsaicin and its analogues, capsaicinoid, in Capsicum fruit 1. Microscopic investigation of the structure of the placenta of Capsicum annuum var. annuum cv. Karayatsubusa. Plant Cell Physiol 21:839–853

    Article  CAS  Google Scholar 

  7. Prasad NBC, Gururaj HB, Kumar V, Giridhar P, Parimalan R, Sharma A, Ravi Shankar GA (2006) Influence of 8-methyl-Nonenoic acid on capsaicin biosynthesis invivo and invitro cell cultures of Capsicum spp. J Agric Federation Chem 54:1854–1859

    Article  CAS  Google Scholar 

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

    Google Scholar 

  9. Iwai K, Suzuki T, Fujiwake H (1986) The formation and accumulation of pungent principle of hot pepper fruits, capsaicin and its analogues in Capsicum annuum var. annuum cv. Karayatsubusa at different growth stages after flowering. Agric Biol Chem 43:2493–2498

    Google Scholar 

  10. 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 

  11. 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  CAS  PubMed  Google Scholar 

  12. Stellari GM, Mazourek M, Jahn M (2010) Contrasting modes for loss of pungency between cultivated and wild species of Capsicum. Heredity 104(460):471

    Google Scholar 

  13. Reddy UK, Almeida A, Abburi VL, Alaparthi SB, Unselt D, Hankins G, Park M, Choi D, Nimmakayala P (2014) Identification of gene-specific polymorphisms and association with capsaicin pathway metabolites in Capsicum annuum L. collections. PLoS ONE 9(1):e86393

    Article  PubMed  PubMed Central  Google Scholar 

  14. Arce-Rodríguez ML, Ochoa-Alejo N (2015) Silencing AT3 gene reduces the expression of pAMT, BCAT, kas, and acl genes involved in capsaicinoid biosynthesis in chili pepper fruits. Biol Plant 59(3):477–484. https://doi.org/10.1007/s140535-015-0525-y

    Article  Google Scholar 

  15. Ademoyegun OT, Fariyike TA, Aminu-Taiwo RB (2011) Effects of poultry dropping on the biologically active compounds in Capsicum annuum L. (var Nsukka yellow). Agric Biol J N Am 2(4):665–672

    Article  Google Scholar 

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

    Google Scholar 

  17. Bosland PW, Baral JB (2007) Bhut Jolokia-the World’s hottest known chile pepper is a putative naturally occurring interspecific hybrid. Hortic Sci 30:137–139

    Google Scholar 

  18. Popelka P, Jevinova P, Smejkal K, Roba P (2017) Determination of capsaicin content and pungency level of different fresh and dried chilli peppers. Folia Vet 2:11–16

    Article  Google Scholar 

  19. Adluri PK, Borah AR, Nath PD (2017) Study of genetic diversity of Bhut Jolokia germplasm in north east India by SSR markers and morphology. Int J Pure Appl Biosci 5(4):1657–1665

    Article  Google Scholar 

  20. Kirii E, Goto T, Yoshida Y, Yasuba K, Tanaka Y (2017) Non-pungency in a Japanese chilli pepper landrace (Capsicum annum) is caused by a novel loss-of-function PUN1 allele. Hortic J 86:61–69

    Article  CAS  Google Scholar 

  21. Webber HJ (1911) Preliminary notes on pepper hybrids. J Hered 7:188–199

    Google Scholar 

  22. Blum E, Liu K, Mazourek M, Yoo EY, Jahn M, Paran I (2002) Molecular mapping of the C locus for presence of pungency in Capsicum. Genome 45:02–705

    Article  Google Scholar 

  23. Zamora AG, Olvera C, Calleros AA, Hernandez JLG (2020) Genetic variability of Pun 1 gene (Capsaicin synthase) in pungent cultivars of Capsicum annuum of Northern Mexico. Trop Subtrop Agroecosyst 23:1–15

    Google Scholar 

  24. Yumnam JS, Tyagi W, Pandey A, Ngasepam TM (2012) Evaluation of genetic diversity of chilli landraces from North Eastern India based on morphology, SSR markers and the Pun 1 locus. Plant Mol Biol Report 30:1470–1479

    Article  CAS  Google Scholar 

Download references

Acknowledgements

AM and SMZ acknowledge Honorable Vice Chancellor SKUAST-K (Prof. Nazir A. Ganai) for the support and encouragement in carrying out research on applied aspects.

Funding

There was no funding.

Author information

Authors and Affiliations

  1. Division of Vegetable Science, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu & Kashmir, India

    Ariza Gulzar, Ajaz Malik & Khursheed Hussain

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

    Geetika Malik

  3. Division of Agricultural Statistics, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India

    Nageena Nazir

  4. Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India

    Ishfaq Aabidi

  5. CSIR, IIIM-Jammu, Jammu, Jammu & Kashmir, India

    Umar Gani

  6. Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India

    Ammarah Hami, Reetika Mahajan & Sajad Majeed Zargar

  7. Division of Soil Science, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India

    Shabir Bangroo

Authors
  1. Ariza Gulzar
    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. Nageena Nazir
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ishfaq Aabidi
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Umar Gani
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ammarah Hami
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Reetika Mahajan
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Shabir Bangroo
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Sajad Majeed Zargar
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

AG did the experimental work, molecular analysis and wrote the manuscript; GM, KH, NN and IA helped in biochemical and statistical analysis; UG, AH and RM helped in experimental work and analysis; SB helped in manuscript writing; AM and SMZ developed the concept and guided all the field and laboratory work and finalized the manuscript.

Corresponding authors

Correspondence to Ajaz Malik or Sajad Majeed Zargar.

Ethics declarations

Conflict of interest

Authors declare that there are no known conflicts of interest associated with this publication.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Publisher's Note

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

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 13 kb)

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

Gulzar, A., Malik, A., Malik, G. et al. Identification of novel SNPs in Pun1 locus for pungency in Capsicum species. Mol Biol Rep 50, 7571–7579 (2023). https://doi.org/10.1007/s11033-023-08691-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-023-08691-z

Keywords

Search

Navigation