Phaseolus vulgaris: A Diploid Model for Soybean

  • Phillip E. McClean
  • Matt Lavin
  • Paul Gepts
  • Scott A. Jackson
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 2)


Common Bean Soybean Genome Much Recent Common Ancestor Bean Common Mosaic Virus Anthracnose Resistance 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. Adams, M.D., Celniker, S.E., Holt, R.A., Evans, C.A., Gocayne, J.D. et al. (2000) The genome sequence of the Drosophila melanogaster. Science 287, 2185–2195.PubMedCrossRefGoogle Scholar
  2. AGI (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815.CrossRefGoogle Scholar
  3. Aragão, F., Ribeiro, S., Barros, L., Brasileiro, A., Maxwell, D., Rech, E. and Faria, J. (1998) Transgenic beans (Phaseolus vulgaris L.) engineered to express viral antisense RNAs show delayed and attenuated symptoms to bean golden mosaic geminivirus. Mol. Breed. 4, 491–499.CrossRefGoogle Scholar
  4. Aragão, F.J.L., Barros, L.M.G., de Sousa, M.V., Grossi de Sa, M.F., Almeida, E.R.P., Gander, E.S. and Rech, E.L. (1999) Expression of a methionine-rich storage albumin from the Brazil nut (Bertholletia excelsa H.B.K., Lecythidaceae) in transgenic bean plants (Phaseolus vulgaris L., Fabaceae). Genetics & Mol. Biol. 22, 445–449.Google Scholar
  5. Aragão, F.J.L., Vianna, G.R., Albino, M.M.C. and Rech, E.L. (2002) Transgenic dry bean tolerant to the herbicide glufosinate ammonium. Crop Sci. 42, 1298–1302.Google Scholar
  6. Aroca, R., Ferrante, A., Vernieri, P. and Chrispeels, M.J. (2006) Drought, abscisic acid and transpiration rate effects on the regulation of PIP aquaporin gene expression and abundance in Phaseolus vulgaris plants. Ann. Bot. 98, 1301–1310.PubMedCrossRefGoogle Scholar
  7. Arumuganathan, K. and Earle, D.E. (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Report. 9, 208–218.CrossRefGoogle Scholar
  8. Becerra Velásquez, V.L., and Gepts, P.(1994) RFLP diversity in common bean (Phaseolus vulgaris L.). Genome 37, 256–263.Google Scholar
  9. Beebe, S.E., Rojas-Pierce, M., Yan, X., Blair, M.W., Pedraza, F., Muñoz, F., Tohme, J. and Lynch, J.P. (2006) Quantitative trait loci for root architecture traits correlated with phosphorus acquisition in common bean, Crop Sci. 46, 413–423.CrossRefGoogle Scholar
  10. Beebe, S.E., Skroch, P.W., Thome, J., Duque, M.C., Pedraza, F., Nienhuis, J. (2000) Structure of genetic diversity among common bean landraces of middle American origin based on correspondance analysis of RAPD. Crop Sci. 40, 264–273.Google Scholar
  11. Bennett, M. and Leitch, I. (1995) Nuclear DNA amounts in angiosperms. Ann. Bot. 76, 113–176.CrossRefGoogle Scholar
  12. Bennett, M. and Leitch, I. (2005) Plant DNA C-Values database. Release 4.0 http://www. Scholar
  13. Blanc, G., and Wolfe, K.H. (2004) Widespread paeleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 17, 1667–1678.CrossRefGoogle Scholar
  14. Blair, M.W., Giraldo, M.C., Buendia, H.F., Tovar, E., Duque, M.C., and Beebe, S.E. (2006) Microsatellite marker diversity in common bean (Phaseolus vulgaris L.) Theor. Appl. Genet. 113, 100–109.PubMedCrossRefGoogle Scholar
