Genomics of Phaseolus Beans, a Major Source of Dietary Protein and Micronutrients in the Tropics

  • Paul Gepts
  • Francisco J.L. Aragão
  • Everaldo de Barros
  • Matthew W. Blair
  • Rosana Brondani
  • William Broughton
  • Incoronata Galasso
  • Gina Hernández
  • James Kami
  • Patricia Lariguet
  • Phillip McClean
  • Maeli Melotto
  • Phillip Miklas
  • Peter Pauls
  • Andrea Pedrosa-Harand
  • Timothy Porch
  • Federico Sánchez
  • Francesca Sparvoli
  • Kangfu Yu
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 1)


Common bean is grown and consumed principally in developing countries in Latin America, Africa, and Asia. It is largely a subsistence crop eaten by its producers and, hence, is underestimated in production and commerce statistics. Common bean is a major source of dietary protein, which complements carbohydrate-rich sources such as rice, maize, and cassava. It is also a rich source of minerals, such as iron and zinc, and certain vitamins. Several large germplasm collections have been established, which contain large amounts of genetic diversity, including the five domesticated Phaseolus species and wild species, as well as an incipient stock collection. The genealogy and genetic diversity of P. vulgaris are among the best known in crop species through the systematic use of molecular markers, from seed proteins and isozymes to simple sequence repeats, and DNA sequences. Common bean exhibits a high level of genetic diversity, compared with other selfing species. A hierarchical organization into gene pools and ecogeographic races has been established. There are over 15 mapping populations that have been established to study the inheritance of agronomic traits in different locations. Most linkage maps have been correlated with the core map established in the BAT93 x Jalo EEP558 cross, which includes several hundreds of markers, including Restriction Fragment Length Polymorphisms, Random Amplified Polymorphic DNA, Amplified Fragment Length Polymorphisms, Short Sequence Repeats, Sequence Tagged Sites, and Target Region Amplification Polymorphisms. Over 30 individual genes for disease resistance and some 30 Quantitative Trait Loci for a broad range of agronomic traits have been tagged. Eleven BAC libraries have been developed in genotypes that represent key steps in the evolution before and after domestication of common bean, a unique resource among crops. Fluorescence in situ hybridization provides the first links between chromosomal and genetic maps. A gene index based on some P. vulgaris 21,000 expressed sequence tags (ESTs) has been developed. ESTs were developed from different genotypes, organs, and physiological conditions. They resolve currently in some 6,500–6,800 singletons and 2,900 contigs. An additional 20,000 embryonic P. coccineus ESTs provides an additional resource. Some 1,500 M2 Targeting Local Lesions In Genomes populations exist currently. Finally, transformation methods by biolistics and Agrobacterium have been developed, which can be applied for genetic engineering. Root transformation via A. rhizogenes is also possible. Thus, the Phaseomics community has laid a solid foundation towards its ultimate goal, namely the sequencing of the Phaseolus genome. These genomic resources are a much-needed source of additional markers of known map location for marker-assisted selection and the accelerated improvement of common bean cultivars.


Quantitative Trait Locus Hairy Root Common Bean Angular Leaf Spot Common Bacterial Blight 
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. Adam-Blondon A, Sévignac M, Bannerot H, Dron M (1994) SCAR, RAPD and RFLP markers tightly linked to a dominant gene (Are) conferring resistance to anthracnose in common bean. Theor Appl Genet 88:865–870Google Scholar
  2. Aguilar OM, Riva O, Peltzer E (2004) Analysis of Rhizobium etli and of its symbiosis with wild Phaseolus vulgaris supports coevolution in centers of host diversification. Proc Natl Acad Sci USA 101:13548–13553PubMedGoogle Scholar
  3. Alzate-Marin AL, Arruda KM, Souza KA, Barros EG, Moreira MA (2005) Introgression of Co-4 2 and Co-5 anthracnose resistance genes into “Carioca” common bean cultivars with the aid of MAS. Ann Rep Bean Improv Coop 48:70–71Google Scholar
  4. Arag˜ FJL, Rech EL (1997) Morphological factors influencing recovery of transgenic bean plants (Phaseolus vulgaris L) of a Carioca cultivar. Int J Plant Sci 158:157–163Google Scholar
  5. Arag˜ FJL, Desa MFG, Almeida ER, Gander ES, Rech EL (1992) Particle bombardment-mediated transient expression of a Brazil nut methionine-rich albumin in bean (Phaseolus vulgaris L). Plant Mol Biol 20:357–359Google Scholar
  6. Arag˜ FJL, Desa MFG, Davey MR, Brasileiro ACM, Faria JC, Rech EL (1993) Factors influencing transient gene-expression in bean (Phaseolus vulgaris L) using an electrical particle-acceleration device. Plant Cell Rep 12:483–490Google Scholar
