A plant-transformation-competent BIBAC/BAC-based map of rice for functional analysis and genetic engineering of its genomic sequence

Genome

Volumn 50, Issue 3, 2007, Pages 278-288

  Li, Yaning ^a,b   Uhm, Taesik ^a   Ren, Chengwei ^a   Wu, Chengcang ^a   Santos, Teofila S ^a   Lee, Mi Kyung ^a   Yan, Bo ^a   Santos, Felipe ^a   Zhang, Aimin ^a,c   Scheuring, Chantel ^a   Sanchez, Alma ^d   Millena, Anna C ^d   Nguyen, Henry T ^d,e   Kou, Hongda ^b   Liu, Daqun ^b   Zhang, Hong Bin ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b AGRICULTURAL UNIVERSITY OF HEBEI   (China)

^c INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^d TEXAS TECH UNIVERSITY   (United States)

^e UNIVERSITY OF MISSOURI   (United States)

Author keywords

BIBAC; Functional genomics; Genetic engineering; Genetic transformation; Physical mapping; Positional cloning

Indexed keywords

PLANT DNA;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME MAP; CONTIG MAPPING; DNA FINGERPRINTING; GENE LIBRARY; GENETIC ENGINEERING; GENETIC TRANSFORMATION; GENETICS; GENOME; METHODOLOGY; NUCLEOTIDE SEQUENCE; PLANT CHROMOSOME; RICE;

BASE SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; CONTIG MAPPING; DNA FINGERPRINTING; DNA, PLANT; GENE LIBRARY; GENETIC ENGINEERING; GENOME, PLANT; ORYZA SATIVA; PHYSICAL CHROMOSOME MAPPING; TRANSFORMATION, GENETIC;

BACTERIA (MICROORGANISMS);

EID: 34250312835     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G07-006     Document Type: Article

References (53)

