Construction of a Bacterial Artificial Chromosome Library Containing Large BamHI Genomic Fragments from Medicago truncatula and Identification of Clones Linked to Hypernodulating Genes

  • Park So-Yeon (Department of Life Science, Sogang University) ;
  • Nam Young-Woo (Department of Life Science, Sogang University)
  • Published : 2006.02.01

Abstract

In the model legume Medicago truncatula, two mutants, sickle and sunn, exhibit morphologically and genetically distinct hypernodulation phenotypes. However, efforts to isolate the single recessive and single semidominant genes for sickle and sunn, respectively, by map-based cloning have so far been unsuccessful, partly due to the absence of clones that enable walks from linked marker positions. To help resolve these difficulties, a new bacterial artificial chromosome (BAC) library was constructed using BamHI-digested genomic fragments. A total of 23,808 clones were collected from ligation mixtures prepared with double-size-selected high-molecular-weight DNA. The average insert size was 116 kb based on an analysis of 88 randomly selected clones using NotI digestion and pulsed-field gel electrophoresis. About 18.5% of the library clones lacked inserts. The frequency of the BAC clones carrying chloroplast or mitochondrial DNA was 0.98% and 0.03%, respectively. The library represented approximately 4.9 haploid M. truncatula genomes. Hybridization of the BAC clone filters with a $C_{0}t-l$ DNA probe revealed that approximately 37% of the clones likely carried repetitive sequence-enriched DNA. An ordered array of pooled BAC DNA was screened by polymerase chain reactions using 13 sequence-characterized molecular markers that belonged to the eight linkage groups. Except for two markers, one to five positive BAC clones were obtained per marker. Accordingly, the sickle- and sunn-linked BAC clones identified herein will be useful for the isolation of these biotechnologically important genes. The new library will also provide clones that fill the gaps between preexisting BAC contigs, facilitating the physical mapping and genome sequencing of M. truncatula.