  15. Blair, M.W., Pedraza, F., Buendia, H.F., Gaitán-Solís, E., Beebe, S.E., Gepts, P., and Tohme, J. (2003) Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.) Theor. Appl. Genet. 107, 1362–1374.PubMedCrossRefGoogle Scholar
  16. Blyden, E.R., Doerner, P.W., Lamb, C.J. and Dixon, R.A. (1991) Sequence analysis of a chalcone isomerase cDNA of Phaseolus vulgaris L. Plant Mol. Biol. 16, 167–169.PubMedCrossRefGoogle Scholar
  17. Broughton, W.J., Hernandez, G., Blair, M., Beebe, S., Gepts, P. and Vanderleyden, J. (2003) Beans (Phaseolus spp.) - model food legumes. Plant and Soil 252, 55–128.CrossRefGoogle Scholar
  18. Cadle-Davidson, M. and Jahn, M. (2006) Differential gene expression in Phaseolus vulgaris I locus NILs challenged with bean common mosaic virus. Theor. Appl. Genet. 112, 1452–1457.PubMedCrossRefGoogle Scholar
  19. CESC (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012–2018.CrossRefGoogle Scholar
  20. Choi, S.S., and Lahn, B.T. (2003) Adaptive evolution of MRG, a neuron-specific gene family implicated in nociception. Genome Res. 13, 2252–2259.PubMedCrossRefGoogle Scholar
  21. Choi, H.K., Mun, J.H., Kin, D.J., Zhu, H., Baek, J.M., Mudge, J., Roe, B., Ellis, N., Doyle, J., Kiss, G.B., Young, N.D., and Cook, D.R. (2004) Estimating genome conservation between crop and model legume species. Proc. Natl. Acad. Sci., USA 101, 15289–15294.PubMedCrossRefGoogle Scholar
  22. Crepet, W.L., Nixon, K.C., and Gandolfo, M.A. (2004) Fossil evidence and phylogeny: the age of major angiosperm clades based on mesofossil and macrofossil evidence from Cretaceous deposits. Amer. J. Bot. 91, 1666–1682.CrossRefGoogle Scholar
  23. CSAC (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69–87.CrossRefGoogle Scholar
  24. Debouck, D.G., Toro, O., Paredes, O.M., Johnson, W.C., and Gepts, P. (1993) Genetic diversity and ecological distribution of Phaseolus vulgaris in northwestern South America. Econ. Bot. 47, 408–423.Google Scholar
  25. DeClercq, J., Zambre, M., Van Montagu, M., Dillen, W. and Angenon, G. (2002) An optimized Agrobacterium-mediated transformation procedure for Phaseolus acutifolius A. Gray. Pl. Cell Reports 21, 333–340.CrossRefGoogle Scholar
  26. Delgado-Salinas, A.., Bibler, R. and Lavin, M. (2006) Phylogeny of the genus Phaseolus (Leguminosae): a recent diversification in an ancient landscape. Syst. Bot. 56, in press.Google Scholar
  27. Doyle, J.J., and Luckow, M.A. (2003) The rest of the iceberg. Legume diversity and evolution in a phylogenetic context. Plant Phys. 131, 900–910.CrossRefGoogle Scholar
  28. Estrada-Navarrete, G., Alvarado-Affantranger, X., Olivares, J.-E., Díaz-Camino, C., Santana, O., Murillo, E., Guillén, G., Sánchez-Guevara, N., Acosta, J., Quinto, C., Li, D., Gresshoff, P.M,. and Sánchez, F. (2006) Agrobacterium rhizogenes-transformation of the Phaseolus spp.: A tool for functional genomics. Mol. Plant Microbe Interact. 19, 1385–1393.PubMedCrossRefGoogle Scholar
  29. Flicek, P., Keibler, E. Hu, P. Korf, I., and Brent, M.R. (2003) Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res. 13, 46–54.PubMedCrossRefGoogle Scholar
