Development of EST-SSR markers and construction of a linkage map in faba bean (Vicia faba)

Breeding Science

Volumn 64, Issue 3, 2014, Pages 252-263

  El Rodeny, Walid ^a   Kimura, Mitsuhiro ^b   Hirakawa, Hideki ^b   Sabah, Attia ^a   Shirasawa, Kenta ^b   Sato, Shusei ^b   Tabata, Satoshi ^b   Sasamoto, Shigemi ^b   Watanabe, Akiko ^b   Kawashima, Kumiko ^b   Kato, Midori ^b   Wada, Tsuyuko ^b   Tsuruoka, Hisano ^b   Takahashi, Chika ^b   Minami, Chiharu ^b   Nanri, Keiko ^b   Nakayama, Shinobu ^b   Kohara, Mitsuyo ^b   Yamada, Manabu ^b   Kishida, Yoshie ^b   Fujishiro, Tsunakazu ^b   Isobe, Sachiko ^b   more..

^a PLANT PATHOLOGY RESEARCH INSTITUTE   (Egypt)

^b KAZUSA DNA RESEARCH INSTITUTE   (Japan)

Author keywords

Comparative mapping; EST SSR; Faba bean; Genetic diversity; Linkage map

Indexed keywords

EID: 84907516317     PISSN: 13447610     EISSN: 13473735     Source Type: Journal    
DOI: 10.1270/jsbbs.64.252     Document Type: Article

References (68)