  7. Arag˜ F, Barros L, Brasileiro A, Ribeiro S, Smith F, Sanford J, Faria J, Rech E (1996) Inheritance of foreign genes in transgenic bean (Phaseolus vulgaris L) co-transformed via particle bombardment. Theor Appl Genet 93:142–150Google Scholar
  8. Arag˜ FJL, Barros LMG, de Sousa MV, Grossi de Sa MF, Almeida ERP, Gander ES, Rech EL (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). Genet Mol Biol 22:445–449Google Scholar
  9. Arag˜ FJL, Sarokin L, Vianna GR, Rech EL (2000) Selection of transgenic meristematic cells utilizing a herbicidal molecule results in the recovery of fertile transgenic soybean [Glycine max (L.) Merril] plants at a high frequency. Theor Appl Genet 101:1–6Google Scholar
  10. Arag˜ FJL, Vianna GR, Albino MMC, Rech EL (2002) Transgenic dry bean tolerant to the herbicide glufosinate ammonium. Crop Sci 42:1298–1302Google Scholar
  11. Araya CM, Alleyne AT, Steadman JR, Eskridge KM, Coyne AP (2004) Phenotypic and genotypic characterization of Uromyces appendiculatus from Phaseolus vulgaris in the Americas. Plant Dis 88:830–836Google Scholar
  12. Arndt GC, Gepts P (1989) Segregation and linkage for morphological and biochemical markers in a wide cross in common bean (Phaseolus vulgaris). Ann Rep Bean Improv Coop 32:68–69Google Scholar
  13. Awale HE, Kelly JD (2001) Development of SCAR markers linked to Co-4 2 gene in common bean. Ann Rpt Bean Improv Coop 44:119–120Google Scholar
  14. Bai YH, Michaels TE, Pauls KP (1997) Identification of RAPD markers linked to common bacterial blight resistance genes in Phaseolus vulgaris L. Genome 40:544–551Google Scholar
  15. Bassett MJ (1991) A revised linkage map of common bean. HortSci 26:834–836Google Scholar
  16. Becerra-Velásquez VL, Gepts P (1994) RFLP diversity in common bean (Phaseolus vulgaris L ). Genome 37:256–263Google Scholar
  17. Beebe S, Gonzalez AM, Rengifo J (2000a) Research on trace minerals in the common bean. Food and Nutrition Bull 21:387–391Google Scholar
  18. Beebe S, Skroch PW, Tohme J, Duque MC, Pedraza F, et al. (2000b) Structure of genetic diversity among common bean landraces of Middle American origin based on correspondence analysis of RAPD. Crop Sci 40:264–273Google Scholar
  19. Beebe S, Rengifo J, Gaitan E, Duque MC, Tohme J (2001) Diversity and origin of Andean landraces of common bean. Crop Sci 41:854–862Google Scholar
  20. Beebe SE, Rojas-Pierce M, Yan X, Blair MW, Pedraza F, et al. (2006) Quantitative trait loci for root architecture traits correlated with phosphorus acquisition in common bean. Crop Sci 46:413–423Google Scholar
  21. Bennett M, Leitch I (2005) Angiosperm DNA C-Values database. Release 4.0 Scholar
  22. Blair MW, Pedraza F, Buendia HF, Gaitán-Solís E, Beebe SE, et al. (2003) Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L ). Theor Appl Genet 107, 1362–1374PubMedGoogle Scholar
  23. Blair MW, Giraldo MC, Buendia HF, Tovar E, Duque MC, et al. (2006a) Microsatellite marker diversity in common bean (Phaseolus vulgaris L ). Theor Appl Genet 113:100–109Google Scholar
  24. Blair MW, Iriarte G, Beebe S (2006b) QTL analysis of yield traits in an advanced backcross population derived from a cultivated Andean x wild common bean (Phaseolus vulgaris L ) cross. Theor Appl Genet 112:1149–1163Google Scholar
  25. Blair MW, Muñoz C, Garza R, Cardona C (2006c) Molecular mapping of genes for resistance to the bean pod weevil (Apion godmani Wagner) in common bean. Theor Appl Genet 112: 913–923Google Scholar
  26. Boisson-Dernier A, Chabaud M, Garcia F, Becard G, Rosenberg C, et al. (2001) Agrobacterium rhizogenes-transformed roots of Medicago truncatula for the study of nitrogen-fixing and endomycorrhizal symbiotic associations. Molec Plant-Microbe Inter 14:695–700Google Scholar
  27. Bond JE, Gresshoff PM (1993) Soybean transformation to study molecular physiology. In: Gresshoff PM (ed ) Plant responses to the environment. CRC Press, Boca Raton, FL, USA, pp 25–44Google Scholar
  28. Bonfim K, Faria JC, Nogueira EOPL, Mendes EA, Arag˜ FJL (2007) RNAi-Mediated Resistance to Bean Golden Mosaic Virus in genetically engineered common bean (Phaseolus vulgaris) Molec Plant-Microbe Inter 20:717–726Google Scholar
  29. Boutin S, Young N, Olson T, Yu Z, Shoemaker R, et al. (1995) Genome conservation among three legume genera detected with DNA markers. Genetics 38:928–937Google Scholar
  30. Bressani R (1983) Research needs to upgrade the nutritional quality of common beans (Phaseolus vulgaris). Qualitas Plantarum Plant Foods Human Nutrition 32:101–110Google Scholar
  31. Broughton WJ, Hernandez G, Blair M, Beebe S, Gepts P, et al. (2003) Beans (Phaseolus spp.) – model food legumes. Plant Soil 252:55–128Google Scholar
  32. Buso GSC, Amaral ZPS, Brondani RPV, Ferreira ME (2006) Microsatellite markers for the common bean – Phaseolus vulgaris. Mol Ecol Notes 6:252–254Google Scholar
