Skip to main content
SpringerLink
Log in

Development of intron length polymorphic (ILP) markers in onion (Allium cepa L.), and their cross-species transferability in garlic (A. sativum L.) and wild relatives

  • Short Communication
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

Onion (Allium cepa L.) is a popular spice and a plant of high medicinal value. Conventional breeding and genetic improvement efforts were largely limited due to self-incompatibility and heterozygosity. Recently, marker assisted breeding has significantly reduced time and labour in developing elite varieties. But very limited polymorphic and cross-transferable markers are available in onion. There is an urgent need to develop polymorphic markers in Allium to expedite and introgress desirable traits from wild relatives (which are rich bioresource of various biotic and abiotic resistance genes) to A. cepa. Considering limited availability of reliable molecular markers in Allium and wild relatives, in current study, 20,204 ESTs (3750 contigs and 8364 singletons), of A. cepa were successfully utilized for identification of over 2689 intron length polymorphic (ILP) markers. A set of 30 markers was tested for polymorphism in onion and cross-transferability in garlic and related wild species. Among these, eighteen markers amplified at least one of the accessions of A. cepa. Transferability of these ILP markers was ranged from 21.7 to 95.7% in Allium spp. Low level of polymorphism in A. cepa compared to wild Allium species is reported. Based on the Jaccard dissimilarity matrix, a neighbour-joining tree was constructed, which clustered all the 23 varieties/accessions under three groups. All the varieties of A. cepa were clearly clustered separately under group I. However, there was intermixing of varieties/accessions of A. sativum L. and wild relatives, which may possibly be due to less number of markers validated for cross-transferability. In future, larger set of markers will be used to resolve the genetic variations among wild varieties and A. sativum These 18 polymorphic ILP markers could be utilised for diversity characterization of Allium spp., varietal identification, mapping of genes and introgression of desirable traits from wild relatives.

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.

Fig. 1

Image source: PIP database: http://ibi.zju.edu.cn/pgl/pip/methodology.html

Fig. 2
Fig. 3

References

  • Araki N, Masuzaki SI, Tsukazaki H, Yaguchi S, Wako T, Tashiro Y, Yamuchi N, Shigyo M (2010) Development of microsatellite markers in cultivated and wild species of section Cepa and Phyllodolon in Allium. Euphytica 173(3):321–328

    Article  CAS  Google Scholar 

  • Bhandawat A, Sharma H, Nag A, Singh S, Ahuja PS, Sharma RK (2015a) Functionally relevant novel microsatellite markers for efficient genotyping in Stevia rebaudiana Bertoni. J Genet 94(1):75–81

    Article  Google Scholar 

  • Bhandawat A, Sharma V, Sharma H, Sood A, Sharma RK (2015b) Development and crosstransferability of functionally relevant microsatellite markers in Dendrocalamus latiflorus and related bamboo species. J Genet 94(1):48–55

    Article  CAS  Google Scholar 

  • Choi HK, Kim D, Uhm T, Limpens E, Lim H, Mun JH, Kalo P, Penmetsa RV, Seres A, Kulikova O, Roe BA, Bisseling T, Kiss GB, Cook DR (2004) A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa. Genetics 166:1463–1502

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Feltus FA, Singh HP, Lohithaswa HC, Schulze SR, Silva TD, Paterson AH (2006) A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol 140:1183–1191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gupta S, Bansal R, Gopalakrishna T (2012) Development of intron length polymorphism markers in cowpea (Vigna unguiculata (L.) Walp.) and their transferability to other Vigna species. Mol Breed 30:1363–1370

    Article  CAS  Google Scholar 

  • Huang M, Xie F, Chen N, Zhao X, Jojee L et al (2010) Comparative analyses of genetic diversity and structure in rice using ILP and SSR markers. Rice Sci 17:257–268. https://doi.org/10.1016/S1672-6308(09)60025-1

    Article  Google Scholar 

  • Jayaswall K, Bhandawat A, Sharma H, Yadav VK, Mahajan V, Singh M (2019) Characterization of Allium germplasms for conservation and sustainable management using SSR markers. Indian J Tradit Knowl 18(1):193–199

    Google Scholar 

  • Karic L, Golzardi M, Glamocliia P, Sutkovic J (2018) Genetic diversity assessment of Allium cepa L. cultivars from Bosnia and Herzegovina using SSR makers. Genet Mol Res 17(1):gmr16039870

    Article  CAS  Google Scholar 

  • King J, Bradeen J, Bark O, McCallum J, Havey M (1998) A low-density genetic map of onion reveals a role for tandem duplication in the evolution of an extremely large diploid genome. Theor Appl Genet 96:52–62. https://doi.org/10.1007/s001220050708

    Article  CAS  Google Scholar 

  • Kuhl JC, Cheung F, Yuan QP, Martin W, Zewdie Y, McCallum J, Catanach A, Rutherford P, Sink KC, Jenderek M, Prince JP, Town CD, Havey MJ (2004) A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. Plant Cell 16:114–125. https://doi.org/10.1105/tpc.017202

