, Volume 138, Issue 7, pp 709–716 | Cite as

Construction of a BAC library and a physical map of a major QTL for CBB resistance of common bean (Phaseolus vulgaris L.)

  • S. Y. Liu
  • K. Yu
  • M. Huffner
  • S. J. Park
  • M. Banik
  • K. P. Pauls
  • W. Crosby


A major quantitative trait loci (QTL) conditioning common bacterial blight (CBB) resistance in common bean (Phaseolus vulgaris L.) lines HR45 and HR67 was derived from XAN159, a resistant line obtained from an interspecific cross between common bean lines and the tepary bean (P. acutifolius L.) line PI319443. This source of CBB resistance is widely used in bean breeding. Several other CBB resistance QTL have been identified but none of them have been physically mapped. Four molecular markers tightly linked to this QTL have been identified suitable for marker assisted selection and physical mapping of the resistance gene. A bacterial artificial chromosome (BAC) library was constructed from high molecular weight DNA of HR45 and is composed of 33,024 clones. The size of individual BAC clone inserts ranges from 30 kb to 280 kb with an average size of 107 kb. The library is estimated to represent approximately sixfold genome coverage. The BAC library was screened as BAC pools using four PCR-based molecular markers. Two to seven BAC clones were identified by each marker. Two clones were found to have both markers PV-tttc001 and STS183. One preliminary contig was assembled based on DNA finger printing of those positive BAC clones. The minimum tiling path of the contig contains 6 BAC clones spanning an estimated size of 750 kb covering the QTL region.


Common bacterial blight Physical mapping Bacterial artificial chromosome library Common bean Contig 


