Transcriptome characterization and large-scale identification of ssr/snp markers in symbiotic nitrogen fixation crop faba bean (Vicia faba l.)

Turkish Journal of Agriculture and Forestry

Volumn 39, Issue 3, 2015, Pages 459-469

  Suresh, Sundan ^a,b   Kim, Tae Sung ^c   Raveendar, Sebastin ^a   Cho, Joon Hyeong ^d   Yi, Jung Yoon ^a   Lee, Myung Chul ^a   Lee, Sok Young ^a   Baek, Hyung Jin ^a   Cho, Gyu Taek ^a   Chung, Jong Wook ^a  

^a National Institute of Animal Science   (South Korea)

^b MADURAI KAMARAJ UNIVERSITY   (India)

^c Kongju National University   (South Korea)

^d Dongguk University   (South Korea)

Author keywords

454 pyrosequencing; Gene ontology; Molecular marker; Transcriptome analysis

Indexed keywords

CROPS; DNA SEQUENCES; GENES; NUCLEOTIDES;

454-PYROSEQUENCING; GENE ONTOLOGY; MOLECULAR MARKER; SEQUENCE ASSEMBLIES; SIMPLE SEQUENCE REPEATS; SINGLE-NUCLEOTIDE POLYMORPHISMS; SYMBIOTIC NITROGEN FIXATION; TRANSCRIPTOME ANALYSIS;

NITROGEN FIXATION;

CROP PLANT; GENE EXPRESSION; GENETIC MARKER; GENOMICS; LEGUME; NITROGEN FIXATION;

VICIA FABA;

EID: 84930448800     PISSN: 1300011X     EISSN: 13036173     Source Type: Journal    
DOI: 10.3906/tar-1409-3     Document Type: Article

References (49)