  30. Flint, J., Tufarelli, C., Peden, J., Clark, K., Daniels, R.J., Hardison, R., Miller, W., Philipsen, S., Tan-Un, K.C., McMorrow, T., Frampton, J., Alter, B.P., Frischauf, A.M., and Higgs, D.R. (2001) Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the alpha globin cluster. Hum. Mol. Genet. 10, 371–382.PubMedCrossRefGoogle Scholar
  31. Freyre, R., Skroch, P.W., Geffroy, V., Adam-Blondon, A.F., Shirmohamadali, A.., Johnson, W.C., Llaca, V., Nodari, R.O., Pereira, P.A.., Tsai, S.M., Tohme, J., Dron, M., Nienhuis, J., Vallejos, C.E., and Gepts.,P. (1998) Towards an integrated linkage map of common bean. 4. Development of a core linkage map and alignment of RFLP maps. Theor. Appl. Genet. 97:847–856.CrossRefGoogle Scholar
  32. Gepts, P. (1990) Biochemical evidence bearing on the domestication of Phaseolus (Fabaceae) beans. Econ. Bot. 44, 22–38.Google Scholar
  33. Gepts, P. (1998) Origin and evolution of common bean: past events and recent trends. HortSci. 33, 1124–1130.Google Scholar
  34. Gepts, P., Aragão, F., de Barros, E., Blair, M.W., Brondani, R., Broughton, W.J., Galasso, I., Hernández, G., Kami, J., Lariguet, P., McClean, P., Melotto, M., Miklas, P., Pauls, P., Pedrosa-Harand, A., Porch, T., Sánchez, F., Sparvoli, F. and Yu, K. (2007) Genomics of Phaseolus beans, a major source of dietary protein and micronutrients in the Tropics. In: P.H. Moore and R. Ming (Eds), Genomics of Tropical Crop Plants. Springer, Berlin, in press.Google Scholar
  35. Gepts, P., and Bliss, F.A. (1986) Phaseolin variability among wild and cultivated common beans (Phaseolus vulgaris) from Colombia. Econ. Bot. 40, 469–478.Google Scholar
  36. Gepts, P, and Debouck, D. 1991. Origin, domestication, and evolution of common bean (Phaseolus vulgaris L.). In: A. van Schoonhoven and O. Voyest (Eds.) Common Beans: Research for Crop Improvement. C.A.B. Intl., Wallingford, UK and CIAT, Cali, Colombia, pp. 7–53.Google Scholar
  37. González, A., Wong, A., Delgado-Salinas, A., Papa, R., and Gepts, P. (2005) Assessment of inter simple sequence repeat markers to differentiate sympatric wild and domesticated populations of common bean (Phaseolus vulgaris L.). Crop Sci. 35, 606–615.Google Scholar
  38. Guo, H., and Moose, S.P. (2003). Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell 15, 1143–1158.PubMedCrossRefGoogle Scholar
  39. Hoffman, L.M., and Donaldson, D.D. (1985) Characterization of two Phaseolus vulgaris phytohemagglutinin genes closely linked on the chromosome. EMBO J. 4, 883–889.PubMedGoogle Scholar
  40. Inada, D.C., Bashir, A., Lee, C., Thomas, B.C., Ko, C., Goff, S.A., and Freeling, M. (2003). Conserved noncoding sequences in the grasses. Genome Res. 13, 2030–2041.PubMedCrossRefGoogle Scholar
  41. Inoue, S., Konoshita, T., and Simazaki, K. (2005) Possible involvement of phototropins in leaf movement of kidney bean in response to blue light. Plant Physiol. 138, 1994–2004.PubMedCrossRefGoogle Scholar
  42. IRGSP (2005) The map-based sequence of the rice genome. Nature 436, 793–800.CrossRefGoogle Scholar
  43. Islam, F.M.A., Basford, K.E., Jara, C., Redden, R.L., and Beebe, S. (2002) Seed compositional and disease resistance differences among gene pools in cultivated common bean. Genet. Resour. Crop. Evol. 49, 285–293.CrossRefGoogle Scholar