  33. Caixeta ET, Borém A, Kelly JD (2005a) Development of microsatellite markers based on BAC common bean clones. Crop Breed Appl Biotech 5:125–133Google Scholar
  34. Caixeta ET, Borem A, Azate-Marin AL, Fagundes SA, Silva MGM, et al. (2005b) Allelic relationships for genes that confer resistance to angular leaf spot in common bean. Euphytica 145:237–245Google Scholar
  35. Chang YL, Henriquez X, Preuss D, Copenhaver GP, Zhang HB (2003) A plant-transformation-competent BIBAC library from the Arabidopsis thaliana Landsberg ecotype for functional and comparative genomics. Theor Appl Genet 106:269–276PubMedGoogle Scholar
  36. Cheon CI, Lee NG, Siddique ABM, Bal AK, Verma DPS (1993) Roles of plant homologs of Rab1p and Rab7p in the biogenesis of the peribacteroid membrane, a subcellular compartment formed de-novo during root-nodule symbiosis. EMBO J 12:4125–4135PubMedGoogle Scholar
  37. Choi H-K, Mun J-H, Kim D-J, Zhu H, Baek J-M, et al. (2004) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 101:15289–15294PubMedGoogle Scholar
  38. Costa MR, Tanure JPM, Arruda KMA, Carneiro JES, Moreira MA, et al. (2006) Pyramiding of anthracnose, angular leaf spot and rust resistance genes in black and red bean cultivars. Ann Rep Bean Improv Coop 49:187–188Google Scholar
  39. Debouck DG, Toro O, Paredes OM, Johnson WC, Gepts P (1993) Genetic diversity and ecological distribution of Phaseolus vulgaris in northwestern South America. Econ Bot 47:408–423Google Scholar
  40. Díaz CL, Spaink HP, Kijne JW (2000) Heterologous rhizobial lipochitin oligosaccharides and chitin oligomers induce cortical cell divisions in red clover roots, transformed with the pea lectin gene. Molec Plant-Microbe Inter 13:268–276Google Scholar
  41. 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 PM, Sánchez F (2006) Agrobacterium rhizogenes-transformation of the Phaseolus spp.: A tool for functional genomics. Molec Plant-Micr Inter 19:1385–1393Google Scholar
  42. Faria JC, Albino MMC, Dias BBA, Cancado LJ, da Cunha NB, Silva LD, Vianna GR, Aragão FJL (2006) Partial resistance to bean golden mosaic virus in a transgenic common bean (Phaseolus vulgaris L.) line expressing a mutated rep gene. Plant Sci 171:565–571Google Scholar
  43. Foster-Hartnett D, Mudge J, Larsen D, Danesh D, Yan HH, et al. (2002) Comparative genomic analysis of sequences sampled from a small region on soybean (Glycine max) molecular linkage group G. Genome 45:634–645PubMedGoogle Scholar
  44. Frei A, Blair MW, Cardona C, Beebe SE, Gu H, et al. (2005) QTL mapping of resistance to Thrips palmi Karny in common bean. Crop Sci 45:379–387Google Scholar
  45. Freyre, R, Skroch P, Geffroy V, Adam-Blondon A-F, Shirmohamadali A, et al. (1998) Towards an integrated linkage map of common bean. 4. Development of a core map and alignment of RFLP maps. Theor Appl Genet 97:847–856Google Scholar
  46. Gaitán-Solís 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 42:2128–2136Google Scholar
  47. Galasso I, Lioi L, Lanave C, Campion B, Bollini R, et al. (2005) Identification and sequencing of a BAC clone belonging to the Phaseolus vulgaris (L) insecticidal Arc4 lectin locus. Ann Rep Bean Improv Coop 48:40–40Google Scholar
  48. Geffroy V, Sicard D, de Oliveira J, Sévignac M, Cohen S, et al. (1999) Identification of an ancestral resistance gene cluster involved in the coevolution process between Phaseolus vulgaris and its fungal pathogen Colletotrichum lindemuthianum. Molec Plant-Microbe Inter 12:774–784Google Scholar
  49. Geffroy V, Sévignac M, De Oliveira J, Fouilloux G, Skroch P, et al. (2000) Inheritance of partial resistance against Colletotrichum lindemuthianum in Phaseolus vulgaris and co-localization of QTL with genes involved in specific resistance. Molec Plant-Microbe Inter 13:287–296Google Scholar
  50. Genga AM, Allavena A, Ceriotti A, Bollini R (1992) Genetic transformation in Phaseolus by high-velocity particle microprojectiles. Acta Hort. 300:309–313Google Scholar
  51. Gepts P (1988) Provisional linkage map of common bean. Annu Rep Bean Improv Coop 31:20–25Google Scholar
  52. Gepts P (1990) Biochemical evidence bearing on the domestication of Phaseolus beans. Econ Bot 44(3S):28–38Google Scholar
  53. Gepts P, Bliss FA (1984) Enhanced available methionine concentration associated with higher phaseolin levels in common bean seeds. Theor Appl Genet 69:47–53Google Scholar
  54. Gepts P, Bliss FA (1985) F1 hybrid weakness in the common bean: differential geographic origin suggests two gene pools in cultivated bean germplasm. J Hered 76:447–450Google Scholar
  55. Gepts P, Bliss FA (1986) Phaseolin variability among wild and cultivated common beans (Phaseolus vulgaris) from Colombia. Econ Bot 40:469–478Google Scholar
  56. Gepts P, Osborn TC, Rashka K, Bliss FA (1986) Phaseolin-protein variability in wild forms and landraces of the common bean (Phaseolus vulgaris): evidence for multiple centers of domestication. Econ Bot 40:451–468Google Scholar
