Skip to main content
SpringerLink
Log in

Cross-species transferability of IRAP retrotransposon markers and polymorphism in black pepper (Piper nigrum L.)

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

Abstract

Black pepper is one of the most important spices, known for its use worldwide. Retrotransposons, class I mobile elements abundantly appear in the plant genome and can play role in gene activation or silencing by their copy and paste mechanism in the respective genome of an organism. In this study, the Piper nigrum L. genome was scanned for identification of retrotransposon activity in terms of insertional polymorphism using IRAP retrotransposon-based molecular marker system. Seven LTR IRAP primers (Sukkula, Nikita, 3′LTR, 5′LTR1, 5′LTR2, LTR6149, and LTR6150) in single and combination were used to analyse insertional polymorphism among nineteen varieties of black pepper. In single primer analysis Sukkula, Nikita, 3′LTR, and LTR6150 primers showed amplification in all the nineteen varieties. Out of these Sukkula, Nikita and 3′LTR were found to be polymorphic in nature with 33.33%, 53% and 56.25% polymorphism, with PIC values of 0.131, 0.183 and 0.197 respectively. Out of the 21 combinations of primer pairs tried, 16 showed amplification in all the nineteen varieties and 14 combinations among them were polymorphic in nature with the percentage of polymorphism and PIC value in the range between 50–100% and 0.04–0.350 respectively. This is the first report of horizontal transferability and identification of retrotransposons Sukkula, BARE1, and Nikita in black pepper (Piper nigrum L.) indicating an evolutionary relationship between black pepper (Piper nigrum L.) and other genome such as barley (Hordeum vulgare). These polymorphic markers (single and combination of primer pairs) were also useful for the evaluation of genetic diversity among the nineteen varieties of black pepper used in the study.

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

  • Abirami K, Baskaran V, Simachalam P (2018) ISSR marker-based diversity assessment of Piper spp. in Bay Island, India. Indian J Agric Res 52(4):434–438

    Google Scholar 

  • Alavi-Kia SS, Mohammadi SA, Aharizad S, Moghaddam M (2008) Analysis of genetic diversity and phylogenetic relationships in Crocus genus of Iran using inter retrotransposon amplified polymorphism. Biotechnol Biotechnol Equip 22(3):795–800

    Article  CAS  Google Scholar 

  • Arabi ME, Jawhar M (2012) Inter-retrotransposon amplified polymorphism (IRAP) markers for genetic diversity assessment of Pyrenophora graminea. J Plant Bio Res 1(4):138–144

    Google Scholar 

  • Babu KN, Ravindran PN (1992) Improved varieties of black pepper. In: Sarma YR, Devasahayam S, Anandaraj M (eds) Black pepper and cardamom. Indian Society for Spices, Kozhikode, pp 61–64

    Google Scholar 

  • Basirnia A, Darvishzadeh R, Mandoulkani BA (2016) Retrotransposon insertional polymorphism in sunflower (Helianthus annuus L.) lines revealed by IRAP and REMAP markers. Plant Biosyst 150:641–651

    Article  Google Scholar 

  • Branco CJS, Vieira EA, Malone G, Kopp MM, Malone E, Bernarndes A, Mistura CC, Carvalho FIF, Oliveira CA (2007) IRAP and REMAP assessments of genetic similarity in rice. J Appl Genet 48:107–113

    Article  PubMed  Google Scholar 

  • Cakmak B, Marakli S, Gozukirmizi N (2015) SIRE1 retrotransposons in barley (Hordeum vulgare L.). Genetika 51(7):775–786

    CAS  PubMed  Google Scholar 

  • Cakmak B, Marakli S, Gozukirmizi N (2017) Sukkula retrotransposon movements in the human genome. Biotechnol Biotechnol Equip 31(4):756–760

    CAS  Google Scholar 

  • Cheraghi A, Rahmani F, Ghorttapeh AH (2018) IRAP and REMAP based genetic diversity among varieties of Lallemantia iberica. Mol Biol Res Commun 7(3):125–132

    CAS  PubMed  PubMed Central  Google Scholar 

  • Elkina MA, Erkenov TA, Glazko VI (2015) Mobile genetic elements as a tool for the analysis of genetic differentiation of varieties of cultivated plants and breeds of farm animals. IJRSR 6:5893–5900