1. Ahn, S., and Tanksley, S.D. 1993. Comparative linkage maps of the rice and maize genomes. Proc. Natl. Acad. Sci. U.S.A. 90: 7980-7984. doi:10.1073/pnas.90.17.7980.
2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. doi:10.1093/nar/25.17.3389.
3. Arumuganathan, K., and Earle, E.D. 1991. Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9: 208-218.
4. Bennett, M.D., and Smith, J.B. 1991. Nuclear DNA amounts in angiosperms. Philos. Trans. R. Soc. Lond. B Biol. Sci. 334: 309-345.
5. Causse, M.A., Fulton, T.M., Cho, Y.G., Ahn, S.N., Chunwongse, J., Wu, K., et al. 1994. Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics, 138: 1251-1274.
6. Chang, Y.-L., Tao, Q., Scheuring, C., Ding, K., Meksem, K., and Zhang, H.-B. 2001. An integrated map of Arabidopsis thaliana for functional analysis of its genome sequence. Genetics, 159: 1231-1242.
7. Chen, M., Presting, G., Barbazuk, W.B., Goicoechea, J.L., Blackmon, B., Fang, G., et al. 2002. An integrated physical and genetic map of the rice genome. Plant Cell, 14: 537-545. doi:10.1105/tpc.010485.
8. Ding, Y., Johnson, M.D., Colayco, R., Chen, Y.J., Melnyk, J., Schmitt, H., and Shizuya, H. 1999. Contig assembly of bacterial artificial chromosome clones through multiplexed fluorescence-labeled fingerprinting. Genomics, 56: 237-246. doi:10.1006/geno.1998.5734.
9. Dong, J., Teng, W., Buchholz, W.G., and Hall, T.C. 1996. Agrobacterium-mediated transformation of javanica rice. Mol. Breed. 2: 267-276. doi:10.1007/BF00564204.
10. Gale, M.D., and Devos, K.M. 1998. Comparative genetics in the grasses. Proc. Natl. Acad. Sci. U.S.A. 95: 1971-1974. doi:10.1073/pnas.95.5.1971.
11. Goff, S.A., Ricke, D., Lan, T.-H., Presting, G., Wang, R., Dunn, M., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science (Washington, D.C.), 296: 92-100. doi:10.1126/science.1068275.
12. Hamilton, C.M., Frary, A., Lewis, C., and Tanksley, S.D. 1996. Stable transfer of intact high molecular weight DNA into plant chromosomes. Proc. Natl. Acad. Sci. U.S.A. 93: 9975-9979. doi:10.1073/pnas.93.18.9975.
13. Hamilton, C.M., Frary, A., Xu, Y., Tanksley, S.D., and Zhang, H.-B. 1999. Construction of tomato genomic DNA libraries in a binary-BAC (BIBAC) vector. Plant J. 18: 223-229. doi:10.1046/j.1365-313X.1999.00433.x.
14. Harushima, Y., Yano, M., Shomura, A., Sato, M., Shimano, T., Kuboki, Y., et al. 1998. A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics, 148: 479-494.
15. He, R.-F., Wang, Y., Shi, Z., Ren, X., Zhu, L., Weng, Q., and He, G.-C. 2003. Construction of a genomic library of wild rice and Agrobacterium- mediated transformation of large-insert DNA linked to BPH resistance locus. Gene, 321: 113-121. doi:10.1016/j.gene.2003.08.009.
16. Hiei, Y., Ohta, S., Komari, T., and Kumashiro, T. 1994. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J. 6: 271-282. doi:10.1046/j.1365-313X.1994.6020271.x.
17. International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature (London), 436: 793-800. doi:10.1038/nature03895.
18. Jones, J.D.G., Shlumukov, L., Carland, F., English, J., Scofield, S.R., Bishop, G.J., and Harrison, K. 1992. Effective vectors for transformation, expression of heterologous genes, and assaying transposon excision in transgenic plants. Transgenic Res. 1: 285-297. doi:10.1007/BF02525170.
19. Kelley, J.M., Field, C.E., Craven, M.B., Bocskai, D., Kim, U.J., Rounsley, S.D., and Adams, M.D. 1999. High throughput direct end sequencing of BAC clones. Nucleic Acids Res. 27: 1539-1546. doi:10.1093/nar/27.6.1539.
20. Li, J.X., Yu, S.B., Xu, C.G., Tan, Y.F., Gao, Y.J., Li, X.H., and Zhang, Q. 2000. Analyzing quantitative trait loci for yield using a vegetatively replicated F2 population from a cross between the parents of an elite rice hybrid. Theor. Appl. Genet. 101: 248-254.
21. Lin, S.Y., Sasaki, T., and Yano, M. 1998. Mapping quantitative trait loci controlling seed dormancy and heading date of rice, Oryza sativa L., using backcross inbred lines. Theor. Appl. Genet. 96: 997-1003. doi:10.1007/s001220050831.
22. Liu, Y.-G., Shirano, Y., Fukaki, H., Yanai, Y., Tasaka, M., Tabata, S., and Shibata, D. 1999. Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning. Proc. Natl. Acad. Sci. U.S.A. 96: 6535-6540. doi:10.1073/pnas.96.11.6535.
23. Liu, Y.-G., Liu, H., Chen, L., Qiu, W., Zhang, Q., Wu, H., et al. 2002. Development of new transformation-competent artificial chromosome vectors and rice genomic libraries for efficient gene cloning. Gene, 282: 247-255. doi:10.1016/S0378-1119(01) 00849-6.
24. Men, A.E., Meksem, K., Kassem, M.A., Lohar, D., Stiller, J., Lightfoot, D., and Gresshoff, P.M. 2001. A bacterial artificial chromosome library of Lotus japonicus constructed in an Agrobacterium tumefaciens- transformable vector. Mol. Plant Microbe Interact. 14: 422-425.
25. Mohan, M., Sathyanarayanan, P.V., Kumar, A., Srivastava, M.N., and Nair, S. 1997. Molecular mapping of a resistance-specific PCR-based marker linked to a gall midge resistance gene (Gm4t) in rice. Theor. Appl. Genet. 95: 777-782. doi:10.1007/s001220050625.
26. Moore, G., Devos, K.M., Wang, Z., and Gale, M.D. 1995. Cereal genome evolution. Grasses, line up and form a circle. Curr. Biol. 5: 737-739. doi:10.1016/S0960-9822(95)00148-5.
27. Nelson, W.M., Bharti, A.K., Butler, E., Wei, F., Fuks, G., Kim, H., et al. 2005. Whole-genome validation of high-information-content fingerprinting. Plant Physiol. 139: 27-38. doi:10.1104/pp.105.061978.
