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A Sorghum propinquum BAC library, suitable for cloning genes associated with loss-of-function mutations during crop domestication

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Abstract

A large insert Sorghum propinquum BAC library has been constructed to analyze the physical organization of the sorghum genome and to facilitate positional cloning of sorghum genes and QTLs associated with the early stages of grain crop domestication. This library was established from 12 different ligations using high-molecular-weight DNA generated from either one cycle or two cycles of size selection. This library consists of 38 016 BAC clones with an estimated average insert size of 126 kb and coverage of 6.6 genome equivalents. The 6.6 genome-equivalent BAC library of S. propinquum provides a 99.7% probability of finding one or more BACs that contain genes of interest. Twenty mapped DNA probes, ten homologous and ten heterologous, were used to screen the library, and 121 positive clones were identified, 6.05 per locus or 6.37 per probe.

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References

  1. Ahn S, Anderson JA, Sorrells ME, Tanksley SD: Homoeologous relationships of rice, wheat, and maize chromosomes. Mol Gen Genet 241: 483–490 (1993).

    Google Scholar 

  2. Ahn S, Tanksley SD: Comparative linkage maps of rice and maize genomes. Proc Natl Acad Sci USA 90: 7980–7984 (1993).

    Google Scholar 

  3. Arondel V, Lemieux B, Hwang I, Gibson S, Goodman HM, Somerville CR: Map-based cloning of a gene controlling omega-3 fatty acid desaturation in Arabidopsis. Science 258: 1353–1355 (1992).

    Google Scholar 

  4. Arumuganathan K, Earle ED: Nuclear DNA content of some important plant species. Plant Mol Bio Rep 9: 208–218 (1991).

    Google Scholar 

  5. Avramova Z, Tikhonov A, Sanmiguel P, Jin YK, Liu CN, Woo S-S, Wing RA, Bennetzen JL: Gene identification in a complex chromosomal continuum by local genomic crossreferencing. Plant J 10: 1163–1168 (1996).

    Google Scholar 

  6. Battraw MJ, Hall TC: Stable transformation of Sorghum bicolor protoplasts with chimeric neomycin phosphotransferase II and β-glucuronidase genes. Theor Appl Genet 82: 161–168 (1991).

    Google Scholar 

  7. Bennetzen JL, Freeling M: Grasses as a single genetic system: genome composition, collinearity and compatibility. Trends Genet 9: 259–261 (1993).

    Google Scholar 

  8. Berhan AM, Hulbert SH, Butler LG, Bennetzen JL: Structure and evolution of the genomes of Sorghum bicolor and Zea mays. Theor Appl Genet: 598–604 (1993).

  9. Binelli G, Ginafranceschi L, Pe ME, Taramino G, Busso C, Stenhouse J, Ottaviano E: Similarity of maize and sorghum genomes as revealed by maize RFLP probes. Theor Appl Genet 84: 10–16 (1992).

    Google Scholar 

  10. Burke DT, Carle GF, Olson MV: Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 236: 806–812 (1987).

    Google Scholar 

  11. Cai L, Taylor JF, Wing RA, Gallagher DS, Woo S-S, Davis SK: Construction and characterization of a bovine bacterial artificial chromosome library. Genomics 29: 413–425 (1995).

    Google Scholar 

  12. Casas AM, Kononowicz AK, Zehr UB, Tomes DT, Axtell JD, Butler LG, Bressan RA, Hasegawa PM: Transgenic sorghum plants via microprojectile bombardment. Proc Natl Acad Sci USA 90: 11212–11216 (1993).

    Google Scholar 

  13. Chang C, Kwok SF, Bleecker AB, Meyerowitz EM: Arabidopsis ethylene-response gene ETR1: Similarity of product to two-component regulators. Science 262: 539–544 (1993).