1. Abo El-kheir, Z.A., M.S. Abdel-Hady, H.M.H. El-Naggar and A.R. Abd El-Hamed (2010) Molecular and biochemical markers of some Vicia faba L. Cultivars in response to broomrape infestation. Nature and Science 8: 252–260.
2. Akash, M.W and G.O. Myers (2012) The development of faba bean expressed sequence tag-simple sequence repeats (EST-SSRs) and their validity in diversity analysis. Plant Breed. 131: 522–530.
3. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815.
4. Arbaoui, M., W. Link, Z. Satovic and A.M. Torres (2008) Quantitative trait loci of frost tolerance and physiologically related trait in faba bean (Vicia faba L.). Euphytica 164: 93–104.
5. Asamizu, E., Y. Nakamura, S. Sato, H. Fukuzawa and S. Tabata (1999) A large scale structural analysis of cDNA in a unicellular greed alga Chlamydomonas reinhadtill. I. Generation of 3433 non-redundant expressed sequence tags. DNA Res. 31: 369–373.
6. Avila, C.M., J.C. Sillero, D. Rubiales, M.T. Moreno and A.M. Torres (2003) Identification of RAPD markers linked to the Uvf-1gene conferring hypersensitive resistance against rust (Uromyces viciae-fabae) in Vicia faba L. Theor. Appl. Genet. 107: 353–358.
7. Avila, C.M., Z. Satovic, J.C. Sillero, D. Rubiales, M.T. Moreno and A.M. Torres (2004) Isolate and organ-specific QTLs for ascochyta blight resistance in faba bean. Theor. Appl. Genet. 108: 1071–1078.
8. Avila, C.M., Z. Šaypvia, J.C. Sillero, S. Nadal, D. Rubiales, M.T. Morenomt and A.M. Torres (2005) QTL Detection for Agronomic Traits in Faba Bean (Vicia faba L.). Agriculturae Conspectus Scientificus. 70: 65–73.
9. Avila, C.M., S. Nadal, M.T. Moreno and A.M. Torres (2006) Development of a simple PCR-based marker for the determination of growth habit in Vicia faba L. using a candidate gene approach. Mol. Breed. 17: 185–190.
10. Avila, C.M., S. Atienza, M. Moreno and A.M. Torres (2007) Development of a new diagnostic marker for growth habit selection in faba bean (Vicia faba L.) breeding. Theor. Appl. Genet. 115: 1075–1082.
11. Cruz-Izquierdo, S., C.M. Avila, Z. Satovic, C. Palomino, N. Gutierrez, S.R. Ellwood, H.T.T. Phan, J.I. Cubero and A.M. Torres (2012) Comparative genomics to bridge Vicia faba with modeland closelyrelated legume species: stability of QTLs for flowering and yieldrelated traits. Theor. Appl. Genet. 125: 1767–1782.
12. Díaz-Ruiz, R., A. Torres, M.V. Gutierrez, D. Rubiales, J.I. Cubero, M. Kharrat, Z. Satovic and B. Román (2009) Mapping of quantitative trait loci controlling Orobanche foetida Poir. resistance in faba bean (Vicia faba L.). Afr. J. Biotechnol. 8: 2718–2724.
13. Díaz-Ruiz, R., A.M. Torres, Z. Satovic, M.V. Gutierrez, J.I. Cubero and B. Román (2010) Validation of QTLs for Orobanche crenata resistance in faba bean (Vicia faba L.) across environments and generations. Theor. Appl. Genet. 120: 909–919.
14. Duc, G., N. Berthaut, J. Le Guen and J. Picard (1992) Hybrid breeding in faba bean (Vicia faba L.). In: Proc. 1st Conf. on Grain Legumes, Angers, France, pp. 45–46.
15. Duc, G., S. Bao, M. Baumc, B. Redden and M. Sadiki (2010) Diversity maintenance and use of Vicia faba L. genetic resources. Field Crops Res. 115: 270–278.
16. Ellwood, S.R., H.T.T. Phan, M. Jordan, J. Hane, A.M. Torres, C.M. Avila, S. Cruz-Izquierdo and R.P. Oliver (2008) Construction of a comparative genetic map in faba bean (Vicia faba L.); conservation of genome structure with Lens culinaris. BMC Genomics 9: 380.
17. Ewing, B. and P. Green (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186–194.
18. Ewing, B., L. Hillier, M.C. Wendl and P. Green (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175–185.
19. Gong, Y., S. Xu, W. Mao, Q. Hu, G. Zang, J. Ding and Z. Li (2010) Generation and characterization of 11 novel EST-derived microsatellites from Vicia faba (Fabaceae). Am. J. Bot. 97: e69–e71.
20. Gong, Y., S. Xu, W. Mao, Z. Li, Q. Hu, G. Zhang and J. Ding (2011) Genetic diversity analysis of faba bean (Vicia faba L.) based on EST-SSR markers. Agric. Sci. China 10: 838–844.
21. Gresta, F., G. Avola, E. Albertini, L. Raggi and V. Abbate (2010) A study of variability in the Sicilian faba bean landrace ‘Larga di Leonforte’. Genet. Resour. Crop. Ev. 57: 523–531.
22. Gutierrez, N., C. Avila, G. Duc, P. Marget, M. Suso, M. Moreno and A.M. Torres (2006) CAPs markers to assist selection for low vicine and convicine contents in faba bean (Vicia faba L.). Theor. Appl. Genet. 114: 59–66.
