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Microsatellite marker diversity in common bean (Phaseolus vulgaris L.)

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Abstract

A diversity survey was used to estimate allelic diversity and heterozygosity of 129 microsatellite markers in a panel of 44 common bean (Phaseolus vulgaris L.) genotypes that have been used as parents of mapping populations. Two types of microsatellites were evaluated, based respectively on gene coding and genomic sequences. Genetic diversity was evaluated by estimating the polymorphism information content (PIC), as well as the distribution and range of alleles sizes. Gene-based microsatellites proved to be less polymorphic than genomic microsatellites in terms of both number of alleles (6.0 vs. 9.2) and PIC values (0.446 vs. 0.594) while greater size differences between the largest and the smallest allele were observed for the genomic microsatellites than for the gene-based microsatellites (31.4 vs. 19.1 bp). Markers that showed a high number of alleles were identified with a maximum of 28 alleles for the marker BMd1. The microsatellites were useful for distinguishing Andean and Mesoamerican genotypes, for uncovering the races within each genepool and for separating wild accessions from cultivars. Greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool and polymorphism rate between genotypes was consistent with genepool and race identity. Comparisons between Andean genotypes had higher polymorphism (53.0%) on average than comparisons among Mesoamerican genotypes (33.4%). Within the Mesoamerican parental combinations, the intra-racial combinations between Mesoamerica and Durango or Jalisco race genotypes showed higher average rates of polymorphism (37.5%) than the within-race combinations between Mesoamerica race genotypes (31.7%). In multiple correspondance analysis we found two principal clusters of genotypes corresponding to the Mesoamerican and Andean gene pools and subgroups representing specific races especially for the Nueva Granada and Peru races of the Andean gene pool. Intra population diversity was higher within the Andean genepool than within the Mesoamerican genepool and this pattern was observed for both gene-based and genomic microsatellites. Furthermore, intra-population diversity within the Andean races (0.356 on average) was higher than within the Mesoamerican races (0.302). Within the Andean gene pool, race Peru had higher diversity compared to race Nueva Granada, while within the Mesoamerican gene pool, the races Durango, Guatemala and Jalisco had comparable levels of diversity which were below that of race Mesoamerica.

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References

  • Afanador LK, Hadley SD (1993) Adoption of a mini-prep DNA extraction method for RAPD marker analysis in common bean. Bean Improv Coop 35:10–11

    Google Scholar 

  • Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186

    Article  PubMed  CAS  Google Scholar 

  • Becerra-Velazquez L, Gepts P (1994) RFLP diversity of common bean (Phaseolus vulgaris L.) in its centres of origin. Genome 37:256–263

    Article  Google Scholar 

  • Beebe SE, Skroch PW, 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 40:264–273

    Article  Google Scholar 

  • Beebe SE, Rengifo J, Gaitán-Solis E, Duque MC, Tohme J (2001) Diversity and origin of Andean landraces of common bean. Crop Sci 41:854–862

    Article  Google Scholar 

  • Benzecri JP (1992) Correspondence analysis handbook. Marcel Dekker Inc., New York, 688 pp

  • Blair MW, Panaud O, McCouch SR (1999) Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.). Theor Appl Genet 98:780–792

    Article  CAS  Google Scholar 

  • Blair MW, Pedraza F, Buendia HF, Gaitán-Solís E, Beebe SE, Gepts P, Tohme J (2003) Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet 107:1362–1374

    Article  PubMed  CAS  Google Scholar 

  • Broughton WJ, Hernandez G, Blair MW, Beebe SE, Gepts P, Vanderleyden J (2003) Beans (Phaseolus spp.)—model food legumes. Plant Soil 252:55–128

    Article  CAS  Google Scholar 

  • Brown SM, Hopkins MS, Mitchell SE, Senior ML, Wang TY, Duncan RR, Gonzalez-Candelas F, Kresovich S (1996) Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum (Sorghum bicolor (L.) Moench). Theor Appl Genet 93:190–198

    Article  CAS  Google Scholar 

  • 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 110:432–444

    Article  PubMed  CAS  Google Scholar 

  • Chen X, Cho YG , McCouch SR (2002) Sequence divergence of rice microsatellites in Oryza and other plant species. Mol Genet Genom 268:331–343

    Article  PubMed  CAS  Google Scholar 

  • Cheng DL, Fatokun CA, Ubi B, Singh BB, Scoles GJ (2001) Determining genetic similarities and relationships among cowpea breeding lines and cultivars by microsatellite markers. Crop Sci 41:189–197