  57. Graham MA, Ramírez M, Valdés-López O, Lara M, Tesfaye M, et al. (2006) Identification of phosphorus stress induced genes in Phaseolus vulgaris L. through clustering analysis across several species. Funct Plant Biol 33:789–797Google Scholar
  58. Grant JE, Dommiss EM, Conner AJ (1991) Gene transfer to plants using Agrobacterium. In: Murray DR (ed) Advanced methods in plant breeding and biotechnology. CAB International, Wallingford, pp 50–73Google Scholar
  59. Guerra-Sanz JM (2004) New SSR markers of Phaseolus vulgaris from sequence databases. Plant Breed 123:87–89Google Scholar
  60. Guzmán P, Gilbertson RL, Nodari R, Johnson WC, Temple SR, et al. (1995) Characterization of variability in the fungus Phaeoisariopsis griseola suggests coevolution with the common bean (Phaseolus vulgaris). Phytopathology 85:600–607Google Scholar
  61. Guzmán-Maldonado SH, Martínez O, Acosta-Gallegos JA, Guevara-Lara F, Paredes-López O (2003) Putative quantitative trait loci for physical and chemical components of common bean. Crop Sci 43:1029–1035Google Scholar
  62. Hagenblad J, Tang CL, Molitor J, Werner J, Zhao K, et al. (2004) Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci. Genetics 168:1627–1638PubMedGoogle Scholar
  63. Hagiwara WE, dos Santos JB, do Carmo LM (2001) Use of RAPD to aid selection in common bean backcross breeding programs. Crop Breed Appl Biotech 1:355–362Google Scholar
  64. Haley S, Afanador L, Miklas P, Stavely J, Kelly J (1994) Heterogeneous inbred populations are useful as sources of near-isogenic lines for RAPD marker localization. Theor Appl Genet 88:337–342Google Scholar
  65. Henikoff S, Till BJ, Comai L (2004) TILLING. Traditional mutagenesis meets functional genomics. Plant Physiol 135:630–636PubMedGoogle Scholar
  66. Islam FMA, Basford KE, Jara C, Redden RJ, Beebe S (2002) Seed compositional and disease resistance differences among gene pools in cultivated common bean. Genetic Res Crop Evol 49:285–293Google Scholar
  67. Johnson E, Miklas P, Stavely J, Martínez-Cruzado J (1995) Coupling- and repulsion-RAPDs for marker-assisted selection of PI 181996 rust resistance in common bean. Theor Appl Genet 90:659–664Google Scholar
  68. Johnson WC, Guzmán P, Mandala D, Mkandawire A, Temple S, et al. (1997) Molecular tagging of the bc-3 gene for introgression into Andean common bean. Crop Sci 37: 248–254Google Scholar
  69. Johnson WC, Gepts P (2002) The role of epistasis in controlling seed yield and other agronomic traits in an Andean x Mesoamerican cross of common bean (Phaseolus vulgaris L.). Euphytica 125:69–79Google Scholar
  70. Jorde LB (2000) Linkage disequilibrium and the search for complex disease genes. Genome Res 10:1435–1444PubMedGoogle Scholar
  71. Jung G, Coyne D, Skroch P, Nienhuis J, Arnaud-Santana E, et al. (1996) Molecular markers associated with plant architecture and resistance to common blight, web blight, and rust in common beans. J Am Soc Hort Sci 121:794–803Google Scholar
  72. Kami J, Becerra Velásquez B, Debouck DG, Gepts P (1995) Identification of presumed ancestral DNA sequences of phaseolin in Phaseolus vulgaris. Proc Natl Acad Sci USA 92:1101–1104PubMedGoogle Scholar
  73. Kami J, Poncet V, Geffroy V, Gepts P (2006) Development of four phylogenetically-arrayed BAC libraries and sequence of the APA locus in Phaseolus vulgaris. Theor Appl Genet 112:987–998PubMedGoogle Scholar
  74. Kelly J, Miklas PN (1998) The role of RAPD markers in breeding for disease resistance in common bean. Mol Breed 4:1–11Google Scholar
  75. Kelly JD, Vallejo VA (2004) A comprehensive review of the major genes conditioning resistance to anthracnose in common bean. Hortscience 39:1196–1207Google Scholar
  76. Kelly JD, Gepts P, Miklas PN, Coyne DP (2003) Tagging and mapping of genes and QTL and molecular marker-assisted selection for traits of economic importance in bean and cowpea. Field Crop Res 82:135–154Google Scholar
  77. Khairallah MM, Adams MW, Sears BB (1990) Mitochondrial DNA polymorphisms of Malawian bean lines: further evidence for two major gene pools. Theor Appl Genet 80:753–761Google Scholar
  78. Khairallah MM, Sears BB, Adams MW (1992) Mitochondrial restriction fragment polymorphisms in wild Phaseolus vulgaris – insights in the domestication of common bean. Theor Appl Genet 84:915–922Google Scholar
  79. Kim JW, Minamikawa T (1996) Transformation and regeneration of French bean plants by the particle bombardment process. Plant Sci 117:131–138Google Scholar
  80. Koenig R, Gepts P (1989a) Segregation and linkage of genes for seed proteins, isozymes, and morphological traits in common bean (Phaseolus vulgaris). J Hered 80:455–459Google Scholar
  81. Koenig R, Gepts P (1989b) Allozyme diversity in wild Phaseolus vulgaris: further evidence for two major centers of diversity. Theor Appl Genet 78:809–817Google Scholar