Keywords

References

  1. Albrecht, C., R. Geurts, and T. Bisseling. 1999. Legume nodulation and mycorrhizae formation; Two extremes in host specificity meet. EMBO J. 18: 281-288 https://doi.org/10.1093/emboj/18.2.281
  2. Ane, J.-M., G. B. Kiss, B. K. Riely, R. V. Penmetsa, G. E. D. Oldroyd, C. Ayax, J. Levy, F. Debelle, J.-M. Baek, P. Kalo, C. Rosenberg, B. A. Roe, S. R. Long, J. Denarie, and D. R. Cook. 2004. Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes. Science 303: 1364-1367 https://doi.org/10.1126/science.1092986
  3. Baek, C.-H., D.-K. Park, K.-E. Lee, W. Hwang, I.-H. Kim, J. Maeng, and K.-S. Kim. 2004. Genes for the catabolism of deoxyfructosyl glutamine in pAtC58 are attributed to utilization of octopine in Agrobacterium tumefaciens strain NT1. J. Microbiol. Biotechnol. 14: 822-828 https://doi.org/10.1159/000076921
  4. Barker, D. G., S. Bianchi, F. Blondon, Y. Dattee, G. Duc, S. Essad, P. Flament, P. Gallusci, G. Genier, P. Guy, X. Muel, J. Tourneur, J. Denarie, and T. Huguet. 1990. Medicago truncatula, a model plant for studying the molecular genetics of the Sinorhizobium-legume symbiosis. Plant Mol. Biol. Rep. 8: 40-49 https://doi.org/10.1007/BF02668879
  5. Blondon, F., D. Marie, S. Brown, and A. Kondorosi. 1994. Genome size and base composition in Medicago sativa and M. truncatula species. Genome 37: 264-270 https://doi.org/10.1139/g94-037
  6. Catoira, R., C. Galera, F. de Billy, E. P. Journet, F. Maillet, R. V. Penmetsa, C. Rosenberg, C. Gough, D. R. Cook, and J. Denarie. 2000. Identification of four genes of Medicago truncatula controlling steps in Nod factor transduction. Plant Cell 12: 1647-1666 https://doi.org/10.1105/tpc.12.9.1647
  7. Chen, Q., S. Sun, Q. Ye, S. McCuine, E. Huff, and H.-B. Zhang. 2004. Construction of two BAC libraries from the wild Mexican diploid potato, Solanum pinnatisectum, and the identification of clones near the late blight and Colorado potato beetle resistance loci. Theor. Appl. Genet. 108: 1002- 1009
  8. Choi, H.-K., D. Kim, T. Uhm, E. Limpens, H. Lim, J.-H. Mun, P. Kalo, R. V. Penmetsa, A. Seres, O. Kulikova, B. A. Roe, T. Bisseling, G. B. Kiss, and D. R. Cook. 2004. A sequence-based genetic map of Medicago truncatula and comparison of marker co-linearity with Medicago sativa. Genetics 166: 1463-1502 https://doi.org/10.1534/genetics.166.3.1463
  9. Choi, H.-K., J.-H. Mun, D. Kim, H. Zhu, J.-M. Baek, J. Mudge, B. A. Roe, N. Ellis, J. Doyle, G. B. Kiss, N. D. Young, and D. R. Cook. 2005. Estimating genome conservation between crop and model legume species. Proc. Natl. Acad. Sci. USA 101: 15289-15294
  10. Choi, S., R. A. Creelman, J. E. Mullet, and R. A. Wing. 1995. Construction and characterization of a bacterial artificial chromosome library of Arabidopsis thaliana. Plant Mol. Biol. Rep. 13: 124-128 https://doi.org/10.1007/BF02668782
  11. Cullimore, J. and J. Denarie. 2003. How legumes select their sweet talking symbionts. Science 302: 575-578 https://doi.org/10.1126/science.1091269
  12. Dickstein, R., R. Prusty, T. Peng, W. Ngo, and M. E. Smith. 1993. ENOD8, a novel early nodule-specific gene, is expressed in empty alfalfa nodules. Mol. Plant-Microbe Interact. 6: 715-721 https://doi.org/10.1094/MPMI-6-715
  13. Endre, G., A. Kereszt, Z. Kevei, S. Mihacea, P. Kalo, and G. B. Kiss. 2002. A receptor kinase gene regulating symbiotic nodule development. Nature 417: 962-966 https://doi.org/10.1038/nature00842
  14. Grill, E. and D. Somerville. 1991. Construction and characterization of a yeast artificial chromosome library of Arabidopsis which is suitable for chromosome walking. Mol. Gen. Genet. 226: 484-490
  15. Handberg, K. and J. Stougaard. 1992. Lotus japonicus, an autogamous, diploid legume species for classical and molecular genetics. Plant J. 2: 487-496 https://doi.org/10.1111/j.1365-313X.1992.00487.x
  16. Heo, M.-S., J.-H. Kim, S.-H. Park, G.-J. Woo, and H.-Y. Kim. 2004. Detection of genetically modified maize by multiplex PCR method. J. Microbiol. Biotechnol. 14: 1150-1156
  17. Kim, M.-K., H.-S. Kim, B.-O. Kim, S. Y. Yoo, J.-H. Seong, D.-K. Kim, S. E. Lee, S.-J. Choe, J.-C. Park, B.-M. Min, M.- J. Jeong, D. K. Kim, Y.-K. Shin, and J.-K. Kook. 2004. Multiplex PCR using conserved and species-specific 16S rDNA primers for simultaneous detection of Fusobacterium nucleatum and Actinobacillus actinomycetemcomitans. J. Microbiol. Biotechnol. 14: 110-115
  18. Lee, J.-S., S.-H. Kim, and Y.-H. Cho. 2004. Dithiothreitol attenuates the pathogenic interaction between Pseudomonas aeruginosa and Drosophila melanogaster. J. Microbiol. Biotechnol. 14: 367-372
  19. Levy, J., C. Bres, R. Geurts, B. Chalhoub, O. Kulikova, G. Duc, E.-P. Journet, J.-M. Ane, E. Lauber, T. Bisseling, J. Denarie, C. Rosenberg, and F. Debelle. 2004. A putative $Ca^{2+}$ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses. Science 303: 1361-1364 https://doi.org/10.1126/science.1093038
