Skip to main content
Springer Nature Link
Log in

Multi-locus DNA fingerprinting and genetic diversity in jute (Corchorus spp.) based on sequence-related amplified polymorphism

  • Original Article
  • Published:
Journal of Plant Biochemistry and Biotechnology Aims and scope Submit manuscript

Abstract

Sequence-Related Amplified Polymorphism (SRAP) markers were used for genetic diversity assessment and cultivar identification among 31 cultivars of jute belonging to two cultivated species Corchours olitorius L. and C. capsularis L. Forty-three primer-pairs produced a total of 394 bands with an average of 9 bands per primer pair and 89% bands were polymorphic across the genotypes of two species. Average genetic diversity in the cultivars of C. olitorius and C. capsularis was 7.2% (range 2.8–12.3%) and 7.6% (range 2.2–13.1%), respectively. Jute cultivars JRC 698, JRC 7447, TJ 40, S19 and JRO 3690 were more diverse compared to rest of the cultivars. UPGMA cluster analysis grouped all cultivars into two clusters which were representative of C. olitorius and C. capsularis species. All the cultivars could be unequivocally differentiated from one another based on the pooled profile of 43 primer-pairs, however, 24 of 31 cultivars could be identified uniquely. The probability of chance identity of any two cultivars based on SRAP markers was very low and was 6.95 × 10−07 and 2.23 × 10−07 for cultivars of C. capsularis and C. olitorius, respectively. Primer-pairs EM1-ME5, EM4-ME1, EM8-ME1 and EM10-ME1 were found to be useful for genetic diversity and cultivar identification. Our results show that SRAP markers could be effectively used for genetic diversity analyses in jute. For poor genetic diversity and resulting narrow genetic base, these markers will prove to be highly useful for identifying elite germplasm in a jute breeding program.

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+
from $39.99 /Month
  • Starting from 10 chapters or articles per month
  • Access and download chapters and articles from more than 300k books and 2,500 journals
  • Cancel anytime
View plans

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

Explore related subjects

Discover the latest articles and news from researchers in related subjects, suggested using machine learning.

Abbreviations

AFLP:

Amplified fragment length polymorphism

CTAB:

Cetyltrimethylammonium bromide

ISSR:

Inter-simple sequence repeats

PIC:

Polymorphism information content

RAPD:

Random amplified polymorphic DNA

SRAP:

Sequence related amplified polymorphism

SSR:

Simple sequence repeat

UPGMA:

Unweighted pair group method for arithmetic means

References

  • Akter J, Islam MS, Sajib AA, Ashraf N, Haque S, Khan K (2008) Microsatellite markers for determining genetic identities and genetic diversity among jute cultivars. Austral J Crop Sci 1:97–107

    CAS  Google Scholar 

  • Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimising parental selection for genetic linkage maps. Genome 36:181–186

    Article  PubMed  CAS  Google Scholar 

  • Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560. doi:10.1016/j.tplants.2003.09.010

    Article  PubMed  CAS  Google Scholar 

  • Basu A, Ghosh M, Meyer R, Powell W, Basak SL, Sen SK (2004) Analysis of genetic diversity in cultivated jute determined by means of SSR markers and AFLP profiling. Crop Sci 44:678–685

    Article  CAS  Google Scholar 

  • Blair MW, Panaud O, McCouch SR (1999) Intersimple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.). Theor Appl Genet 98:780–792

    Article  CAS  Google Scholar 

  • Das M, Banerjee S, Topdar N, Kundu A, Sakrar D, Sinha MK, Balyan HS, Gupta PK (2011) Development of large scale AFLP markers in jute. J Plant Biochem Biotechnol 20:270–275

    Article  Google Scholar 

  • Gupta PK, Rustgi S (2004) Molecular markers from the transcribed/expressed region of the genome in higher plants. Func Integr Genomics 4:139–162

    Article  CAS  Google Scholar 

  • Hossain M, Hossain F (2002) Breeding for photo-period insensitivity and fibre yield in capsularis jute (Corchorus capsularis L.). Indian J Genet 62:240–241

    Google Scholar 

  • Jaccard P (1908) Nouvelles recherchés sur la distribution florale. Bull Soc Vaud Sci Nat 44:223–270

    Google Scholar 

  • Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461

    Article  CAS  Google Scholar 

  • Li H, Chen H, Zhuang T, Chen J (2010) Analysis of genetic variation in eggplant and related Solanum species using sequence-related amplified polymorphism markers. Sci Hort 125:19–24

    Article  CAS  Google Scholar 

  • Mir RR, Banerjee S, Das M, Gupta V, Tyagi AK, Sinha MK, Balyan HS, Gupta PK (2009) Development and characterization of large-scale simple sequence repeats in jute. Crop Sci 49:1687–1694

    Article  CAS  Google Scholar 

  • Mir RR, Sachin R, Shailendra S, Ravinder S, Aakash G, Jitendra K, Anupama G, Tyagi AK, Haseena K, Sinha MK, Balyan HS, Gupta PK (2008) A preliminary genetic analysis of fibre traits and the use of new genomic SSRs for genetic diversity in jute. Euphytica 161:413–427

    Article  CAS  Google Scholar 

  • Qi J, Zhou D, Wu W, Lin L, Fang P, Wu J (2003a) The application of RAPD technology in genetic diversity detection of Jute. Ying Yong Sheng Tai Xue Bao 30:926–932

