Molecular Breeding

, Volume 2, Issue 1, pp 11–24 | Cite as

Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population

  • Hong-Bin Zhang
  • Sangdun Choi
  • Sung-Sick Woo
  • Zhikang Li
  • Rod A. Wing


Rice is a leading grain crop and the staple food for over half of the “world” population. Rice is also an ideal species for genetic and biological studies of cereal crops and other monocotyledonous plants because of its small genome and well developed genetic system. To facilitate rice genome analysis leading to physical mapping, the identification of molecular markers closely linked to economic traits, and map-based cloning, we have constructed two rice bacterial artificial chromosome (BAC) libraries from the parents of a permanent mapping population (Lemont and Teqing) consisting of 400 F9 recombinant inbred lines (RILs). Lemont (japonica) and Teqing (indica) represent the two major genomes of cultivated rice, both are leading commercial varieties and widely used germplasm in rice breeding programs. The Lemont library contains 7296 clones with an average insert size of 150 kb, which represents 2.6 rice haploid genome equivalents. The Teqing library contains 14208 clones with an average insert size of 130 kb, which represents 4.4. rice haploid genome equivalents. Three single-copy DNA probes were used to screen the libraries and at least two overlapping BAC clones were isolated with each probe from each library, ranging from 45 to 260 kb in insert size. Hybridization of BAC clones with chloroplast DNA probes and fluorescent in situ hybridization using BAC DNA as probes demonstrated that both libraries contain very few clones of chloroplast DNA origin and are likely free of chimeric clones. These data indicate that both BAC libraries should be suitable for map-based cloning of rice genes and physical mapping of the rice genome.

Key words

bacterial artificial chromosome (BAC) cereal genome analysis map-based cloning monocotyledon, rice 


