Molecular Breeding

, Volume 30, Issue 3, pp 1363–1370 | Cite as

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

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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.

Keywords

Intron length polymorphism Cowpea Vigna Molecular markers ESTs 
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Notes

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.

Supplementary material

11032_2012_9722_MOESM1_ESM.pdf (210 kb)
Supplementary material 1 (PDF 210 kb)

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  1. 1.Nuclear Agriculture and Biotechnology DivisionBhabha Atomic Research CentreTrombayIndia

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