    Article  Google Scholar 

  • Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park J, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722

    Article  CAS  Google Scholar 

  • Coburn JR, Temnykh SV, Paul EM, McCouch SR (2002) Design and application of microsatellite marker panels for semi-automated genotyping of rice (Oryza sativa L.). Crop Sci 42:2092–2099

    Article  CAS  Google Scholar 

  • Cregan PB, Jarvik T, Bush AL, Shoemaker RC, Lark KG, Kahler AL, Kaya N, VanToai TT, Lohnes DG, Chung J, Specht JE (1999) An integrated linkage map of the soybean genome. Crop Sci 39:1464–1490

    Article  CAS  Google Scholar 

  • Debouck D, Toro O, Paredes O, Johnson W, Gepts P (1993). Genetic diversity and ecological distribution of Phaseolus vulgaris L. (Fabacea) in northwestern south America. Econ Bot 47:408–423

    Google Scholar 

  • Eujay I, Sorrells ME, Baum M, Wolters P, Powell W (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theor Appl Genet 104:399–407

    Article  PubMed  Google Scholar 

  • Ferguson ME, Burow MD, Schulze SR, Bramel PJ, Paterson AH, Kresovich S, Mitchell S (2004) Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor Appl Genet 108:064–1070

    Article  CAS  Google Scholar 

  • Freyre R, Skroch PW, Geffory V, Adam-Blondon AF, Shirmohamadali A, Johnson WC, Llaca V, Nodari RO, Periera PA, Tsai SM, Tohme 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 97:847–856

    Article  CAS  Google Scholar 

  • 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 42:2128–2136

    Article  Google Scholar 

  • Gomez OJ, Blair MW, Frankow-Lindberg BE, Gullberg U (2004) Molecular and phenotypic diversity of common bean landraces from Nicaragua. Crop Sci 44:1412–1418

    Article  CAS  Google Scholar 

  • Gepts P, Debouck D (1991) Origin, domestication, and evolution of the common bean (Phaseolus vulgaris L.). In: Schoonhoven AV (ed) Common beans: research for crop improvement. CIAT, Cali, pp 7–53

    Google Scholar 

  • Hair JF, Anderson RE, Tatham RL, Black WC (1992) Multivariate data analysis with readings. Macmillan Publishing Company, New York

    Google Scholar 

  • Hopkins MS, Casa AM, Wang T, Mitchell SE, Dean RE, Kochert GD Kresovich S (1999) Discovery and characterization of polymorphic simple sequence repeats (SSRs) in peanut. Crop Sci 39:1243–1247

    Article  CAS  Google Scholar 

  • Huttel B, Winter P, Weising K, Choumane W, Weigand F, Kahl G (1999) Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Genome 42:210–217

    Article  PubMed  CAS  Google Scholar 

  • Johns M, Skroch P, Nienhuis J, Hinrichsen P, Bascur G, Muñoz-Schick C (1997) Gene pool clasification of common bean landraces from Chile based on RAPD and morphological data. Crop Sci 37:605–613

    Article  Google Scholar 

  • Lee M (1995) DNA markers and plant breeding programs. Adv Agron 55:265–344

    Article  CAS  Google Scholar 

  • Mahuku GS (2004) A simple extraction method suitable for PCR based analysis of plant, fungal and bacterial DNA. Plant Mol Biol Rept 22:71–81

    Article  CAS  Google Scholar 

  • Masi P, Spagnoletti Zeuli PL, Donini P (2003) Development of multiplex microsatellite markers sets in common bean (Phaseolus vulgaris L.). Mol Breed 11:303–313

    Article  CAS  Google Scholar 

  • Matus IA, Hayes PM (2002) Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats. Genome 45:1095–1106

    Article  PubMed  CAS  Google Scholar 

  • 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 104:1346–1352

    Article  PubMed  CAS  Google Scholar 

  • Mitchell SE, Kresovich S, Jester CA, Hernandez CJ, Szewc-McFadden AK (1997) Application of multiplex-PR and fluorescence-based, semi-automated allele sizing technology for genotyping palnt genetic resources. Crop Sci 37:617–624

    Article  CAS  Google Scholar 

  • Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182

    Article  PubMed  CAS  Google Scholar 

  • Muñoz LC, Blair MW, Duque MC, Roca W, Tohme J (2004) Level of introgression in inter-specific (Phaseolus vulgaris × P. acutifolius) congruity-backcross lines. Crop Science 44: 637–645