1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al. (2000). Gene Ontology: tool for the unification of biology. Nat Genet 25: 25–29.
2. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007). SNP discovery via 454 transcriptome sequencing. Plant J 51: 910–918.
3. Barrero RA, Chapman B, Yang YF, Moolhuijzen P, Keeble-Gagnere G, Zhang N, Tang Q, Bellgard MI, Qiu DY (2011). De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes. BMC Genomics 12: 600.
4. Blair M, Buendia HF, Giraldo M, Metais I, Peltier D (2008). Characterization of AT-rich microsatellites in common bean (Phaseolus vulgaris L.). Theor Appl Genet 118: 91–103.
5. Blair MW, Torres MM, Giraldo MC, Pedraza F (2009). Development and diversity of Andean-derived, gene-based microsatellites for common bean (Phaseolus vulgaris L.). BMC Plant Biol 9: 100.
6. Blanca J, Canizares J, Roig C, Ziarsolo P, Nuez F, Pico B (2011). Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics 12: 104.
7. Bond DA (1983). Pollination. In: Hebblethwaite PD, editor. The Faba Bean (Vicia faba L.). London, UK: Butterworths, pp. 77–101.
8. Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T et al. (2006). Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. P Natl Acad Sci USA 103: 14959–14964.
9. Cheung F, Win J, Lang JM, Hamilton J, Vuong H, Leach JE, Kamoun S, Levesque CA, Tisserat N, Buell CR (2008). Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches. BMC Genomics 9: 542.
10. Chung JW, Kim TS, Suresh S, Lee SY, Cho GT (2013). Development of 65 novel polymorphic cDNA-SSR markers in common vetch (Vicia sativa subsp. sativa) using next generation sequencing. Molecules 18: 8376–8392
11. Doyle JJ, Luckow MA (2003). The rest of the iceberg. Legume diversity and evolution in a phylogenetic context. Plant Physiol 131: 900–910.
12. Duc G, Bao SY, Baum M, Redden B, Sadiki M, Suso MJ, Vishniakova M, Zong XX (2010). Diversity maintenance and use of Vicia faba L. genetic resources. Field Crop Res 115: 270–278.
13. Elahi E, Ronaghi M (2004). Pyrosequencing: a tool for DNA sequencing analysis. Methods Mol Biol 255: 211–219.
14. Gaitan-Solis E, Duque MC, Edwards KJ, Tohme J (2002). Microsatellite repeats in common bean (Phaseolus vulgaris): isolation, characterization, and cross-species amplification in Phaseolus ssp. Crop Sci 42: 2128–2136.
15. Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT et al. (2011). Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: 419–423.
16. Gohin M, Bobe J, Chesnel F (2010). Comparative transcriptomic analysis of follicle-enclosed oocyte maturational and developmental competence acquisition in two non-mammalian vertebrates. BMC Genomics 11: 18.
17. Gonzalez-Ibeas D, Blanca J, Roig C, Gonzalez-To M, Pico B, Truniger V, Gomez P, Deleu W, Cano-Delgado A, Arus P et al. (2007). MELOGEN: an EST database for melon functional genomics. BMC Genomics 8: 306.
18. Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, Lin C, Holoch D, Lim C, Tuschl T (2008). Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 44: 3–12.
19. Hanai LR, de Campos T, Camargo LEA, Benchimol LL, de Souza AP, Melotto M, Carbonell SAM, Chioratto AF, Consoli L, Formighieri EF et al. (2007). Development, characterization, and comparative analysis of polymorphism at common bean SSR loci isolated from genic and genomic sources. Genome 50: 266–277.
20. Kaur S, Cogan NOI, Pembleton LW, Shinozuka M, Savin KW, Materne M, Forster JW (2011). Transcriptome sequencing of lentil based on second-generation technology permits largescale unigene assembly and SSR marker discovery. BMC Genomics 12: 265.
21. Kaur S, Pembleton LW, Cogan NOI, Savin KW, Leonforte T, Paull J, Materne M, Forster JW (2012). Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers. BMC Genomics 13: 104.
22. Kim D (2004). Developing one step program (SSR manager) for rapid identification of clones with SSRs and primer designing. Thesis, Seoul National University, Seoul, Republic of Korea.
23. Kristiansson E, Asker N, Forlin L, Larsson DGJ (2009). Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing. BMC Genomics 10: 345.
24. Li DJ, Deng Z, Qin B, Liu XH, Men ZH (2012). De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubbertree (Hevea brasiliensis Muell. Arg.). BMC Genomics 13: 192.
25. Li YC, Korol AB, Fahima T, Nevo E (2004). Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21: 991–1007.
26. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P (2003). The power and promise of population genomics: from genotyping to genome typing. Nat Rev Genet 4: 981–994.
27. Ma KH, Kim KH, Dixit A, Chung IM, Gwag JG, Kim TS, Park YJ (2010). Assessment of genetic diversity and relationshipsamong Coix lacryma-jobi accessions using microsatellite markers. Biol Plantarum 54: 272–278.
28. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376–380.
29. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV (2009). Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 10: 219.
30. Michelmore RW, Paran I, Kesseli RV (1991). Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. P Natl Acad Sci USA 88: 9828–9832.
31. Novaes E, Drost D, Farmerie W, Pappas G Jr, Grattapaglia D, Sederoff R, Kirst M (2008). High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9: 132.
32. Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA (2010). Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 11: 180.
33. Pozarkova D, Koblizkova A, Roman B, Torres AM, Lucretti S, Lysak M, Dolezel J, Macas J (2002). Development and characterization of microsatellite markers from chromosome 1-specific DNAlibraries of Vicia faba. Biol Plantarum 45: 337–345.
34. Riley M (1993). Functions of the gene-products of Escherichia coli. Microbiol Rev 57: 862–952.
35. Ronaghi M (2001). Pyrosequencing sheds light on DNA sequencing. Genome Res 11: 3–11.
36. Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Guldener U, Mannhaupt G, Munsterkotter M et al. (2004). The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes Nucleic Acids Res 32: 5539–5545.
37. Serres MH, Riley M (2000). MultiFun, a multifunctional classificationscheme for Escherichia coli K-12 gene products. Microb CompGenomics 5: 205–222.
38. Sjödin J (1971). Induced morphological variation in Vicia faba L. Hereditas 67: 155–179.
39. Terzopoulos PJ, Bebeli PJ (2008). Genetic diversity analysis ofMediterranean faba bean (Vicia faba L.) with ISSR markers.Field Crop Res 108: 39–44.
40. Varshney RK, Close TJ, Singh NK, Hoisington DA, Cook DR (2009).Orphan legume crops enter the genomics era! Curr Opin PlantBiol 12: 202–210.
41. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, CrawfordDL, Hanski I, Marden JH (2008). Rapid transcriptomecharacterization for a nonmodel organism using 454pyrosequencing. Mol Ecol 17: 1636–1647.
42. Weber APM, Weber KL, Carr K, Wilkerson C, Ohlrogge JB (2007).Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 144: 32–42.
43. Wheat CW (2010). Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing.Genetica 138: 433–451.
44. Wicker T, Schlagenhauf E, Graner A, Close TJ, Keller B, Stein N(2006). 454 sequencing put to the test using the complexgenome of barley. BMC Genomics 7: 245.
45. Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, Roe BA, Tabata S (2005). Sequencing the genespaces of Medicago truncatula and Lotus japonicus. Plant Physiol 137: 1174–1181.
46. Young ND, Mudge J, Ellis TH (2003). Legume genomes: more than peas in a pod. Curr Opin Plant Biol 6: 199–204.
47. Zagrobelny M, Scheibye-Alsing K, Jensen NB, Moller BL, GorodkinJ, Bak S (2009). 454 pyrosequencing based transcriptome analysis of Zygaena filipendulae with focus on genes involvedin biosynthesis of cyanogenic glucosides. BMC Genomics 10: 574.
48. Zeid M, Mitchell S, Link W, Carter M, Nawar A, Fulton T, Kresovich S (2009). Simple sequence repeats (SSRs) in faba bean: new loci from Orobanche-resistant cultivar ‘Giza 402’. Plant Breeding 128: 149–155.
49. Zhu H, Choi HK, Cook DR, Shoemaker RC (2005). Bridging model and crop legumes through comparative genomics. Plant Physiol 137: 1189–1196.