  20. Limpens, E., C. Franken, P. Smit, J. Willemse, T. Bisseling, and R. Geurts. 2003. LysM domain receptor kinase regulating rhizobial Nod factor-induced infection. Science 302: 630- 633 https://doi.org/10.1126/science.1090074
  21. Mylona, P., K. Pawlowski, and T. Bisseling. 1995. Symbiotic nitrogen fixation. Plant Cell 7: 869-885 https://doi.org/10.1105/tpc.7.7.869
  22. Nam, Y.-W., R. V. Penmetsa, G. Endre, P. Uribe, D. Kim, and D. R. Cook. 1999. Construction of a bacterial artificial chromosome library of Medicago truncatula and identification of clones containing ethylene-response genes. Theor. Appl. Genet. 98: 638-646 https://doi.org/10.1007/s001220051115
  23. Nam, Y.-W., J.-R. Lee, K.-H. Song, M.-K. Lee, M. D. Robbins, S.-M. Chung, J. E. Staub, and H.-B. Zhang. 2005. Construction of two BAC libraries from cucumber (Cucumis sativus L.) and identification of clones linked to yield component quantitative trait loci. Theor. Appl. Genet. 111: 150-161 https://doi.org/10.1007/s00122-005-2007-7
  24. Penmetsa, R. V. and D. R. Cook. 1997. A legume ethylene-insensitive mutant hyperinfected by its rhizobial symbiont. Science 275: 527-530 https://doi.org/10.1126/science.275.5299.527
  25. Penmetsa, R. V., J. A. Frugoli, L. S. Smith, S. R. Long, and D. R. Cook. 2003. Dual genetic pathways controlling nodule number in Medicago truncatula. Plant Physiol. 131: 998- 1008
  26. Sambrook, J. and D. W. Russell. 2001. Molecular Cloning: A Laboratory Manual, 3rd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, U.S.A
  27. Schauser, L., A. Roussis, J. Stiller, and J. Stougaard. 1999. A plant regulator controlling development of symbiotic root nodules. Nature 402: 191-195 https://doi.org/10.1038/46058
  28. Schnabel, E., O. Kulikova, R. V. Penmetsa, T. Bisseling, D. R. Cook, and J. Frugoli. 2003. An integrated physical, genetic and cytogenetic map around the sunn locus of Medicago truncatula. Genome 46: 665-672 https://doi.org/10.1139/g03-019
  29. Searle, I. R., A. E. Men, T. S. Laniya, D. M. Buzas, I. Iturbe- Ormaetxe, B. J. Carroll, and P. M. Gresshoff. 2003. Long-distance signaling in nodulation directed by a CLAVATA1- like receptor kinase. Science 299: 109-112 https://doi.org/10.1126/science.1077937
  30. Shizuya, H., B. Birren, U.-J. Kim, V. Mancino, T. Slepak, Y. Tachini, and M. Simon. 1992. Cloning and stable maintenance of 300 kilo base pair fragment of human DNA in Escherichia coli using an F-factor based vector. Proc. Natl. Acad. Sci. USA 89: 8794-8797
  31. Stracke, S., C. Kistner, S. Yoshida, L. Mulder, S. Sato, T. Kaneko, S. Tabata, N. Sandal, J. Stougaard, K. Szczyglowski, and M. Parniske. 2002. A plant receptor-like kinase required for both bacterial and fungal symbiosis. Nature 417: 959- 962 https://doi.org/10.1038/nature00841
  32. Tanksley, S. D., M. W. Ganal, and G. B. Martin. 1995. Chromosome landing: A paradigm for map-based gene cloning in plants with large genomes. Trends Genet. 11: 63-68 https://doi.org/10.1016/S0168-9525(00)88999-4
  33. Tao, Q., A. Wang, and H.-B. Zhang. 2002. One large-insert plant-transformation-competent BIBAC library and three BAC libraries of Japonica rice for genome research in rice and other grasses. Theor. Appl. Genet. 105: 1058-1066
  34. Trieu, A. T., S. H. Burleigh, I. V. Kardailsky, I. E. Maldonado-Mendoza, W. K. Versaw, L. A. Blaylock, H. Shin, T. J. Chiou, H. Katagi, G. R. Dewbre, D. Weigel, and M. J. Harrison. 2000. Transformation of Medicago truncatula via infiltration of seedlings or flowering plants with Agrobacterium. Plant J. 22: 531-541 https://doi.org/10.1046/j.1365-313x.2000.00757.x
  35. VandenBosch, K. A. and G. Stacey. 2003. Summaries of legume genomics projects from around the globe. Community resources for crops and models. Plant Physiol. 131: 840- 865 https://doi.org/10.1104/pp.103.020388
  36. Woo, S.-S., J. Jiang, B. S. Grill, A. H. Paterson, and R. A. Wing. 1994. Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucleic Acids Res. 22: 4922-4931 https://doi.org/10.1093/nar/22.23.4922
  37. Wu, C., P. Nimmakayala, F. A. Santos, R. Springman, Q. Tao, K. Meksem, D. A. Lightfoot, and H.-B. Zhang. 2004. Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping. Theor. Appl. Genet. 109: 1041-1050
  38. Zhang, H.-B., X. Zhao, X. Ding, A. H. Peterson, and R. A. Wing. 1995. Preparation of megabase-size DNA from plant nuclei. Plant J. 7: 175-184 https://doi.org/10.1046/j.1365-313X.1995.07010175.x
  39. Zhang, H.-B., S.-S. Woo, and R. A. Wing. 1996. BAC, YAC and cosmid library construction, pp. 75-99. In Foster, G. and D. Twell (eds.), Plant Gene Isolation: Principles and Practices. John Wiley and Sons, England
  40. Zwick, M. S., R. E. Hanson, T. D. Mcknight, M. N. Islam- Faridi, D. M. Stelly, R. A. Wing, and H. J. Price. 1997. A rapid procedure for the isolation of $C_{0}t-1$ DNA from plants. Genome 40: 138-142 https://doi.org/10.1139/g97-020