  1. Bennett MD, Leitch IJ (1995) Nuclear-DNA amounts in angiosperms. Ann Bot 76:113–176CrossRefGoogle Scholar
  2. Broughton WJ, Hernandez G, Blair M, Beebe S, Gepts P, Vanderleyden J (2003) Beans (Phaseolus spp.)—model food legumes. Plant Soil 252:55–128CrossRefGoogle Scholar
  3. Bruno WJ, Knill E, Balding DJ, Bruce DC, Doggett NA, Sawhill WW, Stallings RL, Whittaker CC, Whittaker CC, Torney DC (1995) Efficient pooling designs for library screening. Genomics 26:21–30CrossRefPubMedGoogle Scholar
  4. Chang YL, Tao Q, Scheuring C, Ding K, Meksem K, Zhang HB (2001) An integrated map of Arabidopsis thaliana for functional analysis of its genome sequence. Genetics 159:1231–1242PubMedGoogle Scholar
  5. D’Ovidio R, Raiola A, Capodicasa C, Devoto A, Pontiggia D, Roberti S, Galletti R, Conti E, O’Sullivan D, De Lorenzo G (2004) Characterization of the complex locus of bean encoding polygalacturonase-inhibiting proteins reveals subfunctionalization for defense against fungi and insects. Plant Physiol 135:2424–2435CrossRefPubMedGoogle Scholar
  6. David P, Sevignac M, Thareau V, Catillon Y, Kami J, Gepts P, Langin T, Geffroy V (2008) BAC end sequences corresponding to the B4 resistance gene cluster in common bean: a resource for markers and synteny analyses. Mol Genet Genomics 280:521–533CrossRefPubMedGoogle Scholar
  7. David P, Chen NWG, Pedrosa-Harand A, Thareau V, Sévignac M, Cannon SB, Debouck D, Langin T, Geffroy V (2009) A nomadic subtelomeric disease resistance gene cluster in common bean. Plant Physiol 151:1048–1065CrossRefPubMedGoogle Scholar
  8. Folkertsma RT, Spassova MI, Prins M, Stevens MR, Hille J, Goldbach RW (1999) Construction of a bacterial artificial chromosome (BAC) library of Lycopersicon esculentum cv. Stevens and its application to physically map the Sw-5 locus. Mol Breed 5:197–207CrossRefGoogle Scholar
  9. Fourie D, Herselman L (2002) Breeding for common blight resistance in dry beans in South Africa. Annu Rep Bean Improv Coop 45:50–51Google Scholar
  10. Galasso I, Lioi L, Lanave C, Campion B, Bollini R, Sparvoli F (2005) Identification and sequencing of a BAC clone belonging to the Phaseolus vulgaris (L) insecticidal Arc4 lectin locus. Ann Rep Bean Improv Coop 48:40Google Scholar
  11. Gepts P, Francisco JL, de Barros AE, Blair MW, Brondani R, Broughton W, 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, Yu K (2008) BAC library genomics of Phaseolus beans, a major source of dietary protein and micronutrients in the tropics. In: Moore PH, Ming R (eds) Genomics of tropical crop plants. Springer, New York, pp 113–143CrossRefGoogle Scholar
  12. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. spp. Japonica). Science 296:92–100CrossRefPubMedGoogle Scholar
  13. Guo B, Sleper DA, Lu P, Shannon JG, Nguyen HT, Arelli PR (2006) QTLs associated with resistance to soybean cyst nematode in soybean: meta-analysis of QTL locations. Crop Sci 46:595–602CrossRefGoogle Scholar
  14. Ibarra-Perez FJ, Kelly JD (2005) Molecular markers used to validate reaction of elite bean breeding lines to common bacterial blight. Annu Rep Bean Improv Coop 48:98–99Google Scholar
  15. Innes RW, Ameline-Torregrosa C, Ashfield T, Cannon E, Cannon SB, Chacko B, Chen NWG, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Hans CS, Howell S, Ilut D, Jackson S, Lai HS, Mammadov J, del Campo SM, Metcalf M, Nguyen A, O’Bleness M, Pfeil BE, Podicheti R, Ratnaparkhe MB, Samain S, Sanders I, Segurens B, Sevignac M, Sherman-Broyles S, Thareau V, Tucker DM, Walling J, Wawrzynski A, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MAS, Young ND (2008) Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. Plant Physiol 148:1740–1759CrossRefPubMedGoogle Scholar
  16. 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 112:987–998CrossRefPubMedGoogle Scholar
  17. 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 Crops Res 82:135–154CrossRefGoogle Scholar
  18. Klein PE, Klein RR, Cartinhour SW, Ulanch PE, Dong J, Obert JA, Morishige DT, Schlueter SD, Childs KL, Ale M, Mullet JE (2000) A high-throughput AFLP-based method for constructing integrated genetic and physical maps: progress toward a sorghum genome map. Genome Res 10:789–807CrossRefPubMedGoogle Scholar
