Tropical Plant Biology

, Volume 3, Issue 4, pp 204–218 | Cite as

QTL Analysis and Effect of the fin Locus on Tropical Adaptation in an Inter-Gene Pool Common Bean Population

  • M. Carolina Chavarro
  • Matthew W. Blair


Common bean architecture is in part determined by the determinacy gene fin which can affect yield potential and adaptation to various environments and has many known effects in temperate regions. Tropical adaptation, meanwhile, requires adaptation to rainy and dry seasons where heat and drought stress are major problems. The goal of this research was to determine the effect of the fin gene on plants grown under heat, drought and non-stress conditions in the tropics and to identify quantitative trait loci (QTL) for architectural, phenological and yield traits related to fin in an inter-genepool population derived from a cross between an indeterminate Mesoamerican genotype with erect architecture (A55) and a determinate Andean genotype with heat tolerance (G122). The population was evaluated in four experiments conducted in a tropical location across two rainy seasons and across dry season drought stress and dry season irrigated treatments. A total of 71 SSR loci and 245 AFLP, RAPD, seed protein or phenotypic markers were integrated together into a genetic map with a total distance of 982.8 cM. A total of 36 QTL were identified based on the evaluation of six phenotypic variables differentiating the parents. The A55 parent was high yielding under all conditions; while G122 was confirmed to be resistant to high temperatures, but not to drought. Some QTL for yield were associated with erect growth alleles inherited from the indeterminate parent and were located on linkage group b01 near the fin locus while other QTL for seed weight were found across the genome.


Abiotic stress Heat tolerance Drought resistance Quantitative trait loci Phaseolus vulgaris 



Amplified fragment length polymorphisms




Days After Planting


Days to Flowering


Days to Physiological Maturity


Drought Stress Irrigated


Drought Stress Dry Season


Generalized Linear Model


Likelihood of Odds Ratio


Quantitative Trait Loci


Random Amplified Polymorphic DNA


Restriction Fragment Length Polymorphism


Recombinant Inbred Line


First Rainy Seasons


Second Rainy Seasons


Sequence-Characterized Amplified Region


Single Sequence Repeats


Single-Seed Descent


100-Seed Weight



We thank Ingrid Schuler for her suggestions for this work, Elizabeth Paez for editorial help, Héctor Fabio Buendía for technical assistance, Bill Johnson and Paul Gepts for mapping results, and Steve Magnusson and Phil Miklas for germplasm development and supply. Finally, Agobardo Hoyos helped with statistical analyses.