  44. Jackson, S.A., Rokshar, D., Stacey, G., Shoemaker, R.C., Schmutz, J., and Grimwood, J. (2006) Toward a reference sequence of the soybean genome: a multiagency effort. Crop Sci. 46,S-55–61.Google Scholar
  45. Kami, J., Becerra Velásquez, B., Debouck, D.G., and Gepts, P. (1995) Identification of presumed ancestral DNA sequences of phaseolin in Phaseolus vulgaris. Proc. Natl. Acad. Sci. U.S.A. 92, 1101–1104.PubMedCrossRefGoogle Scholar
  46. Kami, J., Poncet, V., Geffroy, V. and Gepts, P. (2006) Development of four phylogenetically-arrayed BAC libraries and sequence of the APA locus in Phaseolus vulgaris. Theor. Appl. Genet. 112, 987–998.PubMedCrossRefGoogle Scholar
  47. Kaplan, L., and Lynch, T.F. (1999) Phaseolus (Fabaceae) in archaeology: AMS radiocarbon dates and their significance for pre-Columbian agriculture. Econ. Bot. 53, 261–272.Google Scholar
  48. Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 242–254.CrossRefGoogle Scholar
  49. Kelly, J.D., Gepts, P., Miklas, P.N. and Coyne, D.P. (2003) Tagging and mapping of genes and QTL and molecular marker-assisted selection for traits of economic importance in bean and cowpea. Field Crops Res. 82, 135–154.CrossRefGoogle Scholar
  50. Koenig, R., and Gepts, P. (1989) Allozyme diversity in wild Phaseolus vulgaris: further evidence for two major centers of diversity. Theor. Appl. Genet. 78, 809–817.CrossRefGoogle Scholar
  51. Kumar, S., Filipski, A., Swarna, V., Walker A., and Hedges, B.S. (2005) Placing confidence limits on the molecular age of the human–chimpanzee divergence. Proc. Natl, Acad. Sci., U.S.A 102, 18842–18847.CrossRefGoogle Scholar
  52. Lai, J., Ma, J., Swigonova, Z., Ramakrishna, W., Linton, E., Llaca, V., Tanyolac, B., Park, Y.J., Jenong, O.Y., Bennetzen, J.L., and Messing, J. (2004) Gene loss and movement in the maize genome. Genome Res. 14, 1924–1931.PubMedCrossRefGoogle Scholar
  53. Lavin, M., Herendeen, P.S., and Wojciechowski, M.F. (2005) Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the Tertiary. System. Biol. 54, 530–549.CrossRefGoogle Scholar
  54. Lewis, G., Schrire, B., Mackinder, B., and Lock, M. (2005) Legumes of the World. Royal Botanic Gardens, Kew Publishing; London.Google Scholar
  55. Lioi, L., Sparvoli, F., Galasso, I., Lanave, C., and Bollini, R. (2003) Lectin-related resistance factors against bruchids evolved through a number of duplication events. Theor. Appl. Genet. 107, 814–822.PubMedCrossRefGoogle Scholar
  56. Liu, Z.C., Park, B.J., Kanno, A., and Kameya, T. (2005) The novel use of a combination of sonication and vacuum infiltration in Agrobacterium-mediated transformation of kidney bean (Phaseolus vulgaris L.) with lea gene. Mol. Breed. 16, 189–197.CrossRefGoogle Scholar
  57. López, C.E., Acosta, I.F., Jara, C., Pedraza, F., Gaitán-Solís, E., Gallego, G., Beebe, S. and Tohme, J. (2003) Identifying resistance gene analogs associated with resistances to different pathogens in common bean. Phytopathology 93, 88–95.CrossRefPubMedGoogle Scholar
  58. Ma, J. SanMiguel, P., Lai, J., Messing, J., and Bennetzen, J.L. (2005) DNA rearrangement in orthologous orp regions of the maize, rice, and sorghum genomes. Genetics 170, 1209–1220.PubMedCrossRefGoogle Scholar
