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Genes 2015, 6(4), 1164-1182; doi:10.3390/genes6041164

Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement

1
Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 340-702, Korea
2
National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea
3
Department of Botany, Directorate of Distance Education, Madurai Kamaraj University, Madurai 625 021, India
4
Department of Biological and Environmental Science, Dongguk University, Seoul 100-175, Korea
*
Authors to whom correspondence should be addressed.
Academic Editors: Sean Mayes, Festo Massawe, Prakit Somta and Wai Kuan Ho
Received: 15 April 2015 / Revised: 16 October 2015 / Accepted: 19 October 2015 / Published: 2 November 2015
(This article belongs to the Special Issue Genetic Diversity for Crop Improvement)
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Abstract

The vetch (Vicia sativa) is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra) to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program. View Full-Text
Keywords: 454 pyrosequencing; the vetch (Vicia sativa); transcriptome; SSRs; SNPs 454 pyrosequencing; the vetch (Vicia sativa); transcriptome; SSRs; SNPs
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MDPI and ACS Style

Kim, T.-S.; Raveendar, S.; Suresh, S.; Lee, G.-A.; Lee, J.-R.; Cho, J.-H.; Lee, S.-Y.; Ma, K.-H.; Cho, G.-T.; Chung, J.-W. Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement. Genes 2015, 6, 1164-1182.

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