23. Gutierrez, N., C. Avila, C. Rodriguez-Suarez, M. Moreno and A. Torres (2007) Development of SCAR markers linked to a gene controlling absence of tannins in faba bean. Mol. Breed. 19: 305–314.
24. Gutierrez, N., C. Avila, M. Moreno and A. Torres (2008) Development of SCAR markers linked to zt-2, one of the genes controlling absence of tannins in faba bean. Aust. J. Agric. Res. 59: 62–68.
25. Huang, X., J. Wang, S. Aluru, S.P. Yang and L. Hillier (2003) PCAP: a whole-genome assembly program. Genome Res. 13: 2164–2170.
26. Isobe, S.N., H. Hisano, S. Sato, H. Hirakawa, K. Okumura, K. Shirasawa, S. Sasamoto, A. Watanabe, T. Wada, Y. Kishida et al. (2012) Comparative genetic mapping and discovery of linkage disequilibrium across linkage groups in white clover (Trifolium repens L.). G3 (Bethesda) 2: 607–617.
27. Johnston, J.S., M.D. Bennett, A.L. Rayburn, D.W. Galbraith and H.J. Price (1999) Reference standards for determination of DNA content of plant nuclei. Am. J. Bot. 86: 609–613.
28. Kaur, S., L.W. Pembleton, N.O.I. Cogan, K.W. Savin, T. Leonforte, J. Paull, M. Materne and J.W. Forster (2012) Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers. BMC Genomics 13: 104.
29. Käser, H.R. and A.M. Steiner (1983) Subspecific classification of Vicia faba L. by protein and isozyme patterns. Fabis. Newsletter 7: 19–20.
30. Kiss, G.B., A. Kereszt, P. Kiss and G. Endre (1998) Colormapping; a non-mathematical procedure for genetic mapping. Acta Biol. Hung. 19: 125–142.
31. Lander, E.S., P. Green, J. Abrahamson, A. Barlow, M.J. Daly, S.E. Lincoln and L. Newburg (1987) MAPMAKER: an interactive computer program for constructing genetic linkage maps of experimental and natural populations. Genomics 1: 174–181.
32. Lincoin, S.E., M.J. Daly and E.S. Lander (1993) Constructing genetic linkage maps with MAPMAKER/EXP version 3.0: A Tutorial and reference manual. Whitehead Kubtitute o]for Biomedical Resarch. USA.
33. Link, W., W. Ederer, P. Metz, H. Buiel and A.E. Melchinger (1994a) Genotypic and environmental variation for degree of crossfertilization in faba bean. Crop Sci. 34: 960–964.
34. Link, W., D. Stelling and E. Ebmeyer (1994b) Factors determining the performance of synthetics in Vicia faba L. 1. Heterogeneity, heterozygosity, and degree of cross-fertilization. Euphytica 75: 77–84.
35. Link, W., C. Dixkens, M. Singh and M. Schwall (1995) Genetic diversity in European and Mediterranean faba bean germplasm revealed by RAPD markers. Theor. Appl. Genet. 90: 27–32.
36. Liu, K. and S.V. Muse (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128–2129.
37. Liu, Y.J. and X.X. Zong (2008) Morphological diversity analysis of faba bean (Vicia Faba L.), germplasm resources from Qinghai. J. Plant Genet. Res. 9: 79–83.
38. Ma, Y., T. Yang, J. Guan, S. Wang, H. Wang, X. Sun and X. Zong (2011) Development and characterization of 21 EST-derived microsatellite markers in Vicia faba (fava bean). Am. J. Bot. 98: e22–e24.
39. Mancini, R., C. Pace, G.T.S. Mugnozza, V. Delre and D. Vittori (1989) Isozyme gene markers in Vicia faba L. Theor. Appl. Genet. 77: 657–667.
40. Nei, M. (1973) Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. USA 70: 3321–3323.
41. Ouji, A., S. El-Bok, N.H. Syed, R. Abdellaoui, M. Rouaissi, A.J. Flavell and M. El-Gazzah (2012) Genetic diversity of faba bean (Vicia faba L.) populations revealed by sequence specific amplified polymorphism (SSAP) markers. Afr. J. Biotechnol. 11: 2162–2168.
42. Požárková, D., A. Koblížková, B. Román, A.M. Torres, S. Lucretti, M. Lysák, J. Doležel and J. Macas (2002) Development and characterization of microsatellite markers from chromosome 1-specific DNA libraries of Vicia faba. Biologia Plantarum 45: 337–345.
43. Rafalski, J.A., I.M. Vogel, M. Morgant, W. Powell, C. Andre and S.V. Tingey (1996) Generating and using DNA markers in plants. In: Non mammalian, genic analysis: a practical guide Academic, San Diego, ISBN: 0121012859, pp. 75–135.
44. Ramsey, G., W. Van de Ven, R. Waugh, D. Griffiths and W. Powell (1995) Mapping quantitative trait loci in faba beans. In: AEP (eds.) Proceedings of the 2nd European conference on grain legumes, Copenhagen, Denmark, pp. 444–445.