    Article  Google Scholar 

  • Narvel JM, Chu W, Fehr WR, Cregan PB, Shoemaker RC (2000) Development of multiplex sets of simple sequence repeat DNA markers covering the soybean genome. Mol Breed 6:175–183

    Article  CAS  Google Scholar 

  • Nei M (1987) Molecular evolution and genetics. Colombia University Press, New York

    Google Scholar 

  • Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222

    Google Scholar 

  • Santalla M, Rodiño AP, De Ron AM (2002) Allozyme evidence supporting southwestern Europe as a secondary center of genetic diversity for the common bean. Theor Appl Genet 104:934–944

    Article  PubMed  CAS  Google Scholar 

  • Schloss SJ, Mitchell SE, White GM, Kukatla R, Bowers RE, Paterson AH, Kresovich S (2002) Characterization of RFLP probe sequences for gene discovery and SSR development in sorghum (Sorghum bicolor (L.) Moench). Theor Appl Genet 105:912–920

    Article  PubMed  CAS  Google Scholar 

  • Singh SP (1982) A key for identification of different growth habits of Phaseolus vulgaris L. Annu Rept Bean Improv Coop 25:92–95

    Google Scholar 

  • Singh SP, Gepts P, Debouck D (1991a) Races of common bean (Phaseolus vulgaris, Fabaceae). Econ Bot 45:379–396

    Google Scholar 

  • Singh SP, Nodari R, Gepts P (1991b) Genetic diversity in cultivated common bean: I. Allozymes. Crop Sci 31:19–23

    Article  CAS  Google Scholar 

  • Sonnante G, Stockton T, Nodari R, Becerra Velasquez V, Gepts P (1994) Evolution of genetic diversity during the domestication of common bean (Phaseolus vulgaris L.). Theor Appl Genet 89:629–635

    Article  Google Scholar 

  • Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG , Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    Article  CAS  Google Scholar 

  • Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch SR (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452

    Article  PubMed  CAS  Google Scholar 

  • Terán H, Singh SP (2002) Comparison of sources and lines selected for drought resistance in common bean. Crop Sci 42:64–70

    Article  PubMed  Google Scholar 

  • Thoquet P, Ghérardi M, Journet EP, Kereszt A, Ané JM, Prosperi JM, Huguet T (2002) The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes. BMC Plant Biol 2:1

    Article  PubMed  Google Scholar 

  • Tohme J, Gonzlez DO, Beebe S, Duque MC (1996) AFLP analysis of gene pools of a wild bean core collection. Crop Sci 36:1375–1384

    Article  CAS  Google Scholar 

  • Yaish MWF, Pérez de la Vega M (2003) Isolation of (GA)n microsatellite sequences and description of a predicted MADS-box sequence isolated from common bean (Phaseolus vulgaris L.). Genetics Mol Biol 26:337–342

    CAS  Google Scholar 

  • Yu K, Park SJ, Poysa V (1999) Abundance and variation of microsatellite DNA sequences in beans (Phaseolus and Vigna). Genome 42:27–34

    Article  CAS  Google Scholar 

  • Yu K, Park SJ, 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 91:429–434

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

We are grateful to J. Rengifo, A.V. Gonzalez, and F. Pedraza for technical assistance, E. Gaitán-Solís for helpful advice and P. Zamorano for formatting. This work was supported by the Generation Challenge Program and the United States Agency for International Development.

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Authors and Affiliations

  1. CIAT - International Center for Tropical Agriculture, 1380 N.W. 78th Ave., Miami, FL, 33126, USA

    M. W. Blair

  2. CIAT - International Center for Tropical Agriculture, Apartado Aéreo 6713, Cali, Colombia

    M. W. Blair, M. C. Giraldo, H. F. Buendía, E. Tovar, M. C. Duque & S. E. Beebe

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  1. M. W. Blair
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  2. M. C. Giraldo
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  3. H. F. Buendía
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  6. S. E. Beebe
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Correspondence to M. W. Blair.

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Communicated by F. J. Muehlbauer

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Blair, M.W., Giraldo, M.C., Buendía, H.F. et al. Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 113, 100–109 (2006). https://doi.org/10.1007/s00122-006-0276-4

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  • DOI: https://doi.org/10.1007/s00122-006-0276-4

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