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  1. 1.
    Anderson C: Genome shortcut leads to problems. Science 259: 1684–1587 (1993).Google Scholar
  2. 2.
    Ahn S, Anderson JA, Sorrells ME, Tanksley SD: Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet 241: 483–490 (1993).PubMedGoogle Scholar
  3. 3.
    Ahn S, Tanksley SD: Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA, 90: 7980–7984 (1993).PubMedGoogle Scholar
  4. 4.
    Arondel V, Lemieux B, Hwang I, Gibson S, Goodman HN, Somerville CR: Map-based cloning of gene controlling omega-3 fatty acid desaturation in Arabidopsis. Science 258: 1353–1355 (1992).Google Scholar
  5. 5.
    Arumuganathan K, Earle ED: Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: 208–218 (1991).Google Scholar
  6. 6.
    Battraw M, Hall TC: Expression of a chimeric neomycin phosphotransferase II gene in first and second generation transgenic rice plants. Plant Sci 85: 191–202 (1992).Google Scholar
  7. 7.
    Bent AF, Kunkel BN, Dahlbeck D, Brown KL, Schmidt R, Giraudat J, Leung J, Staskawicz BJ: RPS2 of Arabidopsis thaliana: a leucine-rich repeated class of plant disease resistance genes. Science 265: 1855–1860 (1994).Google Scholar
  8. 8.
    Bernatzky R, Tankley SD: Methods fordetection of single or low copy sequence in tomato on Southern blots. Plant Mol Biol Rep 4: 37–41 (1986).Google Scholar
  9. 9.
    Bhave MR, Lawrence S, Barton C, Hannah C: Identification and molecular characterization of Shrunken-2 cDNA clones of maize. Plant Cell 2: 581–588 (1990).Google Scholar
  10. 10.
    Burke DT, Carle GF, Olson MV: Cloning of large artificial chromosome vectors. Science 236: 805–811 (1987).Google Scholar
  11. 11.
    Cao J, Zhang W, McElroy D, Wu R: Assessment of rice genetic transformation techniques. In: Khush GS, Toenniessen GH (eds) Rice Biotechnology, pp. 175–198. CAB International, Wallingford, UK (1991).Google Scholar
  12. 12.
    Causse MA, Fulton TM, Cho YG, Ahn AN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE, Second G, McCouch SR, Tanksley SD: Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138: 1251–1274 (1994).PubMedGoogle Scholar
  13. 13.
    Chang C, Kwok SF, Bleecker AB, Meyerowitz EM: Arabidopsis ethylene-response gene ETRl: similarity of product to two-component regulators. Science 252: 539–544 (1993).Google Scholar
  14. 14.
    Creusot F, Fouilloux E, Dron M, Lafleuriel J, Picard G, Billault A, Le Paslier D, Cohen D, Chaboute M, Durr A, Fleck J, Gigot C, Camilleri C, Bellini C, Caboche M, Bouchez D: The CIC library: a large insert YAC library for genome mapping in Arabidopsis thaliana. Plant J, in press (1995).Google Scholar
  15. 15.
    Ecker JR: PFGE and YAC analysis of the Arabidopsis genome. Methods 1: 186–194 (1992).Google Scholar
  16. 16.
    Edwards KJ, Thompson H, Edwards D, de Saizieu A, Sparks C, Thompson JA, Greenland AJ, Eyers M, Schuch W: Construction and characterization of a yeast artificial chromosome library containing three haploid maize genome equivalents. Plant Mol Biol 19: 299–308 (1992).Google Scholar
  17. 17.
    Eyers M, Edwards K, Schuch W: Construction and characterization of a yeast artificial chromosome library containing two haploid Beta vulgaris L. genome equivalents. Gene 121: 195–201 (1992).Google Scholar
  18. 18.
    Feinberg AP, Vogelstein S: A technique for radio-labeling DNA fragments to high specific activity. Anal Biochem 137: 266–267 (1984).PubMedGoogle Scholar
  19. 19.
    Giraudat J, Hauge BM, Valon C, Smalle J, Parcy F, Goodman HM: Isolation of the Arabidopsis 3 AB1 gene by positional cloning. Plant Cell 4: 1251–1251 (1992).CrossRefPubMedGoogle Scholar
  20. 20.
    Grill E, Somerville: Construction and characterization of a yeast artificial chromosome library of Arabidopsis which is suitable for chromosome walking. Mol Gen Genet 226: 484–490 (1991).Google Scholar
  21. 21.
    Hall TC, Xu Y, Huntley CC, Yu H, Seay J, Connell JC, Lepetit M, Dong J, Wallace D, Way MO, Buchholz WG: Transgene expression and agronomic improvement of rice. Phil Trans R Soc London B 341: 351–374 (1993).Google Scholar
  22. 22.
    Hodges TK, Peng J, Lyznik LA, Koetje D: Transformation and regeneration of rice protoplasts. In: Khush GS, Toenniessen GH (eds) Rice Biotechnology, pp. 157–176. CAB International, Wallingford, UK (1991).Google Scholar
  23. 23.
    Jiang J, Gill B, Wang G, Ronald P, Ward D: Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci USA 92: 4487–4491 (1995).PubMedGoogle Scholar
  24. 24.
    Khush GS, Kinoshita T: Rice karyotype, marker genes, and linkage groups. In: Khush GS, Toenniessen GH (eds), Rice Biotechnology, pp. 83–108. CAB International, Wallingford, UK (1991).Google Scholar
  25. 25.
    Kleine M, Michalek W, Graner A, Herrmann RG, Jung C: Construction of a barley (Hordeum vulgare L.) YAC library and isolation of a Horl-specific clone. Mol Gen Genet 240: 255–272 (1993).Google Scholar
  26. 26.
    Kurata N, Nagamura Y, Yamamoto K, Harushima Y, Sue N, Wu J, Antonio BA, Shomura A, Shimizu T, Lin S-Y, Inoue T, Fukuta A, Shimano T, Kuboki Y, Toyama, Miyamoto Y, Kirihara T, Hayasaka K, Miyao A, Monna L, Zhong HS, Tamura Y, Wang Z-X, Momma T, Umehara Y, Yano M, Sasaki T, Minobe Y: A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nature Genet 8: 365–372 (1994).Google Scholar