28. Quackenbush, J., Liang, F., Holt, I., Pertea, G., and Upton, J. 2000. The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res. 28: 141-145. doi:10.1093/nar/28.1.141.
29. Ren, C., Lee, M.-K., Yan, B., Ding, K., Cox, B., Romanov, M.N., et al. 2003. A BAC-based physical map of the chicken genome. Genome Res. 13: 2754-2758. doi:10.1101/gr.1499303.
30. Ren, C., Xu, Z.Y., Sun, S., Lee, M.-K., Wu, C., and Zhang, H.-B. 2005. Genomic libraries for physical mapping. In The handbook of plant genome mapping: genetic and physical mapping. Edited by K. Meksem and G. Kahl. Wiley-VCH Verlag GmbH, Weinheim, Germany. pp. 173-213.
31. Saji, S., Umehara, Y., Antonio, B.A., Yamane, H., Tanoue, H., Baba, T., et al. 2001. A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes. Genome, 44: 32-37. doi:10.1139/gen-44-1-32.
32. Soderlund, C., Longden, I., and Mott, R. 1997. FPC: a system for building contigs from restriction fingerprinted clones. Comput. Appl. Biosci. 13: 523-535.
33. Soderlund, C., Humphrey, S., Dunham, A., and French, L. 2000. Contigs built with fingerprints, markers, and FPC V4.7. Genome Res. 10: 1772-1787. doi:10.1101/gr.GR-1375R.
34. Sulston, J., Mallet, F., Staden, R., Durbin, R., Horsnell, T., and Coulson, A. 1988. Software for genome mapping by fingerprinting techniques. Comput. Appl. Biosci. 4: 125-132.
35. Tao, Q., and Zhang, H.-B. 1998. Cloning and stable maintenance of DNA fragments over 300 kb in Escherichia coli with conventional plasmid-based vectors. Nucleic Acids Res. 26: 4901-4909. doi:10.1093/nar/26.21.4901.
36. Tao, Q., Chang, Y.-L., Wang, J., Chen, H., Schuering, C., Islam-Faridi, M.N., et al. 2001. BAC-based physical map of the rice genome constructed by restriction fingerprint analysis. Genetics, 158: 1711-1724.
37. Tao, Q., Wang, A., and Zhang, H.-B. 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.
38. Tripathy, J.N., Zhang, J., Robin, S., Nguyen, T.T., and Nguyen, H.T. 2000. QTLs for cell-membrane stability mapped in rice (Oryza sativa L.) under drought stress. Theor. Appl. Genet. 100: 1197-1202. doi:10.1007/s001220051424.
39. Uhm, T. 2004. Genomic organization of chromosomal centromeres in the cultivated rice, Oryza sativa L., and its wild progenitor, O. rufipogon Griff. Ph.D. thesis, Texas A&M University, College Station.
40. Wu, C., Sun, S., Nimmakayala, P., Santos, F.A., Springman, R., Meksem, K., et al. 2004a. A BAC and BIBAC-based physical map of the soybean genome. Genome Res. 14: 319-326. doi:10.1101/gr.1405004.
41. Wu, C., Xu, Z., and Zhang, H.-B. 2004b. DNA Libraries. In Encyclopedia of molecular cell biology and molecular medicine, Vol. 3. Edited by R.A. Meyers. Wiley-VCH Verlag GmbH, Weinheim, Germany, pp. 385-425.
42. Wu, C., Sun, S., Lee, M.-K., Xu, Z.Y., Ren, C., and Zhang, H.-B. 2005. Whole genome physical mapping: An overview on methods for DNA fingerprinting. In The handbook of plant genome mapping: genetic and physical mapping. Edited by K. Meksem and G. Kahl. Wiley-VCH Verlag GmbH, Weinheim, Germany, pp. 257-284.
43. Wu, C., Wang, S., and Zhang, H.-B. 2006. Interactions among genomic structure, function, and evolution revealed by comprehensive analysis of the Arabidopsis thaliana genome. Genomics, 88: 394-406. doi:10.1016/j.ygeno.2006.05.003.
44. Wu, Y., Tulsieram, L., Tao, Q., Zhang, H.-B., and Rothstein, S.J. 2000. A binary vector-based large insert library for Brassica napus and identification of clones linked to a fertility restorer locus for Ogura cytoplasmic male sterility (CMS). Genome, 43: 102-109. doi:10.1139/gen-43-1-102.
45. Xiong, L.Z., Liu, K.D., Dai, X.K., Xu, C.G., and Zhang, Q. 1999. Identification of genetic factors controlling domestication-related traits of rice using an F2 population of a cross between Oryza sativa and O. rufipogon. Theor. Appl. Genet. 98: 243-251. doi:10.1007/ s001220051064.
46. Xu, Z., Sun, S., Covaleda, L., Ding, K., Zhang, A., Wu, C., Scheuring, C., and Zhang, H.-B. 2004. Genome physical mapping with large-insert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage and contig map quality. Genomics, 84: 941-951. doi:10.1016/j.ygeno.2004.08. 014.
47. Xu, Z., van den Berg, M., Scheutring, C., Colaveda, L., Lu, H., Santos, F.A., et al. 2005. Genome-wide physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: a robust physical map of Penicillium chrysogenum. Nucleic Acids Res. 33: e50. doi:10.1093/nar/gni037.
48. Yano, M., Harushima, Y., Nagamura, Y., Kurata, N., Minobe, Y., and Sasaki, T. 1997. Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map. Theor. Appl. Genet. 95: 1025-1032. doi:10.1007/s001220050658.
49. Yu, J., Hu, S., Wang, J., Wong, G.K.-S., Li, S., Liu, B., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (Washington, D.C.), 296: 79-92. doi:10.1126/science.1068037.
50. Zhang, H.-B., and Wing, R.A. 1997. Physical mapping of the rice genome with BACs. Plant Mol. Biol. 35: 115-127. doi:10.1023/A:1005733909099.
51. Zhang, H.-B., Choi, S., Woo, S.-S., Li, Z., and Wing, R.A. 1996. Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population. Mol. Breed. 2: 11-24.
52. Zhao, S., Shatsman, S., Ayodeji, B., Geer, K., Tsegaye, G., Krol, M., et al. 2001. Mouse BAC ends quality assessment and sequence analyses. Genome Res. 11: 1736-1745. doi:10.1101/gr.179201.
53. Zhao, Q., Zhang, Y., Cheng, Z., Chen, M., Wang, S., Feng, Q., et al. 2002. A fine physical map of the rice chromosome 4. Genome Res. 12: 817-823. doi:10.1101/gr.48902.