  59. Magallón, S., Crane, P.R., and Herendeen, P.S. (1999) Phylogenetic pattern, diversity, and diversification of eudicots. Ann. Mo. Bot. Gard. 86, 297–372.CrossRefGoogle Scholar
  60. Magallón, S., and Sanderson, M.J. (2001) Absolute diversification rates in angiosperms. Evolution 55, 1762–1780.PubMedGoogle Scholar
  61. Maréchal, R. (1971) Observations sur quelques hybrides dans le genre Phaseolus. II. Les phénomènes méiotiques. Bull. Rech. Agron. Gembloux 6, 461–489.Google Scholar
  62. Margis-Pinheiro, M., Martivet, J. and Burkard, G. (1994) Bean class IV chitinase gene: structure, developmental expression and induction by heat stress Plant Sci. 98, 163–173.CrossRefGoogle Scholar
  63. Margulies, E.H., and Green, E.D. (2003) Detecting highly conserved regions of the human genome by multispecies sequence comparison. Cold Spring Harb. Symp. Quant. Biol. 68,255–263.PubMedCrossRefGoogle Scholar
  64. Margulies, E.H., Blanchette, M., Haussler, D., and Green, E.D. (2003) Identification and characterization of multi-species conserved sequences. Genome Res. 13, 2507–2518.PubMedCrossRefGoogle Scholar
  65. Margulies, E.H., Vinson, J.P., Miller, W., Jaffe, D.B., Lindblad-Toh, K., Chang, J.L., Green, E.D., Lander, E.S., Mullikin, J.C., and Clamp, M. (2005) An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing. Proc. Natl. Acad. Sci., USA. 102, 4795–4800.PubMedCrossRefGoogle Scholar
  66. Matsuoka, Y., Vigouroux, Y., Goodman, M.M., Sanchez, G.J., Buckler IV, E., and Doebley, J. (2002) A single domestication for maize shown by multilocus microsatellite genotyping. Proc. Natl. Acad. Sci., USA. 99, 6080–6084.PubMedCrossRefGoogle Scholar
  67. McCallum, C.M., Comai, L., Greene, E.A. and Henikoff, S. (2000) Targeting induced local lesions in genomes (TILLING) for plant functional genomics. Pl. Physiol. 123, 439–442.CrossRefGoogle Scholar
  68. McClean, P.E., Kami, J., and Gepts, P. (2004a) Genomics and genetic diversity in common bean. In: R.F. Wilson, H.T. Stalker, and E.C. Brummer (Eds.) Legume Crop Genomics. AOCS Press, Champaign, Illinois, USA, pp. 60–82.Google Scholar
  69. McClean, P.E., Lee, R.K. and Miklas, P.N. (2004b) Sequence diversity analysis of dihydroflavanol reductase intron 1 in common bean. Genome 47, 266–280.Google Scholar
  70. Melotto, M., Coelho, M.F., Pedrosa-Harand, A., Kelly, J.D. and Camargo, L.E.A. (2004) The anthracnose resistance locus Co-4 of common bean is located on chromosome 3 and contains putative disease resistance-related genes. Theor. Appl. Genet. 109, 690–699.PubMedCrossRefGoogle Scholar
  71. Melotto, M., Monteiro-Vitorello, C.B., Bruschi, A.G., and Camargo, L.E. (2005) Comparative bioinformatic analysis of genes expressed in common bean (Phaseolus vulgaris L.) seedlings. Genome, 48, 562–570.PubMedCrossRefGoogle Scholar
  72. Miklas, P.N., Kelly, J.D., Beebe, S.E. and Blair, M.W. (2006) Common bean breeding for resistance against biotic and abiotic stresses: from classical to MAS breeding. Euphytica 147,106–131.CrossRefGoogle Scholar
