Development of 65 novel polymorphic cDNA-SSR markers in common vetch (Vicia sativa subsp. sativa) using next generation sequencing

Molecules

Volumn 18, Issue 7, 2013, Pages 8376-8392

  Chung, Jong Wook ^a   Kim, Tae Sung ^b   Suresh, Sundan ^a   Lee, Sok Young ^a   Cho, Gyu Taek ^a  

^a National Institute of Animal Science   (South Korea)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

454 sequencing; CDNA SSR; Genetic diversity; Vicia stiva subsp. Sativa

Indexed keywords

COMPLEMENTARY DNA; GENETIC MARKER; MICROSATELLITE DNA;

ALLELE; COMMON VETCH; DNA SEQUENCE; GENETIC MARKER; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; NUCLEOTIDE SEQUENCE; ARTICLE;

ALLELES; BASE SEQUENCE; DNA, COMPLEMENTARY; GENETIC MARKERS; GENETIC VARIATION; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROSATELLITE REPEATS; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; VICIA SATIVA;

EID: 84880842598     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules18078376     Document Type: Article

References (27)

1. Hueze, V.; Tran, G.; Baumont, R. Common vetch (Vicia sativa). Feedipedia 2011, 12, 53-62.
2. Sullivan, P. Overview of cover crops and green manures. ATTRA 2003, 1-16.
3. Tate, M.; Ennenking, D. Common vetch (Vicia sativa ssp. sativa): Feed or future food. Grain Legumes 2006, 16-17.
4. Tate, M.E.; Enneking, D. A mess of red pottage. Nature 1992, 359, 357-358.
5. Tate, M.E.; Rathjen, J.; Delaere, I.; Enneking, D. Covert trade in toxic vetch continues. Nature 1999, 400, 207-207.
6. Thavarajah, P.; Thavarajah, D.; Premakumara, G.A.; Vandenberg, A. Detection of Common Vetch (Vicia sativa L.) in Lentil (Lens culinaris L.) using unique chemical fingerprint markers. Food Chem. 2012, 135, 2203-2206.
7. Uzun, A.; Gucer, S.; Acikgoz, E. Common vetch (Vicia sativa L.) germplasm: correlations of crude protein and mineral content to seed traits. Plant Foods Hum. Nutr. 2011, 66, 254-260.
8. Firincioglu, H.K.; Unal, S.; Erberkas, E.; Dogruyol, L. Relationships between seed yield and yield components in common vetch (Vicia sativa ssp. sativa) populations sown in spring and autumn in central Turkey. Field Crop. Res. 2010, 116, 30-37.
9. Firincioglu, H.K.; Erbektas, E.; Dogruyol, L.; Mutlu, Z.; Unal, S.; Karakurt, E. Phenotypic variation in autumn and spring-sown vetch (Vicia sativa ssp.) populations in central Turkey. Span. J. Agric. Res. 2009, 7, 596-606.
10. Mutz, K.O.; Heilkenbrinker, A.; Lonne, M.; Walter, J.G.; Stahl, F. Transcriptome analysis using next-generation sequencing. Curr. Opin. Biotechnol. 2012, 24, 22-30.
11. Ronaghi, M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 2001, 11, 3-11.
12. Varshney, R.K.; Close, T.J.; Singh, N.K.; Hoisington, D.A.; Cook, D.R. Orphan legume crops enter the genomics era! Curr. Opin. Plant Biol. 2009, 12, 202-210.
13. Luro, F.L.; Costantino, G.; Terol, J.; Argout, X.; Allario, T.; Wincker, P.; Talon, M.; Ollitrault, P.; Morillon, R. Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics 2008, 9, 287-310.
14. Kim, T.S.; Booth, J.G.; Gauch, H.G., Jr.; Sun. Q.; Park. J.; Lee, Y.H.; Lee, K.G. Simple sequence repeats in Neurospora crassa: Distribution, Polymorphism and evolutionary inference. BMC Genomics 2008, 9, 31-48.
15. Wang, Z.; Fang, B.; Chen, J.; Zhang, X.; Luo, Z.; Huang, L.; Chen, X.; Li, Y. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genomics 2010, 11, 726-739.
16. Blanca, J.; Canizares, J.; Roig, C.; Ziarsolo, P.; Nuez, F.; Pico, B. Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics 2011, 12, 104-119.
17. Moe, K.T.; Chung, J.W.; Cho, Y.I, Moon, J.K.; Ku, J.H.; Jung, J.K.; Lee, J.; Park, Y.J. Sequence information on simple sequence repeats and single nucleotide polymorphisms through transcriptome analysis of mungbean. J. Integr. Plant Biol. 2011, 53, 63-73.
18. Kaur, S.; Pembleton, L.W.; Cogan, N.O.; Savin, K.W.; Leonforte, T.; Paull. J.; Materne, M.; Forster, J.W. Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers. BMC Genomics 2012, 13, 104-116.
19. Tanase, K.; Nishitani, C.; Hirakawa, H.; Isobe, S.; Tabata, S.; Ohmiya, A.; Onozaki, T. Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology. BMC Genomics 2012, 13, 292-303.
20. Yang , T.; Bao, S.Y.; Ford, R.; Jia, T.J.; Guan, J.P.; He, Y.H.; Sun X.L.; Jiang, Hao, J.; Zhang, X.; Zong, X. High-throughput novel microsatellite marker of faba bean via next generation sequencing. BMC Genomics 2012, 13, 602-613.
21. Dangi, R.S.; Lagu, M.D.; Choudhary, L.B.; Ranjekar, P.K.; Gupta, V.S. Assessment of genetic diversity in Trigonella foenum-graecum and Trigonella caerulea using ISSR and RAPD markers. BMC Plant Biol. 2004, 4, 13-24.
22. Elahi, E.; Ronaghi, M. Pyrosequencing: a tool for DNA sequencing analysis. Methods Mol. Biol. 2004, 255, 211-219.
23. Margulies, M.; Egholm, M.; Altman, W.E.; Attiya, S.; Bader, J.S.; Bemben, LA.; Berka, J.; Braverman, MS.; Chen, Y.J.; Chen, Z.; et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437, 376-380.
24. Riley, M. Functions of the gene products of Escherichia coli. Microbiol. Mol. Biol. Rev. 1993, 57, 862-952.
25. Peakall, R.; Smouse, P.E. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 2012, 28, 2537-2539.
26. Botstein, D.; White, R.L.; Skolnick, M.; Davis, R.W.; Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 1980, 32, 314-331
27. Cavalli-Sforza, L.L.; Edwards, A.W.F.; 1967. Phylogenetic Analysis: Models and Estimation Procedures. Am. J. Hum. Genet. 1967, 19, 233-257.