    Google Scholar 

  14. Chen M, Sanmiguel P, Bennetzen JL: Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148: 435–443 (1998).

    Google Scholar 

  15. Chen M, Sanmiguel P, De Oliveira AC, Woo S S, Zhang H, Wing RA, Bennetzen JL: Microcollinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc Natl Acad Sci USA 94: 3431–3435 (1997).

    Google Scholar 

  16. Chittenden LM, Schertz KF, Lin Y-R, Wing RA, Paterson AH: A detailed RFLP map of Sorghum bicolor _ S. propinquum, suitable for high-density mapping, suggests ancestral duplication of Sorghum chromosomes or chromosomal segments. Theor Appl Genet 87: 925–933 (1994).

    Google Scholar 

  17. Choi S, Creelman RA, Mullet JE, and Wing RA: Construction and characterization of a bacterial artificial chromosome library of Arabidopsis thaliana. Weeds World 2: 17–20 (1995).

    Google Scholar 

  18. Chumakov IM, Rigault P, Le Gall I, Bellanne Chantelot C, Billault A, Guillou S, Soularue P, Guasconi G, Poullier E, Gros I, Belova M, Sambucy JL, Susini L, Gervy P, Gilbert F, Beaufils S, Bui H, Massart C, De Tand MF, Dukasz F, Lecoulant S, Ougen P, Perrot V, Saumier M, Soravito C, Bahouayila R, Cohen Akenine A, Barillot E, Bertrand S, Codani JJ, Caterina D, Georges I, Lacroix B, Lucotte G, Sahbatou M, Schmit C, Sangouard M, Tubacher E, Dib C, Faure S, Fizames C, Gyapay G, Millasseau P, Nguyen S, Muselet D, Vignal A, Morissette J, Menninger J, Lieman J, Desai T, Banks A, Bray Ward P, Ward D, Hudson T, Gerety S, Foote S, Stein L, Page DC, Lander ES, Weissenbach J, Le Paslier D, Cohen D: A YAC contig map of the human genome. Nature 377: 175–297 (1995).

    Google Scholar 

  19. Clarke L and Carbon J: A colony bank containing synthetic ColE1 hybrid plasmids representative of the entire E. coli genome. Cell 9: 91–100 (1976).

    Google Scholar 

  20. Cohen D, Chumakov I, Weissenbach J: A first-generation physical map of the human genome. Nature 366: 698–701 (1993).

    Google Scholar 

  21. Danesh D, Penuela S, Mudge J, Denny RL, Nordstrom H, Martinez JP, Young ND: A bacterial artificial chromosome library for soybean and identification of clones near a major cyst nematode resistance gene. Theor Appl Genet 96: 196–202 (1998).

    Google Scholar 

  22. Doebley J, Stec A: Genetic analysis of the morphological differences between maize and teosinte. Genetics 129: 285–295 (1991).

    Google Scholar 

  23. Doebley J, Stec A: Inheritance of the morphological differences between maize and teosinte: comparison of results for two F2 populations. Genetics 134: 559–570 (1993).

    Google Scholar 

  24. Doggett H: Sorghum, 2nd ed John Wiley, New York (1988).

    Google Scholar 

  25. Frijters AC, Zhang Z, Damme MV, Wang GL, Ronald PC, Michelmore RW: Construction of a bacterial artificial chromosome library containing large EcoRI and HindIII genomic fragments of lettuce. Theor Appl Genet 94: 390–399 (1997).

    Google Scholar 

  26. Haldi M, Perrot V, Saumier M, Desai T, Cohen D, Cherif D, Ward D, Lander ES: Large human YACs constructed in a rad52 strain show a reduced rate of chimerism. Genomics 24: 478–484 (1994).

    Google Scholar 

  27. Hamilton CM, Frary A, Lewis C, and Tanksley SD: Stable transfer of intact high molecular weight DNA into plant chromosomes. Proc Natl Acad Sci USA 93: 9975–9979 (1996).