    Google Scholar 

  • Fan F, Cui B, Zhang T, Ding J, Wen X (2014) LTR-retrotransposon activation, IRAP marker development and its potential in genetic diversity assessment of masson pine (Pinus massoniana). Tree Genet Genomes 10:213–222

    Article  Google Scholar 

  • Fatmawati Y, Setiawan AB, Purwantoro A, Respatie DW, Teo CH (2021) Analysis of genetic variability in F2 interspecific hybrids of mung bean (Vigna radiata) using inter-retrotransposon amplified polymorphism marker system. Biodiversitas 22(11):4880–4889

    Article  Google Scholar 

  • Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trends Genet 5:103–107

    Article  CAS  PubMed  Google Scholar 

  • Fortune PM, Roulin A, Panaud O (2008) Horizontal transfer of transposable elements in plants. Commun Integr Biol 1(1):74–77

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Haerinasab M, Farouji AE (2022) Contribution to the knowledge of the genetic diversity and taxonomy of some Iranian Trifolium species. Genet Resour Crop Evol 69:699–717

    Article  Google Scholar 

  • Hosseini M, Yassaie M, Rashed-Mohasse MH, Ghorbani R, Niazi A (2022) Genetic diversity of Iranian wild barley (Hordeum spontaneum Koch.) populations. J Crop Sci Biotechnol 25:301–311

    Article  CAS  Google Scholar 

  • Igiebor FC, Marakli S, Gozukirmizi N (2016) Effects of cadmium on Sukkula retrotransposon polymorphism in Ailanthus altissima (Mill.) Swingle. J Mol Biol Genet 1:33–36

    Google Scholar 

  • Kalendar R (2011) The use of retrotransposon-based molecular markers to analyze genetic diversity. Ratar Povrt Field Veg Crop Res 48:261–274

    Google Scholar 

  • Kalendar R, Schulman AH (2006) IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nat Prot 1(5):2478–2484

    Article  CAS  Google Scholar 

  • Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98:704–711

    Article  CAS  Google Scholar 

  • Khaleghi E, Sorkheh K, Chaleshtori MH, Ercisli S (2017) Elucidate genetic diversity and population structure of Olea europaea L. germplasm in Iran Using AFLP and IRAP molecular markers. 3 Biotech 7(1):71

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar BM, Sasikumar B, Kunhamu TK (2021) Agroecological aspects of black pepper (Piper nigrum L.) cultivation in Kerala: a review. AGRIVITA J Agric Sci 43(3):648–664

    Google Scholar 

  • Kumari R, Wankhede DP, Bajpai A, Maurya A, Prasad K et al (2019) Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): a valuable resource for boosting genomics applications. PLoS ONE 14(12):e0226002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leigh F, Kalendar R, Lea V, Lee D, Donini P, Schulman AH (2003) Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques. Mol Gen Genomics 269:464–474. https://doi.org/10.1007/s00438-003-0850-2

  • Mamaghani RA, Mohammadi SB, Aharizad S (2015) Transferability of barley retrotransposon primers to analyse genetic structure in Iranian Hypericum perforatum L. population. Turk J Bot 39(4):664–672

    Article  Google Scholar 

  • Mandoulakani BA, Sadigh P, Azizi H, Piri Y, Nasri S, Arzahang S (2015) Comparative assessment of IRAP, REMAP, ISSR, and SSR markers for evaluation of genetic diversity of alfalfa (Medicago sativa L.). J Agr Sci Technol 17:999–1010

    Google Scholar 

  • Mansour A (2008) Utilization of genomic retrotransposon as cladistic molecular marker. J Cell Mol Boil 7(1):17–28

    CAS  Google Scholar 

  • Marakli S (2018) Transferability of barley retrotransposons (Sukkula and Nikita) to investigate genetic structure of Pimpinella anisum L. Marmara Fen Bilimleri Dergisi 3:299–304

    Article  Google Scholar 

  • Marakli S (2019) Retrotransposon analyses in Cucurbitaceae family. Int J Sci Lett 1(1):68–76

    Article  Google Scholar 

  • Mia S, Ahmed NU, Islam MZ, Rashad MI, Islam M, Zaman M (2022) Genetic diversity and yield performance among T. Aman rice (Oryza sativa L.) landraces in Barishal region of Bangladesh. J Crop Sci Biotechnol 25:123–132