    Article  PubMed  PubMed Central  Google Scholar 

  • Le Thierry DM, Panaud O, Robert T, Ricroch A (1997) Assessment of genetic relationships among sexual and asexual forms of Allium cepa using morphological traits and RAPD markers. Heredity 78:403–409

    Article  Google Scholar 

  • Mahajan V, Negi KS, Gupta AJ (2015) Biosystematics, botany and genetic resources. In: Krishna Kumar NK, Gopal J, Parthasarthy VA (eds) The Onion. Indian Council of Agricultural research, New Delhi, pp 30–35

    Google Scholar 

  • Martin WJ, McCallum J, Shigyo M, Jakse J, Kuhl JC, Yamane N, Pither-Joyce M, Gokce AF, Sink KC, Town CD et al (2005) Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity. Mol Genet Genom 274:1–8

    Article  CAS  Google Scholar 

  • Masoudi-Nejad A, Tonomura K, Kawashima S, Moriya Y, Suzuki M, Itoh M, Kanehisa M, Endo T, Goto S (2006) EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res 34((suppl_2)):W459–W462

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mitrová K, Svoboda P, Ovesná J (2015) The selection and validation of a marker set for the differentiation of onion cultivars from the Czech Republic. Czech J Genet Plant Breed 51:62–67

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muthamilarasan M, Suresh BV, Pandey G, Kumari K, Parida SK, Prasad M (2014) Development of 5123 intron-length polymorphic markers for large-scale genotyping applications in foxtail millet. DNA Res 21(1):41–52

    Article  CAS  PubMed  Google Scholar 

  • Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P, Bernard M, Sourdille P (2004) Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet 109(4):800–805

    Article  CAS  PubMed  Google Scholar 

  • Nikhil BSK, Jadhav AS (2017) Characterization of onion genotype using molecular markers. Int J Trop Agric 35:1

    Google Scholar 

  • Perrier X, Jacquemoud-Collet J (2006) DARwin software. http://darwin.cirad.fr/. Accessed Aug 2018.

  • Poczai P, Cernák I, Gorji AM, Nagy S, Taller J, Polgár Z (2010) Development of intron targeting (IT) markers for potato and cross-species amplification in Solanum nigrum (Solanaceae). Am J Bot 97(12):e142–e145

    Article  CAS  PubMed  Google Scholar 

  • Tanikawa T, Takagi M, Ichii M (2002) Cultivar identification and genetic diversity in onion (Allium cepa L.) as evaluated by random amplified polymorphic DNA (RAPD) analysis. J Jpn Soc Hortic Sci 71:249–251

    Article  Google Scholar 

  • Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106(3):411–422

    Article  CAS  PubMed  Google Scholar 

  • Villano C, Esposito S, Carucci F, Iorizzo M, Frusciante L, Carputo D, Aversano R (2019) High-throughput genotyping in onion reveals structure of genetic diversity and informative SNPs useful for molecular breeding. Mol Breed 39(1):5

    Article  CAS  Google Scholar 

  • Wang XS, Zhao XQ, Zhu J, Wu WR (2005) Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.). DNA Res 12:417–427

    Article  CAS  PubMed  Google Scholar 

  • Yang L, Jin G, Zhao X, Zheng Y, Xu Z, Wu W (2007) PIP: a database of potential intron polymorphism markers. Bioinformatics 23(16):2174–2177. https://doi.org/10.1093/bioinformatics/btm296

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

Financial assistance for the research by Indian Council of Agricultural Research is gratefully acknowledged.

Author information

Author notes

  1. Kuldip Jayaswall, Himanshu Sharma, and Abhishek Bhandawat contributed equally to this work.

Authors and Affiliations

  1. ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, Maharashtra, India

    Kuldip Jayaswall, Vijay Mahajan & Major Singh

  2. Agri-Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, India

    Himanshu Sharma, Abhishek Bhandawat & Joy Roy

  3. Department of Botany, Banaras Hindu University, Varanasi, India

    Ram Sagar & Vinod Kumar Yadav

  4. Sant Baba Bhag Singh University, Jalandhar, Punjab, India

    Vikas Sharma

Authors
  1. Kuldip Jayaswall
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Himanshu Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Abhishek Bhandawat
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ram Sagar
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Vinod Kumar Yadav
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Vikas Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Vijay Mahajan
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Joy Roy
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Major Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kuldip Jayaswall.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

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

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jayaswall, K., Sharma, H., Bhandawat, A. et al. Development of intron length polymorphic (ILP) markers in onion (Allium cepa L.), and their cross-species transferability in garlic (A. sativum L.) and wild relatives. Genet Resour Crop Evol 66, 1379–1388 (2019). https://doi.org/10.1007/s10722-019-00808-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-019-00808-3

Keywords

Search

Navigation