  82. Koenig R, Singh SP, Gepts P (1990) Novel phaseolin types in wild and cultivated common bean (Phaseolus vulgaris, Fabaceae). Econ Bot 44:50–60Google Scholar
  83. Koinange EMK, Singh SP, Gepts P (1996) Genetic control of the domestication syndrome in common-bean. Crop Sci 36:1037–1045Google Scholar
  84. Kolkman JM, Kelly JD (2003) QTL conferring resistance and avoidance to white mold in common bean. Crop Sci 43:539–548Google Scholar
  85. Kulikova O, Gualtieri G, Geurts R, Kim DJ, Cook D, et al. (2001) Integration of the FISH pachytene and genetic maps of Medicago truncatula. Plant J 27:49–58PubMedGoogle Scholar
  86. Larsen RC, Miklas PN (2004) Generation and molecular mapping of a sequence characterized amplified region marker linked with the Bct gene for resistance to Beet curly top virus in common bean. Phytopathology 94:320–325Google Scholar
  87. Lavin M, Herendeen PS, Wojciechowski MF (2005) Evolutionary rates analysis of Leguminosae implicates a rapid diversification of the major family lineages immediately following an Early Tertiary emergence. Syst Biol 54:575–594PubMedGoogle Scholar
  88. Lee JM, Grant D, Vallejos CE, Shoemaker RC (2001) Genome organization in dicots. II. Arabidopsis as a ‘bridging species’ to resolve genome evolution events among legumes. Theor Appl Genet 103:765–773Google Scholar
  89. Lee, NG, Stein B, Suzuki H, Verma DPS (1993) Expression of antisense nodulin-35 RNA in Vigna aconitifolia transgenic root nodules retards peroxisome development and affects nitrogen availability to the plant. Plant J 3:599–606PubMedGoogle Scholar
  90. Liu ZC, Park BJ, Kanno A, 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 16:189–197Google Scholar
  91. López CE, Acosta IF, Jara C, Pedraza F, Gaitán-Solís E, et al. (2003) Identifying resistance gene analogs associated with resistances to different pathogens in common bean. Phytopathology 93:88–95Google Scholar
  92. Mackay TFC (2001) The genetic architecture of quantitative traits. Ann Rev Genet 35:303–339PubMedGoogle Scholar
  93. Maréchal R, Mascherpa J-M, Stainier F (1978) Etude taxonomique d'un groupe complexe d'espèces des genres Phaseolus et Vigna (Papilionaceae) sur la base de données morphologiques et polliniques, traitées par l'analyse informatique. Boissiera 28:1–273Google Scholar
  94. Mauro Herrera M (2003) Wild bean populations as source of genes to improve the yield of cultivated Phaseolus vulgaris L. Ph.D. thesis, University of California, DavisGoogle Scholar
  95. McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeting induced local lesions in genomes (TILLING) for plant functional genomics. Plant Physiol 123:439–442PubMedGoogle Scholar
  96. McClean PE, Lee RK, Otto C, Gepts P, , Bassett MJ (2002) Molecular and phenotypic mapping of genes controlling seed coat pattern and color in common bean (Phaseolus vulgaris L). J Hered 93:148–152PubMedGoogle Scholar
  97. McClean PE, Lee RK, Miklas PN (2004) Sequence diversity analysis of dihydroflavonol 4-reductase intron 1 in common bean. Genome 47:266–280PubMedGoogle Scholar
  98. McClean PE, Lee RD, McConnell MD, Mamidi S, White CP (2006) Sequence and marker-based diversity in common bean. Plant Animal Genome 14:W144, p 40Google Scholar
  99. McConnell M, Mamidi S, Lee R, McClean P (2006) DNA sequence polymorphism among common bean genes. Ann Rept Bean Improv Coop 49:143–144Google Scholar
  100. Melotto M, Fransisco C, Camargo LEA (2003) Towards cloning the Co-4 2 locus using a bean BAC library. Ann Rep Bean Improv Coop 46:51–52Google Scholar
  101. Melotto M, Coelho MF, Pedrosa-Harand A, Kelly JD, Camargo LEA (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 109:690–699PubMedGoogle Scholar
  102. Melotto M, Monteiro-Vitorello CB, Bruschi AG, Camargo LEA (2005) Comparative bioinformatic analysis of genes expressed in common bean (Phaseolus vulgaris L.) seedlings. Genome 48:562–570PubMedGoogle Scholar
  103. Métais I, Hamon B, Jalouzot R, Peltier D (2002) Structure and level of genetic diversity in various bean types evidenced with microsatellite markers isolated from a genomic enriched library.Google Scholar
  104. Michaels TE, Smith TW, Larsen J, Beattie AD, Pauls KP (2005) OAC Rex common bean. Can J Plant Sci 86:733–736Google Scholar
  105. Mienie C, Liebenberg M, Pretorius Z, Miklas P (2005) SCAR markers linked to the common bean rust resistance gene Ur-13. Theor Appl Genet 111:972–979PubMedGoogle Scholar
  106. Miklas PN (2005) List of SCAR marker for disease resistance: Aug 2005 update Scholar
  107. Miklas PN, Kelly JD (2002) Registration of two cranberry bean germplasm lines resistant to Bean Common Mosaic and Necrosis Potyviruses: USCR-7 and USCR-9. Crop Sci 42:673–674Google Scholar
  108. Miklas PN, Stavely JR, Kelly JD (1993) Identification and potential use of a molecular marker for rust resistance in common bean. Theor Appl Genet 85:745–749Google Scholar