    Article  CAS  Google Scholar 

  • Nazeem PA, Kesavachandran R, Babu TD, Achuthan CR, Girija D, Peter KV (2005) Assessment of genetic variability in black pepper (Piper nigrum L.) varieties through RAPD and AFLP analysis. In: Proceeding of national symposium on biotechnological interventions for improvement of horticultural crops: issues and strategies, Trissur, Kerala, pp 226–228

  • Nisha J, Abraham Z, Soniya EV (2007) A preliminary assessment of genetic relationships among agronomically important cultivars of black pepper. BMC Genet 8:42

    Article  Google Scholar 

  • Otwe EP, Agyirifo DS, Galyuon IK, Heslop-Harrison JS (2017) Molecular diversity in some Ghanaian cowpea [Vigna unguiculata L. (Walp)] accessions. Trop Plant Biol 10:57–67

    Article  CAS  Google Scholar 

  • Pradeepkumar T, Karihaloo JL, Archak S, Baldev A (2003) Analysis of genetic diversity in Piper nigrum L. using RAPD markers. Genet Resour Crop Evol 50:469–475

    Article  CAS  Google Scholar 

  • Rashid K, Othman RY, Ali BS, Yusof YM, Nezhadahmadi A (2014) The application of Irap marker in the breeding of Papaya (Carica papaya L.). Indian J Sci Technol 7(11):1720–1728

    Article  CAS  Google Scholar 

  • Roldán-Ruiz I, Calsyn E, Gilliland TJ, Coll R, van Eijk MJT, Loose MD (2000) Estimating genetic conformity between related ryegrass (Lolium) varieties. 2. AFLP characterization. Mol Breed 6:593–602

    Article  Google Scholar 

  • Saeidi H, Rahiminejad MR, Harrison JS (2008) Retroelement insertional polymorphism, diversity and phylogeohraphy within diploid, D genome Aegilops tauschii (Triticeae, Poaceae) sub taxa in Iran. Ann Bot 101(6):855–861

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saleh B (2013) Genetic diversity in Ficus sycomorus L. species (Moraceae) using RAPD and IRAP markers. Agriculture (poľnohospodárstvo) 59(3):120–130

    CAS  Google Scholar 

  • Saraswathi SM, Uma S, Ramaraj S, Durai P, Mustaffa MM, Kalaiponmani K, Chandrasekar A (2019) Inter retrotransposon based genetic diversity and phylogenetic analysis among the Musa germplasm accessions. J Plant Biochem Biotechnol 29(1):114–124

    Article  Google Scholar 

  • Sheidai M, Riazifar M, Hoordadian A, Alishah O (2018) Genetic fingerprinting of salt and drought-tolerant cotton cultivars (Gossypium hirsutum) by IRAP-REMAP and SRAP molecular marker. Plant Gene 14:12–19

    Article  CAS  Google Scholar 

  • Shivashankar M (2014) Genetic diversity and relationships of piper species using molecular marker. Int J Curr Microbiol Appl Sci 3:1101–1109

    Google Scholar 

  • Soengas P, Velasco P, Padilla G, Ordas A, Cartea ME (2006) Genetic relationships among Brassica napus crops based on SSR markers. Horticult Sci 41(5):1195–1199

    CAS  Google Scholar 

  • Sreedevi M, Syamkumar S, Sasikumar B (2005) Molecular and morphological characterization of new promising black pepper (Piper nigrum L.) lines. J Spices Aromat Crops 14(1):1–9

    Google Scholar 

  • Srinivasan K (2007) Black pepper and its pungent principle Piperine: a review of diverse physiological effects. Crit Rev Food Sci Nutr 47(8):735–748

    Article  CAS  PubMed  Google Scholar 

  • Strioto DK, Kuhn BC, Nagata WS, Marinelli G, Oliveira-Collet SA, Mangolin CA, Machado MF (2019) Development and use of retrotransposons-based markers (IRAP/REMAP) to assess genetic divergence among table grape cultivar. Plant Genet Resour 17(3):272–279

    Article  CAS  Google Scholar 

  • Subba A, Alex S, Soni KB, Nair DS, Reghunath BR (2014) Isolation of genomic DNA from mature leaves and spikes of black pepper (Piper nigrum L.). J Plant Sci Res 30(1):21–25