  1. Acosta-Gallegos JA, Adams MW (1991) Plant traits and yield stability of dry bean (Phaseolus vulgaris L.) cultivars under drought stress. J Agric Sci 117:213–219CrossRefGoogle Scholar
  2. Acosta-Gallegos JA, Kohashi-Shibata J (1989) Effect of water stress on growth and yield of indeterminate dry bean (Phaseolus vulgaris L.) cultivars. Field Crops Res 20:81–93CrossRefGoogle Scholar
  3. Arndt GC, Gepts P (1989) Inheritance study for heat tolerance in common bean Phaseolus vulgaris. Bean Improv Coop 32:22–23Google Scholar
  4. Baudoin J, Camarena F, Lobo M (1997) Improving Phaseolus genotypes for multiple cropping systems. Euphytica 96:115–123CrossRefGoogle Scholar
  5. Beebe S, Rao I, Cajiao C, Grajales M (2008) Selection for drought resistance in common bean also improves yield in phosphorus limited and favorable environments. Crop Sci 48:582–592CrossRefGoogle Scholar
  6. Blair MW, Pedraza F, Buendía HF, Gaitán-Solís E, Beebe SE, Gepts P, Thome J (2003) Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet 107:1362–1374CrossRefPubMedGoogle Scholar
  7. Blair MW, Giraldo MC, Buenda HF, Tovar E, Duque MC, Beebe SE (2006a) Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 113:100–109CrossRefPubMedGoogle Scholar
  8. Blair MW, Iriarte GA, Beebe SE (2006b) QTL analysis of yield traits in an advanced backcross population derived from a cultivated Andean × wild common bean (Phaseolus vulgaris L.) cross. Theor Appl Genet 112:1149–1163CrossRefPubMedGoogle Scholar
  9. Broughton WJ, Hernandez G, Blair MW, Beebe SE, Gepts P, Venderleyden J (2003) Bean Phaseolus spp - model food legumes. Plant Soil 252:55–128CrossRefGoogle Scholar
  10. Caixeta ET, Borém A, Kelly JD (2005) Development of microsatellite markers based on BAC common bean clones. Crop Breed Appl Biot 5:125–133Google Scholar
  11. Checa OE, Blair MW (2008) Mapping QTL for climbing ability and component traits in common bean (Phaseolus vulgaris L.). Mol Breed 22:201–215CrossRefGoogle Scholar
  12. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971PubMedGoogle Scholar
  13. Coyne DP (1967) Photoperiodism: inheritance and linkage studies in Phaseolus vulgaris. J Hered 58:313–314Google Scholar
  14. Dellaporta SJ, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Rep 1:19–21CrossRefGoogle Scholar
  15. Evans AM (1986) Beans. Longman Scientific and Technical, Hong KongGoogle Scholar
  16. Fischer RA, Maurer R (1978) Drought resistance in spring wheat cultivars. I. Grain yield responses. Aust J Agric Res 29:897–912CrossRefGoogle Scholar
  17. Frahm MA, Rosas JC, Mayek-Pérez N, López-Salinas E, Acosta-Gallegos JA, Kelly JD (2004) Breeding beans for resistance to terminal drought in the lowland tropics. Euphytica 136:223–232CrossRefGoogle Scholar
  18. Freyre R, Skroch PW, Geffroy V, Adam-Blondon AF, Shirmo-hamadali A, Johnson WC, Llaca V, Nodari RO, Pereira PA, Tsai SM, Thome J, Dron M, Nienhuis J, Vallejos CE, 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 97:847–856CrossRefGoogle Scholar
  19. Gaitán-Solís E, Duque MC, Edwards KJ, Thome J (2002) Microsatellite repeats in common bean (Phaseolus vulgaris): isolation, characterization, and cross-species amplification in Phaseolus ssp. Crop Sci 42:2128–2136CrossRefGoogle Scholar
  20. Guerra-Sanz JM (2004) Short communication. New SSR markers of Phaseolus vulgaris from sequence databases. Plant Breed 123:87–89CrossRefGoogle Scholar
  21. Hang AN, Miklas PN, Silbernagel MJ, Hosfield GN (2006) Registration of ‘Quincy’ pinto bean. Crop Sci 46:991CrossRefGoogle Scholar
  22. Johnson WC (1997) Improving the efficiency of common bean (Phaseolus vulgaris L.) breeding programs using molecular markers. Dissertation. Univ. of California, Davis, CAGoogle Scholar
  23. Johnson WC, Gepts P (1999) Segregation for performance in recombinant inbred populations resulting from inter-gene pool crosses of common bean (Phaseolus vulgaris L.). Euphytica 106:45–56CrossRefGoogle Scholar
  24. Johnson WC, Menéndez C, Nodari R, Koinange EM, Magnusson S, Singh SP, Gepts P (1996) Association of a seed weight factor with the phaseolin seed storage protein locus across genotypes, environments, and genomes in Phaseolus-Vigna spp.: Sax (1923) revisited. J Agric Genomics (previously Journal of Quantitative Trait Loci) 2:Article 5Google Scholar
  25. Kelly JD, Kolkman J, Schneider K (1998) Breeding for yield in dry bean (Phaseolus vulgaris L.). Euphytica 102:343–356CrossRefGoogle Scholar
  26. Kelly JD, Schneider KA, Kolkman JM (1999) Breeding to improve yield. In: Singh SP (ed) Common bean improvement in the twenty-first century, vol 7. Kluwer Academic Publishers, Kimberly, pp 185–222Google Scholar
  27. Koinange EM, Singh S, Gepts P (1996) Genetic control of the domestication syndrome in common bean. Crop Sci 36:1037–1045CrossRefGoogle Scholar
  28. Kolkman JM, Kelly JD (2003) QTL conferring resistance and avoidance to white mold in common bean. Crop Sci 43:539–548CrossRefGoogle Scholar
  29. Kwak M, Velasco D, Gepts P (2008) Mapping homologous sequences for determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris). J Hered 99:283–291CrossRefPubMedGoogle Scholar
  30. Lander E, Green P, Abrahamson J, Barlow A, Daly M, Lincoln D, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181CrossRefPubMedGoogle Scholar