    CAS  Google Scholar 

  • Qi J, Zhou D, Wu W, Lin L, Wu J, Fang P (2003b) Application of ISSR technology in genetic diversity detection of jute. Ying Yong Sheng Tai Xue Bao 14:1473–1477

    PubMed  CAS  Google Scholar 

  • Ramakrishana W, Lagu MD, Gupta VS, Ranjekar PK (1994) DNA fingerprinting in rice using oligonucleotide probes specific for simple repetitive DNA sequences. Theor Appl Genet 88:402–406

    Google Scholar 

  • Rana MK, Singh S, Bhat KV (2009) Fingerprinting Indian lentil (Lens culinaris ssp. culinaris Medik.) cultivars and landraces for diversity analysis using Sequence-Related Amplified Polymorphism (SRAP) markers. In: Kharkwal MC (eds) Proceedings of Fourth International Food and Legumes Research Conference, New Delhi, pp 617-624.

  • Riaz A, Li G, Quresh Z, Swati MS, Quiros CF (2001) Genetic diversity of oilseed Brassica napus inbred lines based on sequence-related amplified polymorphism and its relation to hybrid performance. Plant Breed 120:411–415

    Article  CAS  Google Scholar 

  • Rohlf FJ (2004) NTSYS-pc Numerical Taxonomy and Multivariate Analysis System, 2.11V. Exeter Software, Setauket, New York

    Google Scholar 

  • Roy A, Bandyopadhyay A, Mahapatra AK, Ghosh SK, Singh NK, Bansal KC, Koundal KR, Mohapatra T (2006) Evaluation of genetic diversity in jute (Corchorus species) using STMS, ISSR and RAPD markers. Plant Breed 125:292–297

    Article  CAS  Google Scholar 

  • Ruiz JJ, García-Martínez S, Picó B, Gao MQ, Quiros CF (2005) Genetic variability and relationship of closely related Spanish traditional cultivars of tomato as detected by SRAP and SSR markers. J Am Soc Hort Sci 130:88–94

    CAS  Google Scholar 

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphism in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Nat Acad Sci USA 81:8014–8018

    Article  PubMed  CAS  Google Scholar 

  • Smutkupt S, Peyachoknagul S, Kowitwanich K, Onto S, Thanananta N, Julsrigival S, Kunkaew W, Punsupa V (2006) Varietal determination and genetic relationship analysis of highland legumes using SRAP markers. SABRAO J Breed Genet 38:19–27

    Google Scholar 

  • Uzun A, Yesiloglu T, Aka-Kacar Y, Tuzcu O, Gulsen O (2009) Genetic diversity and relationships within Citrus and related genera based on sequence related amplified polymorphism markers (SRAPs). Sci Hort 121:306–312

    Article  CAS  Google Scholar 

  • Vos P, Hogers R, Blecker M, Reijans M, Lee TVD, Homes M, Frijters A, Pot L, Peleman I, Kuiper M, Zabeau M (1995) AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  PubMed  CAS  Google Scholar 

  • Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218

    Article  PubMed  CAS  Google Scholar 

  • Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535. doi:10.1093/nar/18.22.6531

    Article  PubMed  CAS  Google Scholar 

  • Xu M, Jin Z, Li X, Zhang Z, Liu H, Zhang F, Zhao S, Zhang H (2009) Comparison of genetic distance among seven cultivars of japonica rice based on SSR and SRAP and its relationship with heterosis of yield traits. Mol Plant Breed 7:1084–1092

    CAS  Google Scholar 

  • Yang P, Liu X, Liu X, Yang W, Feng Z (2010) Diversity analysis of the developed qingke (hulless barley) cultivars representing different growing regions of the Qinghai-Tibet Plateau in China using sequence-related amplified polymorphism (SRAP) markers. African J Biotechnol 9:8530–8538

    CAS  Google Scholar 

  • Youssef M, James AC, Rivera-Madrid R, Ortiz R, Escobedo-Graciamedrano RM (2011) Musa genetic diversity revealed by SRAP and AFLP. Mol Biotechnol 47:189–199

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

Authors are grateful to the Indian Council of Agricultural Research for financial support. We are also thankful to Director, National Bureau of Plant Genetic Resources.

Author information

Authors and Affiliations

  1. National Research Centre on DNA Fingerprinting, National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110 012, India

    M. K. Rana, Kashika Arora, Sonika Singh & Amit Kumar Singh

Authors
  1. M. K. Rana
    View author publications

    Search author on:PubMed Google Scholar

  2. Kashika Arora
    View author publications

    Search author on:PubMed Google Scholar

  3. Sonika Singh
    View author publications

    Search author on:PubMed Google Scholar

  4. Amit Kumar Singh
    View author publications

    Search author on:PubMed Google Scholar

Corresponding author

Correspondence to M. K. Rana.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rana, M.K., Arora, K., Singh, S. et al. Multi-locus DNA fingerprinting and genetic diversity in jute (Corchorus spp.) based on sequence-related amplified polymorphism. J. Plant Biochem. Biotechnol. 22, 1–8 (2013). https://doi.org/10.1007/s13562-012-0104-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13562-012-0104-7

Keywords