Skip to main content
Log in

Development of intron length polymorphism markers in cowpea [Vigna unguiculata (L.) Walp.] and their transferability to other Vigna species

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Expressed sequence tag (EST) sequences available in the public databases provide a cost-effective and valuable genomic resource for the development of molecular markers. Introns which are non-coding DNA sequences of the gene could be used as potential molecular markers as they are highly variable compared to the coding sequences. This study reports the development of intron length polymorphism markers in cowpea [Vigna unguiculata (L.) Walp.]. The ESTs of cowpea were aligned with genomic sequences of Arabidopsis and soybean to predict the position and number of introns in cowpea. Of the 110 PCR primer pairs designed to amplify the intronic regions, 98 primer pairs resulted in successful amplification and were identified as cowpea intron length polymorphism (CILP) markers. Out of the 45 randomly selected CILP markers, 36 % markers produced length variation in the ten cowpea genotypes, collectively yielding 33 alleles with an average of 2.0 alleles/locus. The polymorphism information content of the CILP markers ranged from 0.18 to 0.64 with an average of 0.34. Of the 98 CILP markers, 93 markers (95 %) showed transferability to other Vigna species. Dendrograms based on CILP markers clearly distinguished the cowpea genotypes as well as other Vigna species, demonstrating the utility of CILP markers in genetic diversity and phylogenetic studies. These CILP markers will be very useful in the genome analysis and marker-assisted breeding of cowpea and other Vigna species.

This is a preview of subscription content, log in via an institution to check access.

Access this article

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

Similar content being viewed by others

References

  • Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186. doi:10.1139/g93-024

    Article  PubMed  CAS  Google Scholar 

  • Bartolomé C, Maside X, Charlesworth B (2002) On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. Mol Biol Evol 19:926–937

    Article  PubMed  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

    PubMed  CAS  Google Scholar 

  • Carmel L, Wolf YI, Rogozin IB, Koonin EV (2007) Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res 17:1034–1044. doi:10.1101/gr.6438607

    Article  PubMed  CAS  Google Scholar 

  • Choi HK, Kim DJ, Uhm T, Limpens E, Lim H, Mun J-H, 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. doi:10.1534/genetics.166.3.1463

    Article  PubMed  CAS  Google Scholar 

  • Fatokun CA, Danesh D, Young ND, Stewart EL (1993) Molecular taxonomic relationships in the genus Vigna based on RFLP analysis. Theor Appl Genet 86:97–104. doi:10.1007/BF00223813

    Article  CAS  Google Scholar 

  • Gupta SK, Gopalakrishna T (2010) Development of unigene-derived SSR markers in cowpea (Vigna unguiculata) and their transferability to other Vigna species. Genome 53:508–523. doi:10.1139/G10-028

    Article  PubMed  CAS  Google Scholar 

  • Gupta S, Kumari K, Das J, Lata C, Puranik S, Prasad M (2011) Development and utilization of novel intron length polymorphic markers in foxtail millet [Setaria italica (L.) P. Beauv.]. Genome 54:586–602. doi:10.1139/g11-020

    Article  PubMed  CAS  Google Scholar 

  • Holland JB, Helland SJ, Sharopova N, Rhyne DC (2001) Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat. Genome 44:1065–1076. doi:10.1139/g01-110

    Article  PubMed  CAS  Google Scholar 

  • Huang M, Xie F-M, Chen L-Y, Zhao X-Q, Jojee L, Madonna D (2010) Comparative analysis of genetic diversity and structure in rice using ILP and SSR markers. Rice Sci 17:257–268. doi:10.1016/S1672-6308(09)60025-1

    Article  Google Scholar 

  • Liang C, Liu L, Ji G (2009) WebGMAP: a web service for mapping and aligning cDNA sequences to genomes. Nucleic Acids Res 37:W77–W83. doi:10.1093/nar/gkp389

    Article  PubMed  CAS  Google Scholar 

  • Marechal R, Mascherpa JM, Stainer F (1978) Etude taxonomique d’un groupe complexe d’espèces des genres Phaseolus et Vigna (Papilionaceae) sur la base de données morphologiques et polliniques, traitées par l’analyse informatique. Boissiera 28:1–273

    Google Scholar 

  • Petrov DA, Sangster TA, Johnston JS, Hartl DL, Shaw KL (2000) Evidence for DNA loss as a determinant of genome size. Science 287:1060–1062. doi:10.1126/science.287.5455.1060

    Article  PubMed  CAS  Google Scholar 

  • Rohlf FJ (1998) NTSYS-Pc: numerical taxonomy and multivariate analysis system, version 2.0. Exeter publications, Setauket

  • Roy SW (2006) Intron-rich ancestors. Trends Genet 22:468–471. doi:10.1016/j.tig.2006.07.002

    Article  PubMed  CAS  Google Scholar 

  • Shu Y, Li Y, Zhu Y, Zhu Z, Lv D, Bai X, Cai H, Ji W, Guo D (2010) Genome-wide identification of intron fragment insertion mutations and their potential use as SCAR molecular markers in the soybean. Theor Appl Genet 121:1–8. doi:10.1007/s00122-010-1285-x

    Article  PubMed  CAS  Google Scholar 

  • Tautz D, Renz P (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genome. Nucleic Acids Res 12:4127–4138. doi:10.1093/nar/12.10.4127

    Article  PubMed  CAS  Google Scholar 

  • Verdcourt B (1970) Studies in the Leguminosae-Papilionoidae for the ‘Flora of Tropical East Africa: IV’. Kew Bull 24:507–569. doi:10.2307/4102859

    Article  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414. doi:10.1093/nar/23.21.4407

    Article  PubMed  CAS  Google Scholar 

  • Wang X, Zhao X, Zhu J, Wu W (2005) Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.). DNA Res 12:417–427. doi:10.1093/dnares/dsi019

    Article  PubMed  CAS  Google Scholar 

  • Wang ML, Barkley NA, Gillaspie GA, Pederson GA (2008) Phylogenetic relationships and genetic diversity of the USDA Vigna germplasm collection revealed by gene-derived markers and sequencing. Genet Res 90:467–480. doi:10.1017/S0016672308009889

    Article  CAS  Google Scholar 

  • Wang Y, Chen J, Francis DM, Shen H, Wu T, Yang W (2010) Discovery of intron polymorphisms in cultivated tomato using both tomato and Arabidopsis genomic information. Theor Appl Genet 121:1199–1207. doi:10.1007/s00122-010-1381-y

    Article  PubMed  CAS  Google Scholar 

  • Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218. doi:10.1093/nqr/18.24.7213

    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 

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

    Article  PubMed  CAS  Google Scholar 

  • Zhao X, Yang L, Zheng Y, Xu Z, Wu W (2009) Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice (Oryza rufipogon L.) in relation to the domestication of cultivated rice (O. sativa L.). J Genet Genomics 36:435–442. doi:10.1016/S1673-8527(08)60133-2

    Article  PubMed  CAS  Google Scholar 

  • Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183. doi:10.1006/geno.1994.1151

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors thank AVRDC, Taiwan and NBPGR, India for providing the seed material of various Vigna species, and also Mr. P. Dhanasekar, NABTD, BARC and Dr. N. Nadarajan, TNAU, India for providing the seed material.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to S. K. Gupta.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 210 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gupta, S.K., Bansal, R. & Gopalakrishna, T. Development of intron length polymorphism markers in cowpea [Vigna unguiculata (L.) Walp.] and their transferability to other Vigna species. Mol Breeding 30, 1363–1370 (2012). https://doi.org/10.1007/s11032-012-9722-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11032-012-9722-y

Keywords

Navigation