  109. Miklas PN, Johnson E, Stone V, Beaver JS, Montoya C, et al. (1996) Selective mapping of QTL conditioning disease resistance in common bean. Crop Sci 36:1344–1351Google Scholar
  110. Miklas PN, Larsen RC, Riley R, Kelly JD (2000) Potential marker-assisted selection for bc-1 2 resistance to bean common mosaic potyvirus in common bean. Euphytica 116:211–219Google Scholar
  111. Miklas PN, Johnson WC, Delorme R, Gepts P (2001) QTL conditioning physiological resistance and avoidance to white mold in dry bean. Crop Sci 41:309–315Google Scholar
  112. Miklas PN, Hang AN, Kelly JD, Strausbaugh CA, Forster RL (2002) Registration of three kidney bean germplasm lines resistant to Bean Common Mosaic and Necrosis Potyviruses: USLK-2 Light Red Kidney, USDK-4 Dark Red Kidney, and USWK-6 White Kidney. Crop Sci 42:674–675Google Scholar
  113. Miklas PN, Delorme R, Riley R (2003a) Identification of QTL conditioning resistance to white mold in snap bean. J Am Soc Hort Sci 128:564–570Google Scholar
  114. Miklas PN, Kelly JD, Singh SP (2003b) Registration of anthracnose resistant pinto bean germplasm line USPT ANT 1. Crop Sci 43:1889–1890Google Scholar
  115. Miklas PN, Hu J, Grünwald NJ, Larsen KM (2006a) Potential application of TRAP (Targeted Region Amplified Polymorphism) markers for mapping and tagging disease resistance traits in common bean. Crop Sci 46:910–916Google Scholar
  116. Miklas PN, Kelly JD, Beebe SE, Blair MW (2006b) Common bean breeding for resistance against biotic and abiotic stresses: from classical to MAS breeding. Euphytica 147:106–131Google Scholar
  117. Miklas PN, Smith JR, Singh SP (2006c) Registration of common bacterial blight resistant dark red kidney bean germplasm line USDK-CBB-15 10.2135/cropsci2005.06-0110. Crop Sci 46:1005–1007Google Scholar
  118. Miklas PN, Smith JR, Singh SP (2006d) Release of common bacterial blight resistant pinto bean germplasm lines USPT-CBB-5 and USPT-CBB-6. Ann Rep Bean Improv Coop 49:283–284Google Scholar
  119. Mkandawire ABC, Mabagala RB, Guzman P, Gepts P, Gilbertson RL (2004) Genetic diversity and pathogenic variation of common blight bacteria (Xanthomonas campestris pv. phaseoli and X. campestris pv. phaseoli var. fuscans) suggests pathogen coevolution with the common bean. Phytopathology 94:593–603Google Scholar
  120. Moffett MD, Weeden NF (2006) Investigation of synteny conservation between Pisum and Phaseolus. Abstract, Plant & Animal Genome XIV, 2006: http://www.intl-pag. org/14/abstracts/PAG14_P442.html Moscone EA, Klein F, Lambrou M, Fuchs J, Schweizer D (1999) Quantitative karyotyping and dual-color FISH mapping of 5S and 18S-25S rDNA probes in the cultivated Phaseolus species (Leguminosae). Genome 42:1224–1233Google Scholar
  121. Murray J, Larsen J, Michaels TE, Schaafsma A, Vallejos CE, et al. (2002) Identification of putative genes in bean (Phaseolus vulgaris) genomic (Bng) RFLP clones and their conversion to STSs. Genome 45:1013–1024PubMedGoogle Scholar
  122. Mutlu N, Miklas PN, Coyne DP (2006) Resistance gene analog polymorphism (RGAP) markers co-localize with disease resistance genes and QTL in common bean. Mol Breed 17: 127–135Google Scholar
  123. Mutlu N, Miklas P, Reiser J, Coyne D (2005a) Backcross breeding for improved resistance to common bacterial blight in pinto bean (Phaseolus vulgaris L.). Plant Breed 124:282–287Google Scholar
  124. Mutlu N, Miklas PN, Steadman JR, Vidaver AV, Lindgren D, et al. (2005b) Registration of pinto bean germplasm line ABCP-8 with resistance to common bacterial blight. Crop Sci 45:806Google Scholar
  125. Nagl W (1969) Banded polytene chromosomes in the legume Phaseolus vulgaris. Nature 221:70–71PubMedGoogle Scholar
  126. Nanni L, Losa A, Bellucci E, Kater M, Gepts P, et al. (2005) Identification and molecular diversity of a genomic sequence similar to SHATTERPROOF (SHP1) in Phaseolus vulgaris L. Plant Animal Genome XIII:P470, p 188Google Scholar
  127. Nodari RO, Koinange EMK, Kelly JD, 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 84:186–192Google Scholar
  128. Nodari RO, Tsai SM, Gilbertson RL, Gepts P (1993a) Towards an integrated linkage map of common bean. II. Development of an RFLP-based linkage map. Theor Appl Genet 85:513–520Google Scholar
  129. Nodari RO, Tsai SM, Guzmán P, Gilbertson RL, Gepts P (1993b) Towards an integrated linkage map of common bean. 3. Mapping genetic factors controlling host-bacteria interactions. Genetics 134:341–350Google Scholar
  130. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, et al. (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biology 3:e196PubMedGoogle Scholar
  131. Ochoa IE, Blair MW, Lynch JP (2006) QTL analysis of adventitious root formation in common bean under contrasting phosphorus availability 10.2135/cropsci2005.12-0446. Crop Sci 46:1609–1621Google Scholar
