Theoretical and Applied Genetics

, Volume 114, Issue 1, pp 143–154 | Cite as

Race structure within the Mesoamerican gene pool of common bean (Phaseolus vulgaris L.) as determined by microsatellite markers

Original Paper

Abstract

Common bean (Phaseolus vulgaris L.) cultivars are distinguished morphologically, agronomically and ecologically into specific races within each of the two gene pools found for the species (Andean and Mesoamerican). The objective of this study was to describe the race structure of the Mesoamerican gene pool using microsatellite markers. A total of 60 genotypes previously described as pertaining to specific Mesoamerican races as well as two Andean control genotypes were analyzed with 52 markers. A total of 267 bands were generated with an average of 5.1 alleles per marker and 0.297 heterozygosity across all microsatellites. Correspondence analysis identified two major groups equivalent to the Mesoamerica race and a group containing both Durango and Jalisco race genotypes. Two outlying individuals were classified as potentially of the Guatemala race although this race does not have a defined structure and previously classified members of this race were classified with other races. Population structure analysis with K = 1–4 agreed with this classification. The genetic diversity based on Nei’s index for the entire set of genotypes was 0.468 while this was highest for the Durango–Jalisco group (0.414), intermediate for race Mesoamerica (0.340) and low for race Guatemala (0.262). Genetic differentiation (GST) between the Mesoamerican races was 0.27 while genetic distance and identity showed race Durango and Jalisco individuals to be closely related with high gene flow (Nm) both between these two races (1.67) and between races Durango and Mesoamerica (1.58). Observed heterozygosity was low in all the races as would be expected for an inbreeding species. The analysis with microsatellite markers identified subgroups, which agreed well with commercial class divisions, and seed size was the main distinguishing factor between the two major groups identified.

Keywords

Population structure Genetic differentiation Gene flow Races Durango (D) Jalisco (J) Mesoamerica (M) Simple sequence repeats (SSR) 

