Skip to main content
SpringerLink
Log in

Development and characterization of genic SSR-FDM for stem gall disease resistance in coriander (Coriandrum sativum L.) and its cross species transferability

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

Abstract

Coriander (Coriandrum sativum L.) is well known vegetable and spice crop grown globally for its leaves and seeds. Stem gall (Protomyces macrosporus L.) is a fungal disease affecting its quality and yield. However, no information is available on SSR markers linked to disease resistance in coriander. Hence, development of co-dominant genetic markers is prerequisite for disease investigations in coriander. In-house stem gall resistance and susceptible cultivars transcriptome data were utilized. Totally, 59,933 and 56,861 transcripts were examined, 9141 and 8346 Simple Sequence Repeats (SSR) were identified and the most abundant type was the tri, followed by di, tetra, penta and hexa nucleotide repeats. A total of ten selected SSR-Functional Domain Markers (FDM) were developed based on functional annotation terms associated with pathogen response and validated among ten coriander cultivars and their transferability was examined in five fennel (Foeniculum vulgare L.) cultivars. Nine primer pairs resulted from amplified bands. Marker ACorSGD-1 shown monomorphic bands among coriander genotypes except Acr-1 showed heterologouse and multiple bands in fennel cultivars. Markers ACorSGD-4, 5, 7 and 9 shown presence in resistant cultivars and absence of bands among susceptible cultivars of coriander and thus, considered to be the candidate markers for disease screening. Marker ACorSGD-6 shown monomorphic bands among coriander. Markers ACorSGD-1, 2, 3, and 5 shown transferability among fennel cultivars. A total of 136 alleles in coriander and fennel were produced. Using UPGMA clustering method a dendrogram was generated and cultivars were grouped into two separate clusters with coriander and fennel. Identified and developed SSR-FDM markers are useful for linkage mapping for disease resistant in coriander.

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

Similar content being viewed by others

Abbreviations

SSR:

Simple sequence repeats

FDM:

Functional domain marker

ACorSGD:

Ajmer coriander stem gall disease

References

  1. Sharma MM, Sharma RK (2004) Coriander. In: Peter KV (ed) Hand book of herbs and spices, vol 2. Woodhead Publishing Limited, Cambridge

    Google Scholar 

  2. Aruna G, Baskaran V (2010) Comparative study on the levels of carotenoids lutein, zeaxanthin and b-carotene in Indian spices of nutritional and medicinal importance. Food Chem 123:404–409

    Article  CAS  Google Scholar 

  3. Choudhary S, Pereira A, Basu S (2014) Effect of cryogenic and conventional grinding on the anti-oxidative potential of coriander and turmeric. Int J Seed Spices 2:85–90

    Google Scholar 

  4. Choudhary S, Pereira A, Basu S, Verma AK (2017) Differential antioxidant composition and potential of some commonly used Indian spices. J Agrisearch 4:160–166

    Google Scholar 

  5. Choudhary S, Jethra G, Sharma R, Verma AK (2017) Microsatellite in coriander: a cross species amplification within Apiaceae family. Int J Curr Microbiol Appl Sci 5:2714–2721

    Article  Google Scholar 

  6. Al-Kordy MA, Abou El-Nasr THS, Sherin AM (2013) Assessing phenotypic and molecular variability in coriander (Coriandrum sativum L.) cultivars. J Appl Sci Res 9:3880–3889

    CAS  Google Scholar 

  7. Singh RK, Verma SS, Meena RS, Kumar R (2013) Characterization of coriander (Coriandrum sativum L.) varieties using SDS-PAGE and RAPD markers. Afr J Biotechnol 12(11):1189–1195

    CAS  Google Scholar 

  8. Choudhary S, Sharma R, Jethra G, Vishal MK, Tripathi A (2019) Molecular diversity in coriander (Coriandrum sativum) using RAPD and ISSR markers. Indian J Agric Sci 89:193–198