    Google Scholar 

  28. Hulbert SH, Richter TE, Axtell JD, Bennetzen JL: Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. Proc Natl Acad Sci USA 87: 4251–4255 (1990).

    Google Scholar 

  29. Jiang J, Gill BS, Wang GL, Ronald PC, Ward DC: 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).

    Google Scholar 

  30. Kinoshita T, Takahashi M: The one hundredth report of genetical studies on the rice plant: linkage studies and future prospects. J Fac Agric Hokkaido Univ 65 (Pt. 1): 1–61 (1991).

    Google Scholar 

  31. Lin Y-R, Schertz KF, Paterson AH: Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population. Genetics 141: 391–411 (1995).

    Google Scholar 

  32. Marra MA, Kucaba TA, Dietrich NL, Green ED, Brownstein B, Wilson RK, McDonald KM, Hillier LW, McPherson JD, Waterston RH: High throughput fingerprint analysis of large-insert clones. Genome Res 7: 1072–1084 (1997).

    Google Scholar 

  33. Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED, Tanksley SD: Mapbased cloning of a protein kinase gene conferring disease resistance in tomato. Science 262: 1432–1436 (1993).

    Google Scholar 

  34. Moore G, Gale MD, Kurata N, Flavell R: Molecular analysis of small grain cereal genomes: Current status and prospects. Bio/technology 11: 584–589 (1993).

    Google Scholar 

  35. Mullins LJ, Kotelevtseva N, Boyd AC, Mullins JJ: Efficient Cre-lox linearisation of BACs: Applications to physical mapping and generation of transgenic animals. Nucl Acids Res 25: 2539–2540 (1997).

    Google Scholar 

  36. Ogi Y, Kato H, Maruyama K, Saito A, Kikuchi F: Identification of RFLP markers closely linked to the semidwarfing gene at the sd-1 locus in rice. Japan Breed 43: 141–146 (1993).

    Google Scholar 

  37. Okumoto Y, Ichitani K, Inoue H, Tanisaka T: Photoperiod insensitivity gene essential to the varieties grown in the northern limit region of paddy rice (Oryza sativa L.) cultivation. Euphytica 92: 63–66 (1996).

    Google Scholar 

  38. Paterson AH, Lin Y-R, Li Z, Schertz KF, Doebley JF, Pinson SRM, Liu S-C, Stansel JW, Irvine JE: Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269: 1714–1718 (1995).

    Google Scholar 

  39. Paterson AH; Schertz KF; Lin Y-R, Li Z: Case history in plant domestication; Sorghum, an example of cereal evolution. In: Paterson AH (ed) Molecular Dissection of Complex Traits, pp. 187–196. CRC Press, Boca Raton, FL (1997).

    Google Scholar 

  40. Paterson AH, Schertz KF, Lin Y-R, Liu S-C, Chang Y-L: The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of johnsongrass, Sorghum halepense (L.) Pers. ). Proc Natl Acad Sci USA 92: 6127–6131 (1995).

    Google Scholar 

  41. Pereira MG, Lee M, Bramel-Cox P, Woodman W, Doebley J, Whitkus R: Construction of an RFLP map in sorghum and comparative mapping in maize. Genome 37: 236–243 (1994).

    Google Scholar 

  42. Ragab RA, Dronavalli S, Maroof MAS, Yu YG: Construction of a sorghum RFLP linkage map using sorghum and maize DNA probes. Genome 37: 590–594 (1994).

    Google Scholar 

  43. Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor, Laboratory, Cold Spring Harbor, NY (1989).

    Google Scholar 

  44. Schmidt R, Putterill J, West J, Cnops G, Robson F, Coupland G, Dean C: Analysis of clones carrying repeated DNA sequences in two YAC libraries of Arabidopsis thaliana DNA. Plant J: 735–744 (1994).

  45. Shizuya H, Birren B, Kim U-J, Mancino V, Slepak T, Tachiiri Y, and 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).