  19. Liu S, Yu K, Park SJ (2008) Development of STS markers and QTL validation for common bacterial blight resistance in common bean. Plant Breed 127:62–68Google Scholar
  20. Marquez ML, Terán H, Singh SP (2007) Selecting common bean with genes of different evolutionary origins for resistance to Xanthomonas campestris pv. phaseoli. Crop Sci 47:1367–1374CrossRefGoogle Scholar
  21. Marra MA, Kucaba TA, Dietrich NL, Green ED, Brownstein B, Wilson RK, McDonald KM, Hillier LW, McPherson JD, Waterston RH (1997) High throughput fingerprint analysis of large-insert clones. Genome Res 7:1072–1084PubMedGoogle Scholar
  22. Melotto M, Kelly JD (2001) Fine mapping of the Co-4 locus of common bean reveal a resistance gene candidate, COK-4 that encodes for a protein kinase. Theor Appl Genet 103:508–517CrossRefGoogle Scholar
  23. 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
  24. 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 109:690–699CrossRefPubMedGoogle Scholar
  25. Michaels TE, Smith TH, Larsen J, Beattie AD, Pauls KP (2006) ‘OAC Rex’ common bean. Can J Plant Sci 86:733–736Google Scholar
  26. Miklas PN, Smith JR, Singh SP (2006) Registration of common bacterial blight resistant dark red kidney bean germplasms line USDK-CBB-15. Crop Sci 46:1005–1006CrossRefGoogle Scholar
  27. Mutlu N, Miklas PN, Reiser J, Coyne DP (2005) Backcross breeding for improved resistance to common bacterial blight in pinto bean (Phaseolus vulgaris L.). Plant Breed 124:282–287CrossRefGoogle Scholar
  28. Nodari RO, Tsai SM, Guzman P, Gilbertson RL, Gepts P (1993) Towards an integrated linkage map of common bean. III. Mapping genetic factors controlling host–bacteria interactions. Genetics 134:341–350PubMedGoogle Scholar
  29. O’Boyle PD, Kelly JD, Kirk WW (2007) Use of marker assisted selection to breed for resistance to common bacterial blight in common bean. J Am Soc Hort Sci 132:381–386Google Scholar
  30. Park SJ, Dhanvantari BN (1994) Registration of common bean blight-resistant germplasm, HR45. Crop Sci 34:548CrossRefGoogle Scholar
  31. Park SJ, Yu K (2004) Molecular marker-assisted selection techniques for gene pyramiding of multiple disease resistance in common bean: a plant breeder prospective. Annu Rep Bean Improv Coop 47:73–74Google Scholar
  32. Park SJ, Yu K, Liu S, Rupert T (2007) The release of white bean HR67. Annu Rep Bean Improv Coop 50:221–222Google Scholar
  33. Pedrosa-Harand A, Porch TG, Gepts P (2008) Standard nomenclature for common bean chromosomes and linkage groups. Annu Rep Bean Improv Coop 51:106–107Google Scholar
  34. Perry G, Reinprecht Y, Pauls KP (2006) Identification of common bacterial blight resistance genes in Phaseolus vulgaris. In: Joint annual meeting of the American society of plant biologists and the Canadian society of plant physiologists, Boston, Mass., 5–9 August 2006Google Scholar
  35. Schlueter JA, Goicoechea JL, Collura K, Gill N, Lin JY, Yu Y, Kudrna D, Zuccolo A, Vallejos CE, Tohme J, Blair M, McClean P, Wing RA, Jackson SA (2008) BAC-end sequence analysis and a draft physical map of the common bean (Phaseolus vulgaris L.) genome. Trop Plant Biol 1:40–48. doi:10.1007/s12042-007-9003-9 CrossRefGoogle Scholar
  36. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115CrossRefPubMedGoogle Scholar
  37. Seo YS, Rojas MR, Lee JY, Lee SW, Jeon JS, Ronald P, Lucas WJ, Gilbertson RL (2006) A viral resistance gene from common bean functions across plant families and is up-regulated in a non-virus-specific manner. Proc Natl Acad Sci U S A 103:11856–11861CrossRefPubMedGoogle Scholar
  38. Seo YS, Jeon JS, Rojas MR, Gilbertson RL (2007) Characterization of a novel Toll/interleukin-1 receptor (TIR)-TIR gene differentially expressed in common bean (Phaseolus vulgaris cv. Othello) undergoing a defence response to the geminivirus Bean dwarf mosaic virus. Mol Plant Pathol 8:151–162CrossRefPubMedGoogle Scholar
  39. Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89:8794–8797CrossRefPubMedGoogle Scholar
  40. Soderlund C (1999) FPC V4: User’s manual fingerprinted contigs. The Sanger Centre Cambridge, UK. Technical Report SC-01-99Google Scholar