    CAS  Google Scholar 

  9. Song X, Wang J, Li N, Ju J, Meng F, Wei C, Liu C, Chen W, Nie F, Zhang Z, Ke G, Li X, Jingjing Hu, Yang Q, Li Y, Li C, Feng S, He G, Yuan J, Pei Q, Tong Yu, Xi K, Zhao W, Lei T, Sun P, Li W, Ge W, Di G, Duan X, Shen S, Cui C, Ying Yu, Xie Y, Zhang J, Hou Y, Wang J, Wang J, Li X-Q, Paterson AH, Wang X (2020) Deciphering the high-quality genome sequence of coriander that causes controversial feelings. Plant Biotechnol J 18:1444–2145

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Song X, Nie F, Ma X, Gong K, Yang Q, Wang J, Li N, Sun P, Pei Q, Yu T, Hu J, Li X, Wu T, Feng S, Li X, Wang X (2020) Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander. Hortic Res 7:55

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Choudhary S, Naika MBN, Sharma R, Meena RD, Singh R, Lal G (2019) Transcriptome profiling of coriander: a dual purpose crop unravels stem gall resistance genes. J Genet 98:19

    Article  PubMed  Google Scholar 

  12. Tulsani NJ, Hamid R, Jacob F, Umretiya NG, Nandha AK, Tomar RS, Golakiya BA (2019) Transcriptome landscaping for gene mining and SSR marker development in coriander (Coriandrum sativum L.). Genomics 112(2):1545–1553

    Article  PubMed  Google Scholar 

  13. Choudhary S, Naika MBN, Meena RD (2020) Identification and expression analysis for candidate genes associated with stem gall disease in Coriander (Coriandrum sativum L.) cultivars. Mol Biol Rep 47:5403–5409

    Article  PubMed  Google Scholar 

  14. Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334

    Article  CAS  Google Scholar 

  15. Saha MC, Mian MA, Eujayl I, Zwonitzer JC, Wang L et al (2004) Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet 109(4):783–791

    Article  PubMed  Google Scholar 

  16. Yu JK, Paik H, Choi JP, Han JH, 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 

  17. Martins WS, Lucas DC, Neves KF, Bertioli DJ (2009) WebSat—a web software for microsatellite marker development. Bioinformation 3(6):282–283

    Article  PubMed  PubMed Central  Google Scholar 

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

    Google Scholar 

  19. Rohlf FJ (1997) NTSYS-pc Version. 2.02i numerical taxonomy and multivariate analysis system. Applied Biostatistics Inc., Exeter Software. Setauket, New York

    Google Scholar 

  20. Khare MN, Tiwari SP, Sharma YK (2017) Disease problems in the cultivation of coriander (Coriandrum sativum L.) and their management leading to production of high quality pathogen free seed. Int J Seed Spices 7:1–7

    Google Scholar 

  21. Jain S (2018) In vitro studies on dual culture of Protomyces macrosporus on Coriandrum sativum. Int Res J Nat Appl Sci 5(4):118–132

    Google Scholar 

  22. López PA, Widrlechner MP, Simon PW, Rai S, Boylston TD, Isbell TA, Bailey TB, Gardner CA, Wilson LA (2008) Assessing phenotypic, biochemical, and molecular diversity in coriander (Coriandrum sativum L.) germplasm. Genet Resour Crop Evol 55:247–275

    Article  Google Scholar 

  23. Pareek N, Jakhar M, Malik C (2017) Analysis of genetic diversity in coriander (Coriandrum sativum L.) varieties using random amplified polymorphic DNA (RAPD) markers. J Microbiol Biotechnol Res 1:206–215

    Google Scholar 

  24. Choudhary S, Jethra G, Sharma R, Verma AK (2017) Microsatellite in coriander: a cross species amplification within Apiaceae family. Int J Curr Microbiol Appl Sci 6:2714–2721

    Article  CAS  Google Scholar 

  25. Gupta S, Shukla R, Roy S, Sen N, Sharma A (2010) In silico SSR and FDM analysis through EST sequences in Ocimum basilicum. POJ 3(4):121–128