  73. Moscone, E.A., Klein, F., Lambrou, M., Fuchs, J. and Schweizer, D. (1999) Quantitative karyotyping and dual-color FISH mapping of 5S and 18S–25S rDNA probes in the cultivated Phaseolus species (Leguminosae). Genome 42, 1224–1233.PubMedCrossRefGoogle Scholar
  74. Mutlu, N., Miklas, P.N. and Coyne, D.P. (2005) Resistance gene analog polymorphism (RGAP) markers co-localize with disease resistance genes and QTL in common bean. Mol. Breed. 17, 127–135.CrossRefGoogle Scholar
  75. Myers, E.W., Sutton, G.G., Delcher, A.L., Dew, I.M., Fasulo, D.P., et al. (2000) A whole-genome assembly of Drosophila. Science 287, 2196–2204.PubMedCrossRefGoogle Scholar
  76. Nagl, W. (1974) The Phaseolus suspensor and its polytene chromosomes. Z. Pflanzenphysiol. 73, 1–44.Google Scholar
  77. Nanni, L., Losa, A., Bellucci, E., Kater, M., Gepts, P. and Papa, R. (2005) Identification and molecular diversity of a genomic sequence similar to SHATTERPROOF (SHP1) in Phaseolus vulgaris L. Abstract, Plant and Animal Genome XIII, Jan. 15–19, 2005: Scholar
  78. Nenno, M., Schumann, K. and Nagl, W. (1994) Detection of rRNA and phaseolin genes on polytene chromosomes of Phaseolus coccineus by fluorescence in situ hybridization after pepsin treatment. Genome 37, 1018–1021.PubMedGoogle Scholar
  79. Nodari, R.O., Koinange, E.M.K., Kelly, J.D., and Gepts, P. (1992) Towards an integrated linkage map of common bean. I. Development of genomic DNA probes and levels of restriction fragment length polymorphism. Theor. Appl. Genet. 84, 186–192.CrossRefGoogle Scholar
  80. Ochoa, I.E., Blair, M.W., and Lynch, J.P. (2006) QTL analysis of adventitious root formation in common bean under contrasting phosphorus availability. Crop Sci. 46, 1609–1621.CrossRefGoogle Scholar
  81. Pagel, J., Walling, J.G., Young, N.D., Shoemaker, R.C., and Jackson, S.A. (2004) Segmental duplications within the Glycine max genome revealed by fluorescence in situ hybrization of bacterial artificial chromosomes. Genome 47, 764–768.PubMedCrossRefGoogle Scholar
  82. Papa, R., and Gepts, P. (2003) Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica. Theor. Appl. Genet. 106, 239–250.PubMedGoogle Scholar
  83. Pedrosa, A., Vallejos, C.E., Bachmair, A., and Schweizer, D. (2003) Integration of common bean (Phaseolus vulgaris L.) linkage and chromosomal maps. Theor. Appl. Genet. 106,205–212.PubMedGoogle Scholar
  84. Pedrosa-Harand, A., Almeida, C.C.S., Mosiolek, M., Blair, M.W., Schweizer, D. and Guerra, M. (2006) Extensive ribosomal DNA amplification during Andean common bean (Phaseolus vulgaris L.) evolution. Theor. Appl. Genet. 112, 924–933.PubMedCrossRefGoogle Scholar
  85. Powell, W., Morgante, M., Doyle, J.J., McNicol, J.W., Tingey, S.V., and Rafalski, A.J. 1996. Genepool variation in genus Glycine subgenus soja revealed by polymorphic nucler and chloroplast microsatellites. Genetics 144, 793–803.PubMedGoogle Scholar
  86. Ramirez, M., Graham, M.A., Blanco-Lopez, L., Silvente, S., Medrano-Soto, A., Blair, M.W., Hernandez, G., Vance, C.P. and Lara, M. (2005) Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Pl. Physiol. 137, 1211–1227.CrossRefGoogle Scholar
  87. Rivkin, M.I., Vallejos, C.E., and McClean, P.E. 1999. Disease-resistance related sequences in common bean. Genome 42, 41–47.PubMedCrossRefGoogle Scholar