Supplementary material

122_2006_417_MOESM1_ESM.xls (24 kb)
Supplementary material

References

  1. Afanador L, Hadley S, Kelly JD (1993) Adoption of a mini-prep DNA extraction method for RAPD marker analysis in common bean (Phaseolus vulgaris L). Bean Improv Coop 36:10–11Google Scholar
  2. Becerra V, Gepts P (1994) RFLP diversity of common bean (Phaseolus vulgaris) in its centres of origin. Genome 37:256–263Google Scholar
  3. Beebe S, Ochoa I, Skroch P, Nienhuis J, Tivang J (1995) Genetic diversity among common bean breeding lines developed for Central America. Crop Sci 35:1178–1183CrossRefGoogle Scholar
  4. Beebe S, Renjifo J, Gaitán-Solís E, Duque MC, Tohme J (2001) Diversity and origin of Andean landraces of common bean. Crop Sci 41:854–862CrossRefGoogle Scholar
  5. Beebe S, Skroch P, Tohme J, Duque MC, Pedraza F, Nienhuis J (2000) Structure of genetic diversity among common bean landraces of Middle American origin based on correspondence analysis of RAPD. Crop Sci 40:264–273CrossRefGoogle Scholar
  6. Beebe S, Toro O, González AV, Chacón MI, Debouck D (1997) Wild-weed–crop complex of common bean (Phaseolus vulgaris L., Fabaceae) in the Andes of Peru and Colombia, and their implications for conservation and breeding. Genet Resour Crop Evol 44:73–91CrossRefGoogle Scholar
  7. Blair MW, Pedraza F, Buendia H, Gaitan E, Beebe S, Gepts P, Tohme J (2003) Development of a genome wide anchored microsatellite for common bean (Phaseolus vulgaris L). Theor Appl Genet 107:1362–1374PubMedCrossRefGoogle Scholar
  8. Blair MW, Giraldo MC, Buendia HF, Tovar E, Duque MC, Beebe S (2006) Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 113:100–109PubMedCrossRefGoogle Scholar
  9. Broughton WJ, Hernandez G, Blair M, Beebe S, Gepts P, Vanderleyden J (2003) Bean (Phaseolus spp.)—model food legumes. Plant Soil 252:55–128CrossRefGoogle Scholar
  10. Chacón MI, Pickersgill S, Debouck D (2005) Domestication patterns in common bean (Phaseolus vulgaris L.) and the origin of Mesoamerican and Andean cultivated races. Theor Appl Genet 110:432–444CrossRefGoogle Scholar
  11. Duarte J, Dos Santos J, Melo L (1999) Genetic divergence among common beans cultivars from different races based on RAPD markers. Genet Mol Biol 22:419–426Google Scholar
  12. Ferguson ME, PJ Bramel, Chandra S (2004) Gene diversity among botanical varieties in peanut (Arachis hypogaea L.). Crop Sci 44:1847–1854CrossRefGoogle Scholar
  13. Gaitán E, Duque MC, Edwards K, Tohme J (2002) Microsatellite repeats in common bean (Phaseolus vulgaris L.): isolation, characterization, and cross-species amplification in Phaseolus spp. Crop Sci 42:2128–2136CrossRefGoogle Scholar
  14. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638PubMedCrossRefGoogle Scholar
  15. Gepts P (1988) Phaseolin as an evolutionary marker. In: Resources of Phaseolus beans. Kluwer, Dordtrecht, pp 215–241Google Scholar
  16. Gepts P, Osborn T, Rashka K, Bliss F (1986) Phaseolin–protein variability in wild forms and landraces of the common bean (Phaseolus vulgaris L.): evidence for multiple centers of domestication. Econ Bot 40:451–468Google Scholar
  17. Gomez O, Blair MW, Frankow-Lindberg B, Gullberg U (2004) Molecular and phenotypic diversity of common bean landraces from Nicaragua. Crop Sci 4:1412–1418CrossRefGoogle Scholar
  18. Islam FM, Beebe S, Muñoz M, Tohme J, Redden RJ, Basford KE (2004) Using molecular markers to assess the effect of introgression on quantitative attributes of common bean in the Andean gene pool. Theor Appl Genet 108:243–252PubMedCrossRefGoogle Scholar
  19. Kelly JD (2001) Remaking bean plant architecture for efficient production. Adv Agron 71:109–143CrossRefGoogle Scholar
  20. Koenig R, Gepts P (1989) Allozyme diversity in wild Phaseolus vulgaris: further evidence for two mayor centers of genetic diversity. Theor Appl Genet 78:809–817CrossRefGoogle Scholar
  21. Li C-DF, Fatokun CA. Ubib B, Singh BB, Scoles GJ (2001) Determining genetic similarities and relationships among cowpea breeding lines and cultivars by microsatellite markers. Crop Sci 41:189–197CrossRefGoogle Scholar
  22. Liu K, Goodman M, Muse S, Smith S, Buckler E, Doebley J (2003) Genetic structure and diversity among inbred lines of maize as inferred from DNA microsatellites. Genetics 165:2117–2128PubMedGoogle Scholar
  23. Masi P, Spagnoletti ZP, Donini P (2003) Development and analysis of multiplex microsatellite markers sets in common bean (Phaseolus vulgaris L.). Mol Breed 11:303–313CrossRefGoogle Scholar
  24. McClean P, Kami J, Gepts P (2004). Genomics and genetic diversity in common bean. In: Legume crop genomics. AOCS Press, Champaign, IL, pp. 60–82Google Scholar
  25. Metais 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 104:1346–1352PubMedCrossRefGoogle Scholar
  26. Mitchell SE, Kresovich S, Jester CA, Hernandez CJ, Szewc-McFadden AK (1997) Application of multiplex PCR and fluorescence-based, semi-automated allele sizing technology for genotyping plant genetic resources. Crop Sci 37:617–624CrossRefGoogle Scholar
  27. Nei M (1978) Estimation of average heterozygocity and genetic distance from a small number of individuals. Genetics 89:583–590PubMedGoogle Scholar
  28. Pallottini L, Garcia E, Kami J, Barcaccia G, Gepts P (2004) The genetic anatomy of a patented yellow bean. Crop Sci 44:968–977CrossRefGoogle Scholar
  29. Paredes O, Gepts P (1995) Extensive introgression of middle American germplasm into Chilean common bean cultivars. Genet Resour Crop Evol 42:29–41CrossRefGoogle Scholar
  30. Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Enfield, Science Publishers, Montpellier pp 43–76Google Scholar
  31. Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222Google Scholar
  32. Pritchard JK, Stehens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  33. Rohlf F (2002) NTSYS pc. Numerical Taxonomy System Exeter Publishing, Setauket, NYGoogle Scholar
  34. Rosales-Serna R, Hernández-Delgado S, González-Paz M, Acosta-Gallegos JA, Mayek-Pérez N (2005) Genetic relationships and diversity revealed by AFLP markers in Mexican common bean bred cultivars. Crop Sci 45:1951–1957CrossRefGoogle Scholar
  35. Rosenberg NA (2002) Distruct: a program for the graphical display of structure results. http://www.cmb.usc.edu/»noahr/distruct.htmlGoogle Scholar
  36. Singh S (1989) Patterns of variation in cultivated common bean (Phaseolus vulgaris, Fabaceae). Econ Bot 43:39–57Google Scholar
  37. Singh S, Gepts P, Debouck D (1991a) Races of common bean (Phaseolus vulgaris, Fabaceae). Econ Bot 45:379–396Google Scholar
  38. Singh S, Gutierrez A, Molina A, Urrea C, Gepts P (1991b) Genetic diversity in cultivated common bean. II. Marker-based analysis on morphological and agronomic traits. Crop Sci 31:23–29CrossRefGoogle Scholar
  39. Singh S, Nodari R, Gepts P (1991c) Genetic diversity in cultivated common bean. I. Allozymes. Crop Sci 31:19–23CrossRefGoogle Scholar
  40. Skroch P, Nienhuis J, Beebe S, Tohme J, Pedraza F (1998) Comparison of Mexican common bean (Phaseolus vulgaris L.) core and reserve germplasm collections. Crop Sci 38:488–496CrossRefGoogle Scholar
  41. Tohme J, Gonzales D, Beebe S, Duque MC (1996) AFLP analysis of gene pools of a wild bean core collection. Crop Sci 36:1375–1384CrossRefGoogle Scholar
  42. Voysest O, Valencia M, Amezquita M (1994) Genetic diversity among Latin American Andean and Mesoamerican common bean cultivars. Crop Sci 34:1100–1110CrossRefGoogle Scholar
  43. Yeh FY, Boyle R, Ye T, Mao Z (1997) POPGENE, the user-friendly shareware for population genetic analysis, version 1.31. Molecular Biology and Biotechnology Centre, University of Alberta, AlbertaGoogle Scholar
  44. Yu K, Park J, 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 91:429–434PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  1. 1.Centro Internacional de Agricultura Tropical (CIAT)CaliSouth America

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