    Google Scholar 

  • Sun J, Yin H, Li L, Song Y, Fan L, Zhang S, Wu J (2015) Evaluation of new IRAP markers of pear and their potential application in differentiating bud sports and other Rosaceae species. Tree Genet Genomes 11(2):25

    Article  Google Scholar 

  • Taheri MT, Alavi-Kia SM, Mohammadi SA, Vahed MM (2018) Assessment of genetic diversity and relationships among Triticum urartu and Triticum boeoticum populations from Iran using IRAP and REMAP markers. Genet Resour Crop Evol 65:1867–1878

    Article  CAS  Google Scholar 

  • Teo CH, Tan SH, Ho CL, Faridah QZ, Othman YR, Heslop-Harrison JS, Kalendar R, Schulman AH (2005) Genome constitution and classification using retrotransposon-based marker in the orphan crop banana. J Plant Biol 48(1):96–105

    Article  CAS  Google Scholar 

  • Todorovska E (2007) Retrotransposons and their role in plant-genome evolution. Biotechnol Biotechnol Equip 21(3):294–305

    Article  CAS  Google Scholar 

  • Varagona MJ, Purugganan M, Wessler SR (1992) Alternative splicing induced by insertion of retrotransposon into the maize waxy gene. Plant Cell 4:811–820

    CAS  PubMed  PubMed Central  Google Scholar 

  • Varghese JM, Bhat AI (2011) An efficient Agrobacterium-mediated transformation protocol for black pepper (Piper nigrum L.) using embryogenic mass as explant. J Crop Sci Biotechnol 14(4):247–254

    Article  Google Scholar 

  • Vernhettes S, Grandbastien MA, Casacuberta JM (1998) The evolutionary analysis of the Tnt1 retrotransposon in Nicotiana species reveals the high variability of its regulatory sequences. Mol Biol Evol 15(7):827–836

    Article  CAS  PubMed  Google Scholar 

  • Vuorinen AL, Kalendar R, Fahima T, Korpelainen H, Nevo E, Shulman AH (2018) Retrotransposon based genetic diversity assessment in wild emmer wheat (Triticum turgidum spp. dicoccoides). Agronomy 8:107

    Article  CAS  Google Scholar 

  • Widyawan MB, Wulandary S, Taryono, (2020) Genetic diversity analysis of yardlong bean genotypes (Vigna unguiculata subsp. sesquipedalis) based on IRAP marker. Biodiversitas 21(3):1101–1107

    Article  Google Scholar 

  • Zanganeh F, Sheidai M (2022) Population genetic diversity and genetic affinity analyses of sweet orange cultivars (Citrus sinensis (L.) Osbeck) by using IRAP molecular markers. Genet Resour Crop Evol 69:2437–2446

    Article  CAS  Google Scholar 

Download references

Acknowledgements

Kerala Agricultural University is gratefully acknowledged for providing facilities for the conduct of the work and ICAR Indian Institute of Spices and Research (IISR), Kozhikode, Kerala for providing plant samples.

Funding

This study was funded by Kerala Agricultural University, Thiruvananthapuram, Kerala, India.

Author information

Authors and Affiliations

  1. Department of Plant Biotechnology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala, 695 522, India

    Manjushri Dinkar Dongare, Swapna Alex, K. B. Soni, K. P. Sindura & Elizabeth Jose

  2. Department of Plantation Crops and Spices, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala, 695 522, India

    Deepa S. Nair

  3. Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala, 695 522, India

    Roy Stephen

Authors
  1. Manjushri Dinkar Dongare
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Swapna Alex
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. K. B. Soni
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. K. P. Sindura
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Deepa S. Nair
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Roy Stephen
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Elizabeth Jose
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Swapna Alex.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest. All the authors have read and approved the manuscript in its final form.

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

Dongare, M.D., Alex, S., Soni, K.B. et al. Cross-species transferability of IRAP retrotransposon markers and polymorphism in black pepper (Piper nigrum L.). Genet Resour Crop Evol 70, 2593–2605 (2023). https://doi.org/10.1007/s10722-023-01590-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-023-01590-z

Keywords

Search

Navigation