  31. 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. Theor Appl Genet 104:1346–1352CrossRefPubMedGoogle Scholar
  32. Miklas PN (2007) Marker-assisted backcrossing QTL for partial resistance to Sclerotinia white mold in dry bean. Crop Sci 47:935–942CrossRefGoogle Scholar
  33. Miklas PN, Johnson WC, Delorme R, Gepts P (2001) QTL Conditioning physiological resistance and avoidance to white mold in dry bean. Crop Sci 41:309–315CrossRefGoogle Scholar
  34. Muchero W, Ehlers JD, Close TJ, Roberts PA (2009) Mapping QTL for drought stress-induced premature senescence and maturity in cowpea [Vigna unguiculata (L.) Walp.]. Theor Appl Genet 118:849–863CrossRefPubMedGoogle Scholar
  35. Pañeda A, Rodríguez-Suárez C, Campa A, Ferreira JJ, Giraldez R (2008) Molecular markers linked to the fin gene controlling determinate growth habit in common bean. Euphytica 162:241–248CrossRefGoogle Scholar
  36. Park SO, Coyne DP, Bokosi JM, Steadman JR (1999) Molecular Markers linked to genes for specific rust resistance and indeterminate growth habit in common bean. Euphytica 105:133–141CrossRefGoogle Scholar
  37. Porch TG, Jahn M (2001) Effects of high-temperature stress on microsporogenesis in heat-sensitive and heat-tolerant genotypes of Phaseolus vulgaris. Plant Cell Environ 24:723–731CrossRefGoogle Scholar
  38. Rainey K, Griffiths P (2003) Evaluation of common bean yield components under heat stress. Hortic Sci 38:682Google Scholar
  39. Ramírez-Vallejo P, Kelly JD (1998) Traits related to drought resistance in common bean. Euphytica 99:127–136CrossRefGoogle Scholar
  40. Rosales-Serna R, Kohashi-Shibata J, Acosta-Gallegos JA, Trejo-López C, Ortiz-Cereceres J, Kelly JD (2004) Biomass distribution, maturity acceleration and yield in drought-stressed common bean cultivars. Field Crops Res 85:203–212CrossRefGoogle Scholar
  41. Russell WE (1973) Soil conditions and plant growth, 10th edn. Longman, London, 849Google Scholar
  42. SAS Institute Inc (2002–2003) Statistical Analysis System v 9.1, Cary, NC, USAGoogle Scholar
  43. Schneider KA, Rosales-Serna R, Ibarra-Pérez FJ, Cazares-Enríquez B, Acosta-Gallegos JA, Ramírez-Vallejo P, Wassimi N, Kelly JD (1997a) Improving common bean performance under drought stress. Crop Sci 37:43–50CrossRefGoogle Scholar
  44. Schneider KA, Brothers ME, Kelly JD (1997b) Marker-assisted selection to improve drought resistance in common bean. Crop Sci 37:51–60CrossRefGoogle Scholar
  45. Schoonhoven AV, Schwartz HF, Pastor-Corrales MA (1989) Bean production problems in the tropics, 2nd edn. Centro Internacional de Agricultura Tropical, CaliGoogle Scholar
  46. Shonnard G, Gepts P (1994) Genetics of heat tolerance during reproductive development in common bean. Crop Sci 34:1168–1175CrossRefGoogle Scholar
  47. Silbernagel MJ, Mills LJ (1991) A55 is an excellent source of multiple resistance for U.S. bean breeders. Bean Project Ann Rep 54:52–53Google Scholar
  48. Singh SP (1982) A key for identification of different growth habits of (Phaseolus vulgaris L.). Bean Improv Coop 25:92–95Google Scholar
  49. Singh SP (1995) Selection for water-stress tolerance in interracial populations of common bean. Crop Sci 35:118–124CrossRefGoogle Scholar
  50. Singh SP (1999) Common bean improvement in the twenty-first century. Kluwer Academic Publishers, KimberlyGoogle Scholar
  51. Singh SP (2001) Broadening the genetic base of common bean cultivars: a review. Crop Sci 41:1659–1675CrossRefGoogle Scholar
  52. Singh SP, Terán H, Gutierrez JA (2001) Registration of SEA 5 and SEA 13 drought tolerant dry bean germplasm. Crop Sci 41:276CrossRefGoogle Scholar
  53. Singh S, Gutiérrez J, Terán H (2003) Registration of indeterminate tall upright small black-seeded common bean germplasm A55. Crop Sci 43:1887–1888CrossRefGoogle Scholar
  54. Smith JAC, Griffiths H (1993) Integrating plant water deficits from cell to community. In: Davies WJ (ed) Water deficits. Plant responses from cell to community. BIOS Scientific Publishers, OxfordGoogle Scholar
  55. Tar’an B, Michaels TE, Pauls KP (2002) Genetic mapping of agronomic traits in common bean. Crop Sci 42:544–556CrossRefGoogle Scholar
  56. Terán H, Singh SP (2002) Selection for drought resistance in early generations of common bean populations. Can J Plant Sci 82:491–523Google Scholar
  57. Thung M, Rao IM (1999) Integrated management of abiotic stresses. In: Singh SP (ed) Common bean improvement in the twenty-first century, vol 7. Kluwer Academic Publishers, Kimberly, pp 331–370Google Scholar
  58. Vales MI, Schön CC, Capettini F, Chen XM, Corey AE, Mather DE, Mundt CC, Richardson KL, Sandoval-Islas JS, Utz HF, Hayes PM (2005) Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust. Theor Appl Genet 111:1260–1270CrossRefPubMedGoogle Scholar
  59. Wallace DH, Yan W (1998) Plant breeding and whole-system crop physiology, improving adaptation, maturity and yield. Wallingford, OxonGoogle Scholar
  60. Wang S, Basten CJ, Zeng ZB (2005) Windows QTL cartographer, 25th edn. Raleigh North Carolina State University, USAGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.International Center for Tropical Agriculture (CIAT)CaliColombia

Personalised recommendations