  88. Rodriguez-Uribe, L. and O’Connell, M.A. (2006) A root-specific bZIP transcription factor is responsive to water deficit stress in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris). Plant Sci. 171, 300–307.CrossRefGoogle Scholar
  89. Ryder, T.B., Hedrick, S.A., Bell, J.N., Liang, X.W., Clouse, S.D. and Lamb, C.J. (1987) Organization and differential activation of a gene family encoding the plant defense enzyme chalcone synthase in Phaseolus vulgaris. Mol. Gen. Genet. 210, 219–233.PubMedCrossRefGoogle Scholar
  90. Salamov, A.A., and Solovyev, V.V. (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10, 516–522.PubMedCrossRefGoogle Scholar
  91. Schlueter, J.A., Dixon, P., Granger, C., Grant, D., Clark, L., Doyle, J.J., and Shoemaker, R.C. (2004) Mining EST databases to resolve evolutionary events in major crop species. Genome 47, 868–876.PubMedCrossRefGoogle Scholar
  92. Shoemaker, R.C., Polzin, K., Labate, J., Specht, J., Brummer, E.C., Olson, T.K., Young, N., Concibido, V., Wilcox, J., Tamulonis, J.P., Kochert, G., and Boerma, H.R. (1996) Genome duplications in soybean (Glycine subgenus soja). Genetics 144, 329–338.PubMedGoogle Scholar
  93. Shultz, J.L., Kurunam, D., Shopinski, K., Iqbal, M.J., Kazi, S., Zobrist, K., Bashir, R., Yaegashi, S., Lavu, N., Afzal, A.J., Yesudas, C.R., Kassem, M.A., Wu, C.C., Zhang, H.B., Town, C.D., Meksem, K. and Lightfoot, D.A. (2006) The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max. Nucl. Acids Res. 34, D758–D765.PubMedCrossRefGoogle Scholar
  94. Singh, S.P., Gepts, P., and DeBouck, D.G. (1991). Races of common bean (Phaseolus vulgaris, Fabaceae). Econ.Bot. 45, 379–386.Google Scholar
  95. Stevens, P.F. (2001) Angiosperm Phylogeny Website. Version 7, December 2006 and continuously updated ( Scholar
  96. Sun, S.M., Slightom, J.L., and Hall, T.C. (1981) Intervening sequences in a plant gene – comparison of the partial sequence of the cDNA and genomic DNA of French bean phaseolin. Nature 289, 37–41.CrossRefGoogle Scholar
  97. Thomas, J.W., Touchman, J.W., Blakesley, R.W., Bouffard, G.G., Beckstrom-Sternberg, S.M., et al. (2003) Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424, 788–793.PubMedCrossRefGoogle Scholar
  98. Tohme, J., González, D.O., Beebe, S., and Duque, M.C. (1996) AFLP analysis of gene pools of a wild bean core collection. Crop Sci. 36, 1375–1384.Google Scholar
  99. Tuskan, G.A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596–1604.PubMedCrossRefGoogle Scholar
  100. Vallejos, C.E., Astua-Monge, G., Jones, V., Plyler, T.R., Sakiyama, N.S., and Mackenzie, S.A. (2006) Genetic and molecular characterization of the I locus of Phaseolus vulgaris. Genetics 172, 1229–1242.PubMedCrossRefGoogle Scholar
  101. Vallejos, C.E., Sakiyama, N.S., and Chase, C.D. (1992) A molecular marker-based linkage map of Phaseolus vulgaris L. Genetics 131, 733–740.PubMedGoogle Scholar
  102. Veltcheva, M., Svetleva, D., Petkova, S. and Perl, A. (2005) In vitro regeneration and genetic transformation of common bean (Phaseolus vulgaris L.) - problems and progress. Scientia Horticulturae 107, 2–10.CrossRefGoogle Scholar
