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

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.