45. Rice, P., I. Longden and A. Bleasby (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16: 276–277.
46. Román, B., A.M. Torres, D. Rubiales, J.I. Cubero and Z. Satovic (2002) Mapping of quantitative trait loci controlling broomrape (Orobanche crenata Forsk.) resistance in faba bean (Vicia faba L.). Genome 45: 1057–1063.
47. Román, B., Z. Satovic, C.M. Avila, D. Rubiales, M.T. Moreno and A.M. Torres (2003) Locating genes associated with Ascochyta fabae resistance in Vicia faba. Aust. J. Agric. Res. 54: 85–90.
48. Román, B., Z. Satovic, D. Pozarkova, J. Macas, J. Dolezel, J.I. Cubero and A.M. Torres (2004) Development of a composite map in Vicia faba, breeding applications and future prospects. Theor. Appl. Genet. 108: 1079–1088.
49. Rozen, S. and H. Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz, S. and S. Misener (eds.) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press. Totowa, NJ, USA, pp. 365–386.
50. Sato, S., S. Isobe, E. Asamizu, N. Ohmido, R. Kataoka, Y. Nakamura, T. Kaneko, N. Sakurai, K. Okumura, I. Klimenko et al. (2005) Comprehensive structural analysis of the genome of red clover (Trifolium pretense L.). DNA Res. 12: 301–364.
51. Sato, S., Y. Nakamura, T. Kaneko, E. Asamizu, T. Kato, M. Nakao, S. Sasamoto, A. Watanabe, A. Ono, K. Kawashima et al. (2008) Genome structure of the legume, Lotus japonicus. DNA Res. 15: 227–239.
52. Schmutz, J., S.B. Cannon, J. Schlueter, J. Ma, T. Mitros, W. Nelson, D.L. Hyten, Q. Song, J.J. Thelen, J. Cheng et al. (2010) Genome sequence of the paleopolyploid soybean. Nature 463: 178–183.
53. Stoddard, F.L., S. Hovinen, M. Kontturi, K. Lindström and A. Nykänen (2009) Legumes in Finnish agriculture: history, present status and future prospects. Agric. Food Sci. 18: 191–205.
54. Surahman, M. (2001) The construction of genetic map of faba bean Faba bean EST-SSR linkage map 263 (Vicia faba L.) using RAPD markers. Bul. Agron. 29: 31–33.
55. Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei and S. Kumar (2011) MEGA5: Molecular evolutionary genetics analysis using likelihood, distance, and parsimony methods. Mol. Biol. Evol. 28: 2731–2739.
56. Tatusov, R.L., N.D. Fedorova, J.D. Jackson, A.R. Jacobs, B. Kiryutin, E.V. Koonin, D.M. Krylov, R. Mazumder, S.L. Mekhedov, A.N. Nikolskaya et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41–54.
57. Terzopoulos, P.J. and P.J. Bebeli (2008) Genetic diversity analysis of Mediterranean faba bean (Vicia faba L.) with ISSR markers. Field Crops Res. 108: 39–44.
58. Terzopoulos, P.J., P.J. Kaltsikes and P.J. Bebeli (2008) Determining the sources of heterogeneity in Greek faba bean local populations. Field Crops Res. 105: 124–130.
59. van de Ven, M., W. Powell, G. Ramsay and R. Waugh (1990) Restriction fragment length polymorphisms as genetic markers in Vicia. Heredity 65: 329–342.
60. ® 4, Software for the calculation of genetic linkage maps in experimental populations, Kyazma, B.V., Wageningen, Netherlands.
61. Wang, X.J., X.S. Qi and X.R. Wang (2009) Genetic diversity analysis of main agronomic characters in faba bean germplasm. Res. Agric. Modernization 30: 633–636.
62. Yang, T., S.Y. Bao, R. Ford, T.J. Jia, J.P. Guan, Y.H. He, X.L. Sun, J.Y. Jiang, J.J. Hao, X.Y. Zhang et al. (2012) High-throughput novel microsatellite marker of faba bean via next generation sequencing. BMC Genomics 13: 602.
63. Young, N.D., J. Mudge and T.H.N. Ellis (2003) Legume genomes: more than peas in a pod. Curr. Opin. Plant Biol. 6: 199–204.
64. Zeid, M., C.C. Schon and W. Lin (2003) Genetic diversity in recent elite faba bean linesusing AFLP markers. Theor. Appl. Genet. 107: 1304–1314.
65. Zeid, M., S. Mitchell, W. Link, M. Carter, A. Nawar, T. Fulton and S. Kresovich (2009) Simple sequence repeats (SSRs) in faba bean: New loci from Orobanche-resistant cultivar ‘Giza 402’. Plant Breed. 128: 149–155.
66. Zhang, X.T. and Y.J. Liu (2009) Morphological diversity analysis of faba bean (Vicia faba L.) germplasm resources. Qinghai Sci. Tech. 5: 17–19.
67. Zhu, H., H.K. Choi, D.R. Cook and R.C. Shoemaker (2005) Bridging model and crop legumes through comparative genomics. Plant Physiol. 137: 1189–1196.
68. Zong, X., X. Liu, J. Guan, S. Wang, Q. Liu, J.G. Paull and R. Redden (2009) Molecular variation among Chinese and global winter faba bean germplasm. Theor. Appl. Genet. 118: 971–978.