    Google Scholar 

  46. Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH, Fauquet C, Ronald P: A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270: 1804–1806 (1995).

    Google Scholar 

  47. Tanksley SD, Ganal MW, Martin GB: Chromosome landing: A paradigm for map-based gene cloning in plants with large genomes. Trends Genet 11: 63–68 (1995).

    Google Scholar 

  48. Tsumura Y, Kawahara T, Wickneswari R, Yoshimura K: Molecular phylogeny of Dipterocarpaceae in Southeast Asia using RFLP of PCR-amplified chloroplast genes. Theor Appl Genet 93: 22–29 (1996).

    Google Scholar 

  49. Wetzel CM, Rodermel SR: Gentic map of the Zea mays plastid chromosome. Maize Genet Coop Newsl 68: 209 (1994).

    Google Scholar 

  50. Whitkus R, Doebley J, and Lee M: Comparative genome mapping of sorghum and maize. Genetics 132: 119–130 (1992).

    Google Scholar 

  51. Wicking C, Williamson B: From linked marker to gene. Trends Genet 7: 288–293 (1991).

    Google Scholar 

  52. Woo S-S, Jiang J, Gill BS, Paterson AH, and Wing RA: Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucl Acids Res 22: 4922–4931 (1994).

    Google Scholar 

  53. Xu G-W; Magill CW; Schertz KF; Hart GE: A RFLP linkage map of Sorghum bicolor (L.) Moench. Theor Appl Genet 89: 139–145 (1994).

    Google Scholar 

  54. Yang D, Parco A, Nandi S, Subudhi P, Zhu Y, Wang G, Huang N: Construction of a bacterial artificial chromosome (BAC) library and identification of overlapping BAC clones with chromosome 4-specific RFLP markers in rice. Theor Appl Genet 95: 1147–1154 (1997).

    Google Scholar 

  55. Zamir D, Eshed Y: Case history in germplasm introgression: Tomato genetics and breeding using nearly isogenic introgression lines derived from wild species. In: Paterson AH (eds) Molecular Dissection of Complex Traits, pp. 207–218. Press, Boca Raton, FL (1997).

    Google Scholar 

  56. Zhang H-B, Choi S, Woo S-S, Li Z, Wing RA: 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 (1996).

    Google Scholar 

  57. Zhang H-B, Zhao X, Ding X, Paterson AH, and Wing RA: Preparation of megabase-size DNA from plant nuclei. Plant J 7: 175–184 (1995).

    Google Scholar 

  58. Zhao X-P, Zhang H-B, Wing RA, and Paterson AH: A simple method for isolation of megabase DNA from cotton. PlantMol Biol Rep 12: 126–131 (1994).

    Google Scholar 

  59. Zhao X-P, Si Y, Hanson RE, Crane CF, Price HJ, Stelly DM, Wendel JF, Paterson AH: Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton. Genome Res 8: 479–492 (1998).

    Google Scholar 

  60. Zimmer R, Gibbins AMV: Construction and characterization of a large-fragment chicken bacterial artificial chromosome library. Genomics 42: 217–226 (1997).

    Google Scholar 

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Authors and Affiliations

  1. Department of Soil and Crop Sciences, Texas A&M University, College Station, TX , 77843-2474, USA

    Yann-Rong Lin, Linghua Zhu, Shuxin Ren & Andrew H. Paterson

  2. Institute of Genetics, Fudan University, Shanghai, 200433, P.R. China

    Jinshui Yang

  3. USDA-ARS, College Station, TX , 77843-2474, USA

    Keith F. Schertz

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  1. Yann-Rong Lin
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  2. Linghua Zhu
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Lin, YR., Zhu, L., Ren, S. et al. A Sorghum propinquum BAC library, suitable for cloning genes associated with loss-of-function mutations during crop domestication. Molecular Breeding 5, 511–520 (1999). https://doi.org/10.1023/A:1009642201139

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