  132. Pallottini L, Garcia E, Kami J, Barcaccia G, Gepts P (2004) The genetic anatomy of a patented yellow bean. Crop Sci 44:968–977Google Scholar
  133. Papa R, 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 106:239–250PubMedGoogle Scholar
  134. Papa R, Acosta J, Delgado-Salinas A, Gepts P (2005) A genome-wide analysis of differentiation between wild and domesticated Phaseolus vulgaris from Mesoamerica. Theor Appl Genet 111:1147–1158PubMedGoogle Scholar
  135. Payró de la Cruz E, Gepts P, Colunga GarciaMarín P, Zizumbo Villareal D (2005) Spatial distribution of genetic diversity in wild populations of Phaseolus vulgaris L. from Guanajuato and Michoacán, México. Genet Res Crop Evol 52:589–599Google Scholar
  136. Pedrosa A (2003) Chromosomal organisation and physical mapping in legumes. Ph.D. thesis, University of Vienna, 143 pGoogle Scholar
  137. Pedrosa A, Sandal N, Stougaard J, Schweizer D, Bachmair A (2002) Chromosomal map of the model legume Lotus japonicus. Genetics 161:1661–1672PubMedGoogle Scholar
  138. Pedrosa A, Vallejos C, Bachmair A, Schweizer D (2003) Integration of common bean (Phaseolus vulgaris L.) linkage and chromosomal maps. Theor Appl Genet 106:205–212PubMedGoogle Scholar
  139. Pedrosa-Harand A, Almeida CCS, Mosiolek M, Blair MW, Schweizer D, et al. (2006) Extensive ribosomal DNA amplification during Andean common bean (Phaseolus vulgaris L.) evolution. Theor Appl Genet 112:924–933PubMedGoogle Scholar
  140. Perry JA, Wang TL, Welham TJ, Gardner S, Pike JM, et al. (2003) A TILLING reverse genetics tool and a web-accessible collection of mutants of the legume Lotus japonicus. Plant Physiol 131:866–871PubMedGoogle Scholar
  141. Perry G, Reinprecht Y, Pauls KP (2006) Identification of common bacterial blight resistance genes in Phaseolus vulgaris. Abstract P16051, Plant Biology 2006, Joint Annual Meeting of the American Society of Plant Biologists and the Canadian Society of Plant Physiologists, BostonGoogle Scholar
  142. Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  143. Ragagnin VA, Alzate-Marin AL, Souza TLPO, Sanglard DA, Moreira MA, et al. (2005) Use of molecular markers to pyramiding multiple genes for resistance to rust, anthracnose and angular leaf spot in the common bean. Ann Rep Bean Improv Coop 48:94–95Google Scholar
  144. Ramírez M, Graham MA, Blanco-López L, Silvente S, Medrano-Soto A, et al. (2005) Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol 137:1211–1227Google Scholar
  145. Rivkin M, Vallejos C, McClean P (1999) Disease-related sequences in common bean. Genome 42:41–47PubMedGoogle Scholar
  146. Russell DR, Wallace KM, Bathe JH, Martinell BJ (1993) Stable transformation of Phaseolus vulgaris via electric discharge mediated particle acceleration. Plant Cell Rep 12:165–169Google Scholar
  147. Santalla M, Rodino AP, de Ron AM (2002) Allozyme evidence supporting southwestern Europe as a secondary center of genetic diversity for the common bean. Theor Appl Genet 104:934–944PubMedGoogle Scholar
  148. Sarbhoy RK (1978) Cytogenetical studies in genus Phaseolus Linn. I and II. Somatic and meiotic studies in fifteen species of Phaseolus. Cytologia 43:161–180Google Scholar
  149. Schmid K, Ramos-Onsins S, Ringys-Beckstein H, Weisshaar B, Mitchell-Olds T (2005) A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism. Genetics 169:1601–1615PubMedGoogle Scholar
  150. Shahmuradov IA, Akbarova YY, Solovyev VV, Aliyev JA (2003) Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis. Plant Mol Biol 52:923–934PubMedGoogle Scholar
  151. Singh SP, Gepts P, Debouck DG (1991a) Races of common bean (Phaseolus vulgaris L., Fabaceae). Econ Bot 45:379–396Google Scholar
  152. Singh SP, Nodari R, Gepts P (1991b) Genetic diversity in cultivated common bean. I. Allozymes. Crop Sci 31:19–23Google Scholar
  153. Singh SP, Morales FJ, Miklas PN, Teran H (2000a) Selection for bean golden mosaic resistance in intra- and interracial bean populations. Crop Sci 40:1565–1572Google Scholar
  154. Singh SP, Morales FJ, Terán H (2000b) Registration of bean golden mosaic resistant dry bean germplasm GMR 1 and GMR 5. Crop Sci 40:1836Google Scholar
  155. Stavely JR, Kelly JD, Grafton KF (1994) BelMiDak-rust-resistant navy dry beans germplasm lines. HortScience 29:709–710Google Scholar
  156. Stavely JR, McMillan RT, Beaver JS, Miklas PN (2001) Release of three McCaslan type, indeterminate, rust and golden mosaic resistant snap bean germplasm lines BelDade RGMR 4, 5 and 6. Ann Rep Bean Improv Coop 44:197–198Google Scholar
  157. Stiller J, Martirani L, Tuppale S, Chian RJ, Chiurazzi M, et al. (1997) High frequency transformation and regeneration of transgenic plants in the model legume Lotus japonicus. J Exp Bot 48:1357–1365Google Scholar
  158. Tar'an B, Michaels TE, Pauls KP (2001) Mapping genetic factors affecting the reaction to Xanthomonas axonopodis pv. phaseoli in Phaseolus vulgaris L. under field conditions. Genome 44:1046–1056Google Scholar