  27. 27.
    Larkin J, Scowroft W: Somatoclonal variation: a novel source of variability from cell cultures for plant improvement. Theor Appl Genet 60: 197–214 (1981).Google Scholar
  28. 28.
    Leung J, Bouvier-Durand M, Morris P-C, Guerrier D, Chefdor F, Giraudat: Arabidopsis ABA response gene ABll: features of a calcium-modulate protein phosphatase. Science 264: 1448–1452 (1994).Google Scholar
  29. 29.
    Li ZK, Pinson SRM, Stansel JW, Park WD: Identification of QTL for heading date and plant height in rice using RFLP markers. Theor Appl Genet, in press (1995).Google Scholar
  30. 30.
    Li ZK, Pinson SRM, Marchetti MA, Stansel JW, Park WD: Characterization of quantitative trait loci contributing to field resistance to sheath blight (Rhizoctonia solani) in rice. Theor Appl Genet, in press (1995).Google Scholar
  31. 31.
    Martin GB, Ganal MW, Tanksley SD: Construction of a yeast artificial chromosome library of tomato and identification of cloned segments linked to two disease resistance loci. Mol Gen Genet 223: 25–32 (1992).Google Scholar
  32. 32.
    Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED, Tanksley SD: Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science 252: 1432–1438 (1993).Google Scholar
  33. 33.
    McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffman WR, Tanksley SD: Molecular mapping of rice chromosomes. Theor Appl Genet 76: 815–829 (1988).Google Scholar
  34. 34.
    McCouch SR, Tanksley SD (1991) Development and use of restriction fragment length polymorphism in rice breeding and genetics. In: Khush GS, Toenniessen GH (eds) Rice Biotechnology, pp. 109–124. CAB International, Wallingford, UK (1991).Google Scholar
  35. 35.
    Meyer K, Leube MP, Grill E: A protein phosphatase 2C involved in ABA signal transduction in Arabisopsis thaliana. Science 154: 1452–1455 (1994).Google Scholar
  36. 36.
    Oannou PA, Amemiya CT, Garnes J, Kroisel PM, Shizuya H, Chen C, Batzer MA, de Jong PJ: A new bacteriophage Pl-derived vector for the propagation of large human DNA fragments. Nature Genet 5: 84–89 (1994).Google Scholar
  37. 37.
    Putterill J, Robson F, Lee K, Coupland G: Chromosome walking with YAC clones in Arabidopsis: isolation of 1700 kb of contiguous DNA on chromosome 5, including a 300 kb region containing the flowering-time gene CO. Mol Gen Genet 239: 145–157 (1993).Google Scholar
  38. 38.
    Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1989).Google Scholar
  39. 39.
    Shizuya H, Birren B, Kim U-J, Mancino V, Slepak T, Tachiiri Y, Simon M: Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89: 8794–8797 (1992).PubMedGoogle Scholar
  40. 40.
    Timmis JN, Scott NS: Sequence homology between spinach nuclear and chloroplst genomes. Nature 305: 65–67 (1983).Google Scholar
  41. 41.
    Umehara Y, Inagaki A, Tanoue H, Yasukochi Y, Nagamura Y, Saji S, Otsuki Y, Fujimura T, Kurata N, Minobe Y: Construction and characterization of a rice YAC library for physical mapping. Mol Breed 1: 79–89 (1995).Google Scholar
  42. 42.
    Wang G, Holsten T, Wang H, Ronald P: Construction of a rice bacterial artificial chromosome library and identificication of clones linked to the Xa-21 disease resistance locus. Plant J 7: 525–533 (1995).Google Scholar
  43. 43.
    Ward ER, Jen GC: Isolation of single-copy-sequence clones from a yeast artificial chromosome library of randomly-sheared Arabidopsis thaliana DNA. Plant Mol Biol 14: 561–568 (1990).Google Scholar
  44. 44.
    Wing RA, Rastogi VK, Zhang H-B, Paterson AH, Tanksley SD: An improved method of plant megabase DNA isolation in agarose microbeads suitable for physical mapping and YAC cloning. Plant J 4: 893–898 (1993).Google Scholar
  45. 45.
    Woo SS, Jiang J, Gill BS, Paterson AH, Wing RA: Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucl Acids Res 22: 4922–4931 (1994).Google Scholar
  46. 46.
    Woo SS, Rastogi VK, Zhang H-B, Paterson AH, Schertz KF, Wing RA: Isolation of megabase-size DNA from sorghum and applications for physical mapping and bacterial and yeast artificial chromosome library construction. Plant Mol Biol Rep 13: 38–50 (1995).Google Scholar
  47. 47.
    Zhang H-B, Martin GB, Tanksley SD, Wing RA: Mapbased cloning in crop plants: tomato as a model system. II. Isolation and characterization of a set of overlapping YACs encompassing the jointless locus. Mol Gen Genet 224: 513–521 (1994).Google Scholar
  48. 48.
    Zhang H-B, Zhao X, Ding X, Paterson AH, Wing RA: Preparation of megabase-size DNA from plant nuclei. Plant J 7: 175–184 (1995).Google Scholar

Copyright information

© Kluwer Academic Publishers 1996

Authors and Affiliations

  • Hong-Bin Zhang
    • 1
  • Sangdun Choi
    • 1
  • Sung-Sick Woo
    • 1
  • Zhikang Li
    • 1
  • Rod A. Wing
    • 1
  1. 1.Department of Soil and Crop Sciences, Crop Biotechnology CenterTexas A & M UniversityCollege StationUSA

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