Theoretical and Applied Genetics

, Volume 107, Issue 8, pp 1362–1374

Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.)

  • M. W. Blair
  • F. Pedraza
  • H. F. Buendia
  • E. Gaitán-Solís
  • S. E. Beebe
  • P. Gepts
  • J. Tohme

Abstract

A total of 150 microsatellite markers developed for common bean (Phaseolus vulgaris L.) were tested for parental polymorphism and used to determine the positions of 100 genetic loci on an integrated genetic map of the species. The value of these single-copy markers was evident in their ability to link two existing RFLP-based genetic maps with a base map developed for the Mesoamerican × Andean population, DOR364 × G19833. Two types of microsatellites were mapped, based respectively on gene-coding and anonymous genomic-sequences. Gene-based microsatellites proved to be less polymorphic (46.3%) than anonymous genomic microsatellites (64.3%) between the parents of two inter-genepool crosses. The majority of the microsatellites produced single bands and detected single loci, however four of the gene-based and three of the genomic microsatellites produced consistent double or multiple banding patterns and detected more than one locus. Microsatellite loci were found on each of the 11 chromosomes of common bean, the number per chromosome ranging from 5 to 17 with an average of ten microsatellites each. Total map length for the base map was 1,720 cM and the average chromosome length was 156.4 cM, with an average distance between microsatellite loci of 19.5 cM. The development of new microsatellites from sequences in the Genbank database and the implication of these results for genetic mapping, quantitative trait locus analysis and marker-assisted selection in common bean are described.

References

  1. Afanador LK, Hadley SD (1993) Adoption of a mini-prep DNA extraction method for RAPD marker analysis in common bean. Bean Improv Coop 35:10–11Google Scholar
  2. Areshchenkova T, Ganal MW (1999) Long tomato microsatellites are predominantly associated with centromeric regions. Genome 42:536–544CrossRefPubMedGoogle Scholar
  3. Beebe SE, Pedraza F, Rojas M, Gutierrez J, Tohme J (1998) A genetic map combining RFLP, RAPD, SCAR and AFLP markers. Bean Improv Coop 41:95–96Google Scholar
  4. 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 93:190–198Google Scholar
  5. Cheng-Dao L, 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 41:189–197Google Scholar
  6. 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 100:713–722Google Scholar
  7. Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross-transferable to erianthus and sorghum. Plant Sci 160:1115–1123PubMedGoogle Scholar
  8. Cregan PB, Mudge J, Fickus EW, Marek LF, Danesh D, Denny R, Shoemaker RC, Matthews BF, Jarvik T, Young ND (1999a) Targeted isolation of simple-sequence repeat markers through the use of bacterial artificial chromosomes. Theor Appl Genet 98:919–928Google Scholar
  9. Cregan, PB, Jarvik T, Bush AL, Shoemaker RC, Lark KG, Kahler AL, Kaya N, Vantoai TT, Lohnes DG, Chung J, Specht JE (1999b) An integrated genetic linkage map of the soybean genome. Crop Sci 39:1464–1490Google Scholar
  10. Edwards KJ, Baker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. BioTechniques 20:759–760Google Scholar
  11. 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 104:399–407Google Scholar
  12. 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 97:847–856Google Scholar
  13. 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 42:2128–2136Google Scholar
  14. Gepts P (1999) Development of an integrated linkage map. In: Singh SP (ed) Common bean improvement for the twenty first century. Kluwer, Dordrecht, pp 389–400Google Scholar
  15. 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 39:1243–1247Google Scholar
  16. Huttel B, Winter P, Weising K, Choumane W, Weigand F, Kahl G (1999) Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Genome 42:210–217PubMedGoogle Scholar
  17. Jones ES, Dupall MO, Dumsday JL, Hughes LJ, Forster JW (2002) An SSR-based genetic linkage map for perennial ryegrass (Lolium perenne L.). Theor Appl Genet 102:405–415CrossRefGoogle Scholar
  18. Kelly JD, Miklas NP (1998) The role of RAPD markers in breeding for disease resistance in common bean. Mol Breed 4:1–11Google Scholar
  19. Koinange EMK, Singh SP, Gepts P (1996) Genetic control of the domestication syndrome in common-bean. Crop Sci 36:1037–145Google Scholar
  20. Lander ES, Green P, Abrahamson J, Barlow A, Daly M, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181PubMedGoogle Scholar
  21. Mba, REC, Stephenson P, Edwards K, Melzer S, Nkumbira J, Gullberg U, Apel A, Gale M, Tohme J, Fregene M (2001) Simple sequence repeat (SSR) marker survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of casava. Theor Appl Genet 102:21–31Google Scholar
  22. Morgante, M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182PubMedGoogle Scholar
  23. Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222CrossRefGoogle Scholar
  24. Ramsay L, Macaulay M, Cardle L, Morgante M, Degliivanissevich S, Maestri E, Powell W, Waugh R (1999) Intimate association of microsatellite repeats with retrotransposons and other dispersed repetitive elements in barley. Plant J 17:415–425PubMedGoogle Scholar
  25. Ramsay L, Macaulay M, Degliivanissevich S, Maclean K, Cardle L, Fuller J, Edwards KJ, Tuvesson S, Morgante M, Massari A, Maestri E, Marmiroli N, Sjakste K, Ganal M, Powell W, Waugh R (2000) A simple sequence repeat-based linkage map of barley. Genetics 156:1997–2005PubMedGoogle Scholar
  26. 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 105:912–920CrossRefGoogle Scholar
  27. Schoonhoven A, Voysest O (1991) Common beans: research for crop improvement. Redwood Press, Melssham, Wiltshire, UKGoogle Scholar
  28. Scott KD, Eggler P, Seaton G, Rossetto EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726Google Scholar
  29. Singh SP (1999) Production and utilization. In: Singh SP (ed) Common bean improvement for the twenty-first century. Kluwer, Dordrecht, pp 53–91Google Scholar
  30. Tang S, Yu JK, Slabaugh MB, Shintani DK, Knapp SJ (2002) Simple sequence repeat map of the sunflower genome. Theor Appl Genet 105:1124–1136Google Scholar
  31. Temnykh S, DeClerck, 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 11:1441–1452PubMedGoogle Scholar
  32. 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 2:1CrossRefPubMedGoogle Scholar
  33. Vallejos CE, Sakiyama NE, Chase CD (1992) A molecular-marker based linkage map of Phaseolus vulgaris L. Genetics 131:733–740PubMedGoogle Scholar
  34. Xu Y, Zhu L, Xiao J, Huang N, McCouch SR (1997) Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled-haploid, and recombinant inbred populations in rice (Oryza sativa L.) Theor Appl Genet 253:535–545Google Scholar
  35. Yu K, Park SJ, Poysa V (1999) Abundance and variation of microsatellite DNA secuences in beans (Phaseolus and Vigna). Genome 42:27–34Google Scholar
  36. 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.). Journal of Heredity 91:429–434Google Scholar

Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  • M. W. Blair
    • 1
    • 3
  • F. Pedraza
    • 1
  • H. F. Buendia
    • 1
  • E. Gaitán-Solís
    • 1
  • S. E. Beebe
    • 1
  • P. Gepts
    • 2
  • J. Tohme
    • 1
  1. 1.CIAT—International Center for Tropical AgricultureMiamiUSA
  2. 2.Department of Agronomy and Range ScienceUniversity of CaliforniaDavisUSA
  3. 3.CaliColombia

Personalised recommendations