  159. Tar'an B, Michaels TE, Pauls KP (2002) Genetic mapping of agronomic traits in common bean. Crop Sci 42:544–556Google Scholar
  160. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, et al. (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp mays L.). Proc Natl Acad Sci USA 98:9161–9166PubMedGoogle Scholar
  161. Tepfer D (1990) Genetic transformation using Agrobacterium rhizogenes. Physiol Plant 79:140–146Google Scholar
  162. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, et al. (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289PubMedGoogle Scholar
  163. Urrea C, Miklas P, Beaver J, Riley R (1996) A codominant randomly amplified polymorphic DNA (RAPD) marker useful for indirect selection of bean golden mosaic virus resistance in common bean. J Am Soc Hort Sci 121:1035–1039Google Scholar
  164. Vallad G, Rivkin M, Vallejos C, McClean P (2001) Cloning and homology modelling of a Pto-like protein kinase family of common bean (Phaseolus vulgaris L.). Theor Appl Genet 103:1046–1058Google Scholar
  165. Vallejos C, Skroch P, Nienhuis J (2001) Phaseolus vulgaris – The common bean. Integration of RFLP and RAPD-based linkage maps. In: Phillips R, Vasil I (eds), DNA-based markers in plants. Kluwer, Dordrecht, the Netherlands, pp. 301–317Google Scholar
  166. Vallejos CE, Astua-Monge G, Jones V, Plyler TR, Sakiyama NS, et al. (2006) Genetic and molecular characterization of the I Locus of Phaseolus vulgaris. Genetics 172:1229–1242 Vallejos CE, Chase CD (1991) Linkage between isozyme markers and a locus affecting seed size in Phaseolus vulgaris L. Theor Appl Genet 81:413–419PubMedGoogle Scholar
  167. Vallejos CE, Sakiyama NS, Chase CD (1992) A molecular marker-based linkage map of Phaseolus vulgaris L. Genetics 131:733–740PubMedGoogle Scholar
  168. Van de Velde W, Mergeay J, Holsters M, Goormachtig S (2003) Agrobacterium rhizogenes-mediated transformation of Sesbania rostrata. Plant Sci 165:1281–1288Google Scholar
  169. Vanhouten W, Mackenzie S (1999) Construction and characterization of a common bean bacterial artificial chromosome library. Plant Mol Biol 40:977–983PubMedGoogle Scholar
  170. Vianna GR, Albino MMC, Dias BBA, Silva LdM, Rech EL, Aragão FJL (2004) Fragment DNA as vector for genetic transformation of bean (Phaseolus vulgaris L.). Scientia Horticulturae (Amsterdam) 99:371–378Google Scholar
  171. Yaish MWF, de la Vega MP (2003) Isolation of (GA)(n) microsatellite sequences and description of a predicted MADS-box sequence isolated from common bean (Phaseolus vulgaris L.). Genet Mol Biol 26:337–342Google Scholar
  172. Yan HH, Mudge J, Kim DJ, Shoemaker RC, Cook DR, et al. (2004) Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana. Genome 47:141–155PubMedGoogle Scholar
  173. Yu K, Park S, Poysa V, Gepts P (2000) Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.). J Hered 91:429–434PubMedGoogle Scholar
  174. Yu K, Haffne M, Park SJ (2006) Construction and characterization of a common bean BAC library. Ann Rep Bean Improv Coop 49:61–63Google Scholar
  175. Yu KF, Park SJ, Poysa V (1999) Abundance and variation of microsatellite DNA sequences in beans (Phaseolus and Vigna). Genome 42:27–34Google Scholar
  176. Yu Z, Stall R, Vallejos C (1998) Detection of genes for resistance to common bacterial blight of beans. Crop Sci 38:1290–1296Google Scholar
  177. Zambre M, Goossens A, Cardona C, Van Montagu M, Terryn N, et al. (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 110:914–924PubMedGoogle Scholar
  178. Zhang ZY, Coyne DP, Mitra A (1997) Factors affecting Agrobacterium-mediated transformation of common bean. J Am Soc Hort Sci 122:300–305Google Scholar
  179. Zheng J, Nakata M, Uchiyama H, Morikawa H, Tanaka R (1991) Giemsa C-banding patterns in several species of Phaseolus L. and Vigna Savi, Fabaceae. Cytologia 56:459–466Google Scholar
  180. Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, et al. (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134PubMedGoogle Scholar
  181. Zizumbo-Villarreal D, Colunga-GarcíaMarín P, Payró de la Cruz E, Delgado-Valerio P, Gepts P (2005) Population structure and evolutionary dynamics of wild–weedy–domesticated complexes of common bean in a Mesoamerican region. Crop Sci 35:1073–1083Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Paul Gepts
    • 1
  • Francisco J.L. Aragão
  • Everaldo de Barros
  • Matthew W. Blair
  • Rosana Brondani
  • William Broughton
  • Incoronata Galasso
  • Gina Hernández
  • James Kami
  • Patricia Lariguet
  • Phillip McClean
  • Maeli Melotto
  • Phillip Miklas
  • Peter Pauls
  • Andrea Pedrosa-Harand
  • Timothy Porch
  • Federico Sánchez
  • Francesca Sparvoli
  • Kangfu Yu
  1. 1.Department of Plant Sciences / MS1, Section of Crop and Ecosystem SciencesUniversity of CaliforniaDavisUSA

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