Theoretical and Applied Genetics

, Volume 89, Issue 5, pp 629–635 | Cite as

Evolution of genetic diversity during the domestication of common-bean (Phaseolus vulgaris L.)

  • G. Sonnante
  • T. Stockton
  • R. O. Nodari
  • V. L. Becerra Velásquez
  • P. Gepts


M13 DNA fingerprinting was used to determine evolutionary changes that occurred in Latin American germ plasm and USA cultivars of commonbean (Phaseolus vulgaris L.) during domestication. Linkage mapping experiments showed that M13-related sequences in the common-bean genome were either located at the distal ends of linkage groups or that they were unlinked to each other or to any previously mapped markers. Levels of polymorphism observed by hybridization with M13 (1 probe-enzyme combination) were comparable to those observed by hybridization with single-copy random PstI genomic probes (36 enzyme-probe combinations) but were higher than those observed for isozymes (10 loci). Results indicated that the wild ancestor had diverged into two taxa, one distributed in Middle America (Mexico, Central America, and Colombia) and the other in the Andes (Peru and Argentina); they also suggested separate domestications in the two areas leading to two cultivated gene pools. Domestication in both areas led to pronounced reductions in diversity in cultivated descendants in Middle America and the Andes. The marked lack of polymorphism within commercial classes of USA cultivars suggests that the dispersal of cultivars from the centers of origin and subsequent breeding of improved cultivars led to high levels of genetic uniformity. To our knowledge, this is the first crop for which this reduction in diversity has been documented with a single type of marker in lineages that span the evolution between wild ancestor and advanced cultivars.