  103. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J. et al. (2001) The sequence of the human genome. Science 291, 1304–1351.PubMedCrossRefGoogle Scholar
  104. Walling, J.G., Pires, J.C., and Jackson, S.A. (2005) Preparation of samples for comparative studies of plant chromosomes using in situ hybridization methods. Methods in Enzymology 395,442–459.CrossRefGoogle Scholar
  105. Walter, M.H., Liu, J.W., Grand, C., Lamb, C.J. and Hess, D. (1990) Bean pathogenesis-related (PR) proteins deduced from elicitor-induced transcripts are members of a ubiquitous new class of conserved PR proteins including pollen allergens. Mol. Gen. Genet. 222, 353–360.PubMedCrossRefGoogle Scholar
  106. Wei, C., and Brent, M.R. (2006) Using ESTs to improve the accuracy of de novo gene prediction. BMC Bioinformatics 7, 327.PubMedCrossRefGoogle Scholar
  107. Wikström, N., Savlainen, V., and Chase, M.W. (2001) Evolution of the angiosperms: calibrating the family tree. Proc. Royal Soc. London, B, Biol. Sci. 268, 2211–2220.CrossRefGoogle Scholar
  108. Wing, R.A., Ammiraju, J.S., Luo, M., Kim, H. Yu, Y. Kudrna, D., Goicoechea, J.L., Wang, W., Nelson, W., Rao, K., Brar, D., Mackill, D.J., Han, B., Soderlund, C., Stein, L., SanMiguel, P., and Jackson, S. (2005) The Oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species. Plant Mol. Biol. 59, 53–62.PubMedCrossRefGoogle Scholar
  109. Woolfe, A., Goodson, M., Goode, D.K., Snell, P., McEwen, G.K., Vavouri, T., Smith, S.f., North, P., Callaway, H., Kelly, K, Walter, K., Abnizova, I., Gilks, W., Edwards, Y.J., Cooke, J.E., and Elgar, G. (2005) Highly expressed non-coding sequences are associated with vertebrate development. PLoS Biol. 3, e7.PubMedCrossRefGoogle Scholar
  110. Wright, S.I., Bi, I.V., Schroeder, S.G., Yamasaki, M., Doebley, J.F., McMullen, M.D., Gaut, B.S. (2005). The effects of artificial selection on the maize genome. Science 308, 1310–1314.PubMedCrossRefGoogle Scholar
  111. Xu, D.H. and Gai, Y. (2003) Genetic diversity of wild and cultivated soybeans growing in China revealed by RAPD analysis. Plant Breeding 122, 503–506.CrossRefGoogle Scholar
  112. Yamasaki, M., Tenaillon, M.I., Bi, I.V., Schroeder, S.G,, Sanchez-Villeda, H., Doebley, J.F., Gaut, B.S., McMullen, M.D. (2005) A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell 17,2859–2872.PubMedCrossRefGoogle Scholar
  113. Yang, S.H., and Zeevaart, J.A. (2006) Expression of ABA 8-hydroxylases in relation to leaf water relations and seed development in bean. Plant J. 47, 675–686.PubMedCrossRefGoogle Scholar
  114. Zambre, M., Goossens, A., Cardona, C., Van Montagu, M., Terryn, N. and Angenon, G. (2005) A reproducible genetic transformation system for cultivated Phaseolus acutifolius (tepary bean) and its use to assess the role of arcelins in resistance to the Mexican bean weevil. Theor. Appl, Genet. 110, 914–924.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Phillip E. McClean
    • 1
  • Matt Lavin
  • Paul Gepts
  • Scott A. Jackson
  1. 1.Department of Plant SciencesNorth Dakota State UniversityFargoUSA

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