Development of unigene-derived SSR markers in cowpea (Vigna unguiculata) and their transferability to other Vigna species

Gupta, S. K.; Gopalakrishna, T.
July 2010
Genome;Jul2010, Vol. 53 Issue 7, p508
Academic Journal
Unigene sequences available in public databases provide a cost-effective and valuable source for the development of molecular markers. In this study, the identification and development of unigene-based SSR markers in cowpea (Vigna unguiculata (L.) Walp.) is presented. A total of 1071 SSRs were identified in 15 740 cowpea unigene sequences downloaded from the National Center for Biotechnology Information. The most frequent SSR motifs present in the unigenes were trinucleotides (59.7%), followed by dinucleotides (34.8%), pentanucleotides (4%), and tetranucleotides (1.5%). The copy number varied from 6 to 33 for dinucleotide, 5 to 29 for trinucleotide, 5 to 7 for tetranucleotide, and 4 to 6 for pentanucleotide repeats. Primer pairs were successfully designed for 803 SSR motifs and 102 SSR markers were finally characterized and validated. Putative function was assigned to 64.7% of the unigene SSR markers based on significant homology to reported proteins. About 31.7% of the SSRs were present in coding sequences and 68.3% in untranslated regions of the genes. About 87% of the SSRs located in the coding sequences were trinucleotide repeats. Allelic variation at 32 SSR loci produced 98 alleles in 20 cowpea genotypes. The polymorphic information content for the SSR markers varied from 0.10 to 0.83 with an average of 0.53. These unigene SSR markers showed a high rate of transferability (88%) across other Vigna species, thereby expanding their utility. Alignment of unigene sequences with soybean genomic sequences revealed the presence of introns in amplified products of some of the SSR markers. This study presents the distribution of SSRs in the expressed portion of the cowpea genome and is the first report of the development of functional unigene-based SSR markers in cowpea. These SSR markers would play an important role in molecular mapping, comparative genomics, and marker-assisted selection strategies in cowpea and other Vigna species. Les séquences d’unigènes disponibles au sein des banques publiques représentent une source économique et utile pour le développement de marqueurs moléculaires. Dans ce travail, les auteurs rapportent le développement de marqueurs SSR basés sur des unigènes chez le niébé (Vigna unguiculata (L.) Walp.). Au total, 1071 SSR ont été identifiés au sein de 15 740 séquences d’unigènes téléchargées du National Center for Biotechnology Information. Les motifs SSR les plus fréquents au sein des unigènes étaient des trinucléotides (59,7 %), suivis des dinucléotides (34,8 %), des pentanucléotides (4 %) et des tétranucléotides (1,5 %). Le nombre de copies variait entre 6 et 33 chez les dinucléotides, entre 5 et 29 chez les trinucléotides, entre 5 et 7 chez les tétranucléotides et entre 4 et 6 chez les pentanucléotides. Des paires d’amorces ont été conçues pour 803 motifs SSR et 102 marqueurs ont été caractérisés et validés. Une fonction putative a été assignée à 64,7 % des unigènes sur la base d’une homologie significative avec des protéines rapportées. Environ 31,7 % des SSR étaient présents au sein de régions codantes, tandis que 68,3 % étaient situés au sein de régions non-traduites. Environ 87 % des SSR situés dans des régions codantes étaient des trinucléotides. La variation allélique à 32 locus SSR totalisait 98 allèles parmi 20 génotypes de niébé. L’indice PIC pour les marqueurs SSR variait entre 0,10 et 0,83, pour une moyenne de 0,53. Ces SSR dérivés d’unigènes ont affiché une importante transportabilité (88 %) chez d’autres espèces du genre Vigna, ce qui en augmente l’utilité. L’alignement des séquences d’unigènes avec les séquences génomiques du soja a révélé la présence d’introns au sein des amplicons de certains marqueurs SSR. Cette étude présente la distribution des SSR au sein de la portion exprimée du génome du niébé et constitue la première description du développement de marqueurs SSR fonctionnels dérivés d’unigènes chez le niébé. Ces marqueurs SSR pourraient jouer un rôle important dans le cadre de travaux visant la cartographie moléculaire, la génomique comparée et la sélection assistée chez le niébé et d’autres espèces apparentées du genre Vigna.


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