Key words

Crop evolution M13 Fingerprinting Linkage map 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Balazs I, Neuweiler J, Gunn P, Kidd J, Kidd KK, Kuhl J, Mingjun L (1992) Human population genetic studies using hypervariable loci. I. Analysis of Assamese, Australian, Cambodian, Caucasian, Chinese and Melanesian populations. Genetics 131: 191–198Google Scholar
  2. Becerra Velásquez VL, Gepts P (1994) RFLP diversity in common bean (Phaseolus vulgaris L.). Genome 94:256–263Google Scholar
  3. Braithwaite KS, Manners JM (1989) Human hypervariable minisatellite probes detect DNA polymorphisms in the fungus Colletotrichum gloeosporioides. Curr Genet 16:473–475Google Scholar
  4. Dallas JF (1988) Detection of DNA “fingerprints” of cultivated rice by hybridization with a human minisatellite DNA probe. Proc Natl Acad Sci USA 85:6831–6835Google Scholar
  5. Doebley J (1989) Isozymic evidence and the evolution of crop plants. In: Soltis DE, Soltis PS (eds) Isozymes in plant biology. Dioscorides, Portland, Ore. pp 165–191Google Scholar
  6. Doebley J (1992) Molecular systematics and crop evolution. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular systematics of plants. Chapman Hall, New York, pp 202–222Google Scholar
  7. Donis-Keller H, Barker DF, Knowlton RG, Schumm JW, Braman JC, Green P (1986) Highly polymorphic RFLP probes as diagnostic tools. Cold Spring Harbor Symp Quant Biol 51: 317–324Google Scholar
  8. Feinberg AP, Vogelstein B (1984) Addendum: a technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 137:266–267PubMedGoogle Scholar
  9. Fisher RA (1930) The genetic theory of natural selection. Dover, New YorkGoogle Scholar
  10. Gepts P (1988) A Middle American and Andean gene pool. In: Gepts P (ed) Genetic resources of Phaseolus beans. Kluwer, Dordrecht, the Netherlands, pp 375–390Google Scholar
  11. Gepts P (1990) Biochemical evidence bearing on the domestication of Phaseolus beans. Econ Bot 44:28–38Google Scholar
  12. Gepts P (1993a) Linkage map of common bean (Phaseolus vulgaris L.). In: O'Brien SJ (ed) Genetic maps. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. pp 6.101–6.109Google Scholar
  13. Gepts P (1993b) The use of molecular and biochemical markers in crop evolution studies. Evol Biol 27:51–94Google Scholar
  14. Gepts P, Bliss FA (1986) Phaseolin variability among wild and cultivated common beans (Phaseolus vulgaris) from Colombia. Econ Bot 40:469–478Google Scholar
  15. 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
  16. Gepts P, Kmiecik K, Pereira P, Bliss FA (1988) Dissemination pathways of common bean (Phaseolus vulgaris, Fabaceae) deduced from phaseolin electrophoretic variability. I. The Americas. Econ Bot 42:73–85Google Scholar
  17. Gepts P, Nodari R, Tsai R, Koinange EMK, Llaca V, Gilbertson R, Guzmán P (1993) Linkage mapping in common bean. Annu Rep Bean Improv Coop 36:xxiv-xviiiGoogle Scholar
  18. Golding GB, Aquadro CF, Langley CH (1986) Sequence evolution within populations under multiple types of mutation. Proc Natl Acad Sci USA 83:427–431Google Scholar
  19. Haldane JBS (1927) A mathematical theory of natural and artificial selection, part V. Selection and mutation. Proc Camb Philos Soc 23:838–844Google Scholar
  20. Harlan JR (1992) Crops and man. American Society of Agronomy, Madison, Wis.Google Scholar
  21. Hillel J, Schaap T, Haberfeld A, Jeffreys AJ, Plotzky Y, Cahaner A, Lavi U (1990) DNA fingerprints applied to gene introgression in breeding programs. Genetics 124:783–789Google Scholar
  22. Hoyt E (1988) Conserving the wild relatives of crops. International Board for Plant Genetic Resources, RomeGoogle Scholar
  23. Jeffreys AJ, Wilson V, Thein SL (1985) Hypervariable ‘minisatellite’ regions in human DNA. Nature 314:67–73PubMedGoogle Scholar
  24. Jeffreys AJ, Wilson V, Kelly R, Taylor BA, Bulfield G (1987) Mouse DNA ‘fingerprints’: analysis of chromosome localization and germ-line stability of hypervariable loci in recombinant inbred strains. Nucleic Acids Res 15:2823–2836Google Scholar
  25. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge, UKGoogle Scholar
  26. Koenig R, Gepts P (1989) Allozyme diversity in wild Phaseolus vulgaris: further evidence for two major centers of diversity. Theor Appl Genet 78:809–817Google Scholar
  27. 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
  28. Koinange EMK, Gepts P (1992) Hybrid weakness in wild Phaseolus vulgaris L. J Hered 83:135–139Google Scholar
  29. Kornegay J, Cardona C, Posso CE (1993) Inheritance of resistance to Mexican bean weevil in common bean, determined by bioassay and biochemical tests. Crop Sci 33:589–594Google Scholar
  30. Kuhnlein U, Dawe Y, Zadworny D, Gavora JS (1989) DNA finger-printing: a tool for determining genetic distances between strains of poultry. Theor Appl Genet 77:669–672Google Scholar
  31. Ladizinsky G (1985) Founder effect in crop-plant evolution. Econ Bot 39:191–198Google Scholar
  32. Lander ES, Green P, Abrahamson J, Barlow A, Daly M, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linakge maps of experimental and natural populations. Genomics 1:174–181PubMedGoogle Scholar
  33. McClean PE, Myers JR, Hammond JJ (1993) Coefficient of parentage and cluster analysis of North American dry bean cultivars. Crop Sci 33:190–197Google Scholar
  34. Nakamura Y, Leppert M, O'Connell P, Wolff R, Holm T, Culver M, Martin C, Fujimoto E, Hoff M, Kumlin E, White R (1987) Variable number of tandem repeat (VNTR) markers for human gene mapping. Science 235:1616–1622Google Scholar
  35. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
  36. Nodari RO, Koinange EMK, Kelly JS, 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
  37. Nodari RO, Tsai SM, Gilbertson RL, Gepts P (1993) Towards an integrated linkage map of common bean. II. Development of an RFLP-based linkage map. Theor Appl Genet 85:513–520Google Scholar
  38. Nybom H, Hall HK (1991) Minisatellite DNA ‘fingerprints’ can distinguish Rubus and estimate their degree of relatedness. Euphytica 53:107–114Google Scholar
  39. Nybom H, Rogstad SH (1990) DNA “fingerprints” detect genetic variation in Acer negundo (Aceraceae). Plant Syst Evol 173:49–56Google Scholar
  40. O'Connell P, Lathrop GM, Nakamura Y, Leppert ML, Ardinger RH, Murray JC, Lalouel J-M, White R (1989) Twenty-eight loci form a continuous linkage map of markers for human chromosome 1. Genomics 4:352–360Google Scholar
  41. Reeve HK, Westneat DF, Noon WA, Sherman PW, Aquadro CF (1990) DNA “fingerprinting” reveals high levels of inbreeding in colonies of the eusocial naked mole-rat. Proc Natl Acad Sci USA 87:2496–2500PubMedGoogle Scholar
  42. Rogstad SH, Patton JC II, Schaal BA (1988) M13 repeat probe detects DNA minisatellite-like sequences in gymnosperms and angiosperms. Proc Natl Acad Sci USA 85:9176–9178Google Scholar
  43. Rohlf FJ (1991) NTSYS-pc. Exeter Software, Setauket, N.Y.Google Scholar
  44. Royle NJ, Clarkson RE, Wong Z, Jeffreys AJ (1988) Clustering of hypervariable minisatellites in the proterminal regions of human autosomes. Genomics 3:352–360Google Scholar
  45. Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.Google Scholar
  46. Simmonds NW (1976) Evolution of crop plants. Longman, LondonGoogle Scholar
  47. Singh SP, Gepts P, Debouck DG (1991a) Races of common bean (Phaseolus vulgaris L., Fabaceae). Econ Bot 45:379–396Google Scholar
  48. Singh SP, Nodari R, Gepts P (1991b) Genetic diversity in cultivated common bean. I. Allozymes. Crop Sci 31:19–23Google Scholar
  49. Sneath PHA, Sokal R (1973) Numerical taxonomy. Freeman, San Francisco, Calif.Google Scholar
  50. Stockton T, Sonnante G, Gepts P (1992) Detection of minisatellite sequences in Phaseolus vulgaris. Plant Mol Biol Rep 10:47–59Google Scholar
  51. Vassart G, Georges M, Monsieur R, Brocas H, Lequarre AS, Christophe D (1987) A sequence of M13 phage detects hypervariable minisatellites in human and animal DNA. Science 235:683–684Google Scholar
  52. Wells RA, Green P, Reeders ST (1989) Simultaneous genetic mapping of multiple human minisatellite sequences using DNA fingerprinting. Genomics 5:761–772Google Scholar
  53. Wyman AR, White R (1980) A highly polymorphic locus in human DNA. Proc Natl Acad Sci USA 77:6754–6758PubMedGoogle Scholar

Copyright information

© Springer-Verlag 1994

Authors and Affiliations

  • G. Sonnante
    • 1
  • T. Stockton
    • 1
  • R. O. Nodari
    • 1
  • V. L. Becerra Velásquez
    • 1
  • P. Gepts
    • 1
  1. 1.Department of Agronomy and Range ScienceUniversity of CaliforniaDavisUSA

Personalised recommendations