    CAS  Google Scholar 

  26. Sahu J, Sarmah R, Dehury B, Sarma K, Sahoo S, Sahu M, Barooah M, Modi MK, Sen P (2012) Mining for SSRs and FDMs from expressed sequence tags of Camellia sinensis. Bioinformation 8(6):260–266

    Article  PubMed  PubMed Central  Google Scholar 

  27. Sorkheh K, Prudencio AS, Ghebinejad A et al (2016) In silico search, characterization and validation of new EST-SSR markers in the genus Prunus. BMC Res Notes 9:336

    Article  PubMed  PubMed Central  Google Scholar 

  28. Ray M, Pradhan SP, Sahoo S (2019) Computational in sight into identification and analysis of SSR-FDM in Citrus limon. Int J Plant Biol Res 7(1):1111

    Google Scholar 

  29. Singh HB, Singh A, Tripathi A, Rai SK, Katiyar RS, Johri JK, Singh SP (2003) Evaluation of coriander germplasms for stem gall disease. Genet Resour Crop Evol 50(4):339–343

    Article  CAS  Google Scholar 

  30. Malhotra SK, Kakani RK, Sharma YK, Singh DK (2016) Ajmer coriander-1 (NRCSS, ACR-1), resistant to stem gall disease—an innovative farming technology. Indian J Arecanut Spices Med Plants 18(3):3–7

    Google Scholar 

  31. Wei K, Chen J, Wang Y, Chen Y, Chen S, Lin Y, Pan S, Zhong X, Xie D (2012) Genome-wide analysis of bZIP-encoding genes in maize. DNA Res 19:463–476

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Häffner E, Konietzki S, Diederichsen E (2015) Keeping control: the role of senescence and development in plant pathogenesis and defense. Plants 4:449–488

    Article  PubMed  PubMed Central  Google Scholar 

  33. Jethra G, Choudhary S, Sharma V (2018) Development and characterization of novel set of polymorphic SSR markers for Dill (Anethum graveolens L.). Ann Plant Sci 7(6):2347–2351

    CAS  Google Scholar 

  34. Jethra G, Choudhary S, Sharma V (2020) Identification and characterization of microsatellite markers in fenugreek: an inter-family amplification. Legume Res 43:611–616

    Google Scholar 

Download references

Acknowledgements

We thank Director, NRCSS for timely support and encouragement during the research work. The research is supported by the ICAR-NRC on Seed Spices, Ajmer, Rajasthan, India. Authors also acknowledge the support received by the UHS, Bagalkot, Karnataka for infrastructure facilities.

Author information

Authors and Affiliations

  1. ICAR-National Research Centre on Seed Spices, Tabiji, Ajmer, Rajasthan, 305 206, India

    Sharda Choudhary & R. D. Meena

  2. Department of Biotechnology and Crop Improvement, K. R. C. College of Horticulture, Arabhavi, University of Horticultural Sciences, Bagalkot, Karnataka, 591 218, India

    Mahantesha B. N. Naika

Authors
  1. Sharda Choudhary
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mahantesha B. N. Naika
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. R. D. Meena
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization and methodology developed: SC, MBNN, Formal analysis and investigation: SC, MBNN and RDM Writing—original draft preparation: MBNN, SC and RDM.

Corresponding author

Correspondence to Mahantesha B. N. Naika.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

Our research does not include Human Participants and/or Animals.

Consent to participate

Our research does not include Human and/or Animals participants.

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 (XLS 2065 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Choudhary, S., Naika, M.B.N. & Meena, R.D. Development and characterization of genic SSR-FDM for stem gall disease resistance in coriander (Coriandrum sativum L.) and its cross species transferability. Mol Biol Rep 48, 3963–3970 (2021). https://doi.org/10.1007/s11033-021-06396-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-021-06396-9

Keywords

Search

Navigation