  41. Soderlund C, Humphray S, Dunham A, French L (2000) Contigs built with fingerprints, markers, and FPC V4.7. Genome Res 10:772–778CrossRefGoogle Scholar
  42. Strong SJ, Ohta Y, Litman GW, Amemiya CT (1997) Marked improvement of PAC and BAC cloning is achieved using electroelution of pulsed-field gel-separated partial digests of genomic DNA. Nucleic Acids Res 25:3959–3961CrossRefPubMedGoogle Scholar
  43. Tao Q, Chang Y-L, Wang J, Chen H, Schuering C, Islam-Faridi MN, Wang B, Stelly DM, Zhang H-B (2001) Bacterial artificial chromosome-based physical map of the rice genome constructed by restriction fingerprint analysis. Genetics 158:1711–1724PubMedGoogle Scholar
  44. Tar’an B, Michaels TE, Pauls KP (2001) Mapping genetic factors affecting the reaction to Xanthomonas axonopodis pv. phaseoli in Phaseolus vulgaris under field conditions. Genome 44:1046–1056CrossRefGoogle Scholar
  45. TheArabidopsisGenome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815CrossRefGoogle Scholar
  46. Thomas CV, Waines JG (1984) Fertile backcross and allotetraploid plants from crosses between tepary bean and common bean. Heredity 75:93–98Google Scholar
  47. Vallejos CE, Astua-Monge G, Jones V, Plyler TR, Sakiyama NS, Mackenzie SA (2006) Genetic and molecular characterization of the I Locus of Phaseolus vulgaris. Genetics 172:1229–1242CrossRefPubMedGoogle Scholar
  48. Vandemark GJ, Fourie D, Miklas PN (2008) Genotyping with real-time PCR reveals recessive epistasis between independent QTL conferring resistance to common bacterial blight in dry bean. Theor Appl Genet 117:513–522CrossRefPubMedGoogle Scholar
  49. Vanhouten W, MacKenzie S (1999) Construction and characterization of a common bean bacterial artificial chromosome library. Plant Mol Biol 40:977–983CrossRefPubMedGoogle Scholar
  50. Wawrzynski A, Ashfield T, Chen NWG, Mammadov J, Nguyen A, Podicheti R, Cannon SB, Thareau V, Ameline-Torregrosa C, Cannon E, Chacko B, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Howell S, Ilut D, Lai HS, del Campo SM, Metcalf M, O’Bleness M, Pfeil BE, Ratnaparkhe MB, Samain S, Sanders I, Segurens B, Sevignac M, Sherman-Broyles S, Tucker DM, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MAS, Young ND, Innes RW (2008) Replication of nonautonomous retroelements in soybean appears to be both recent and common. Plant Physiol 148:1760–1771CrossRefPubMedGoogle Scholar
  51. Yim YS, Moak P, Sanchez-Villeda H, Musket T, Close P, Klein P, Mullet J, McMullen M, Fang Z, Schaeffer M, Gardiner J, Coe E, Davis G (2007) A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps. BMC Genomics 8(47):1–12Google Scholar
  52. Yu K, Park SJ, Poysa V (2000) Marker-assisted selection of common beans for resistance to common bacterial blight: efficacy and economics. Plant Breed 119:411–415CrossRefGoogle Scholar
  53. Yu K, Park SJ, Zhang B, Haffner M, Poysa V (2004) An SSR marker in the nitrate reductase gene of common bean is tightly linked to a major gene conferring resistance to common bacterial blight. Euphytica 138:89–95CrossRefGoogle Scholar
  54. Yu K, Haffner M, Park SJ (2006) Construction and characterization of a common bean BAC library. Annu Rep Bean Improv Coop 49:78–79Google Scholar
  55. Zhang H-B, Wu C (2001) BAC as tools for genome sequencing. Plant Physiol Biochem 39:195–209CrossRefGoogle Scholar
  56. Zhang H-B, Zhao X, Ding X, Paterson AH, Wing RA (1995) Preparation of megabase-size DNA from plant nuclei. Plant J 7:175–184CrossRefGoogle Scholar

Copyright information

© UK Crown 2010

Authors and Affiliations

  • S. Y. Liu
    • 1
    • 3
  • K. Yu
    • 1
  • M. Huffner
    • 1
  • S. J. Park
    • 1
  • M. Banik
    • 1
    • 4
  • K. P. Pauls
    • 2
  • W. Crosby
    • 5
  1. 1.Agriculture Agri-Food CanadaGreenhouse and Processing Crops Research CenterHarrowCanada
  2. 2.Department of Plant Agriculture, Crop Science BuildingUniversity of GuelphGuelphCanada
  3. 3.Crop and Soil Environmental ScienceVirginia Polytechnic Institute and State UniversityBlacksburgUSA
  4. 4.Cereal Research CenterAgriculture and Agri-Food CanadaWinnipegCanada
  5. 5.Department of BiologyUniversity of WindsorWindsorCanada

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