Rice molecular genetic map using RFLPs and its applications

Plant Molecular Biology

Volumn 35, Issue 1-2, 1997, Pages 79-87

  Nagamura, Yoshiaki ^a   Antonio, Baltazar A ^a   Sasaki, Takuji ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

Author keywords

Application; Comparative mapping; Molecular genetic map; RFLP marker

Indexed keywords

ARABIDOPSIS;

EID: 0031239532     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/978-94-011-5794-0_8     Document Type: Article

References (98)

1. Arumuganathan K, Earle ED: Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: 208-218 (1991).
2. Ahn S, Tanksley SD: Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90: 7980-7984 (1993).
3. Ahn S, Anderson JA, Sorrells ME, Tanksley SD: Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet 241: 483-490 (1993).
4. Antonio BA, Inoue T, Kajiya H, Nagamura Y, Kurata N, Minobe Y, Yano M, Nakagahra M, Sasaki T: Comparison of genetic distance and order of DNA markers in five populations of rice. Genome 39: 946-956 (1996).
5. Ashikawa I, Kurata N, Nagamura Y, Minobe Y: Cloning and mapping of telomere-associated sequences from rice. DNA Res 1: 67-76 (1994).
6. Beckmann JS, Soller M: Restriction fragment length polymorphisms in genetic improvement: methodologies, mapping and costs. Theor Appl Genet 67: 35-43 (1983).
7. Beckmann JS, Soller M: Restriction fragment length polymorphisms and genetic improvement of agricultural species. Euphytica 35: 111-124 (1986).
8. Bent AF, Kunkel BN, Dahlbeck D, Brown KL, Schmidt R, Giraudat J, Leung J, Staskawicz: RPS2 of Arabidopsis thaliana: a leucine-rich repeat class of plant disease resistance genes. Science 265: 1856-1860 (1994).
9. Bernatzky R, Tanksley SD: Towards a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics 112: 887-898 (1986).
10. Binelli G, Gianfranceschi L, Pe ME, Taramino, 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).
11. Bonierbale M, Plaisted RL, Tanksley SD: RFLP maps of potato and tomato based on a common set of clones reveal modes of chromosomal evolution. Genetics 120: 1095-1103 (1988).
12. Botstein D, White RL, Skolnick M, Davis R: Construction of a genetic linkage map in man using restriction fragment polymorphism. Am J Hum Genet 32: 314-331 (1980).
13. Burr B, Burr FA, Thompson KH, Albertson MC, Stuber CW: Gene mapping with recombinant inbreds in maize. Genetics 118: 519-526 (1988).
14. Burr B, Burr FA, Matz EC: Maize molecular map (Zea mays L.) (2N=20) In: O'Brien SJ (ed) Genetic Maps, Book 6: Plants, pp. 6.39-6.60. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1993).
15. Causse MA, Fulton TM, Cho YG, Ahn SN, 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).
16. Cho YG, Eun MY, McCouch, Chae YA: The semidwarf gene, sd-1, of rice (Oryza sativa L.). II. Molecular mapping and marker-assisted selection. Theor Appl Genet 89: 54-59 (1994).
17. Devos KM, Gale MD: Extended genetic maps of the homoeologous group 3 chromosomes of wheat, rye and barley. Theor Appl Genet 85: 649-652 (1993).
18. Devos K, Gale M: The genetic maps of wheat and their potential in plant breeding. Outlook Agric 22: 93-99 (1993).
19. Dufour P, Grivet L, D'Hont A, Deu M, Trouche G, Glaszmann, Hamon P: Comparative genetic mapping between duplicated segments on maize chromosomes 3 and 8 and homoeologous regions in sorghum and sugarcane. Theor Appl Genet 92: 1024-1030 (1996).
20. Dunford RP, Kurata N, Laurie DA, Money TA, Minobe Y, Moore G: Conservation of fine-scale DNA marker order in the genomes of rice and the Triticeae. Nucl Acids Res 23: 2724-2728 (1995).
21. Fukuoka S, Inoue T, Miyao A, Monna L, Zhong HS, Sasaki T, Minobe Y: Mapping of sequence-tagged sites in rice by single strand conformation polymorphism. DNA Res 1: 271-277 (1994).
22. 2 population. Genetics 134: 917-930 (1993).
23. Graner A, Jahoor A, Schondelmaier J, Siedler H, Pillen K, Fischbeck G, Wenzel G, Hermann RG: Construction of an RFLP map of barley. Theor Appl Genet 83: 250-256 (1991).
24. Grant MR, Godiard L, Straube E, Ashfield T, Lewald, Sattler A, Innes RW, Dangl JL: Structure of the Arabidopsis RPM1 gene enabling dual specificity disease resistance. Science 269: 843-846 (1995).
25. Hart GE, Gale MD: Biochemical/molecular loci of hexaploid wheat (Triticum aestivum 2n=42 genomes AABBDD). In: O'Brien SJ (ed) Genetic Maps. Book 6, pp. 628-638. Cold Spring Harbor Laboratory Press, NY (1990).
26. Harushima Y, Kurata N, Yano M, Nagamura Y, Sasaki T, Minobe Y, Nakagahra M: Detection of segregation distortions in an indica-japonica rice cross using a high-resolution molecular map. Theor Appl Genet 92: 145-150 (1996).
27. Helentjaris T, Slocum M, Wright S, Schaefer A: Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms. Theor Appl Genet 72: 761-769 (1986).
28. Hirabayashi H, Ogawa T: RFLP mapping of Bph-1 (brown plant hopper resistance gene) in rice. Breed Sci 45: 369-371 (1995).
29. Huang N, McCouch S, Mew T, Parco A, Guiderdoni E: Doubled haploid population in rice. Rice Genet Newsl 11: 134-137 (1994).
30. Hulbert SH, Richer 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).
31. Ideta O, Yoshimura A, Matsumoto H, Tsunematsu H, Iwata N: Integration of conventional and RFLP linkage maps in rice. I. Chromosomes 1, 2, 3 and 4. Rice Genet Newsl 9: 128-129 (1992).
32. Ideta O, Yoshimura A, Matsumoto H, Tsunematsu H, Saito H, Iwata N: Integration of conventional and RFLP linkage maps in rice. II. Chromosomes 6, 9, 10 and 11. Rice Genet Newsl 10: 87-89 (1993).
33. Ideta O, Yoshimura A, Ashikari M, Iwata N: Integration of conventional and RFLP linkage maps in rice. III. Chromosomes 5, 7, 8 and 12. Rice Genet Newsl 11: 116-117 (1994).
34. Inoue T, Zhong HS, Miyao A, Ashikawa I, Monna L, Fukuoka S, Miyadera N, Nagamura Y, Kurata N, Sasaki T, Minobe Y: Sequence-tagged sites (STSs) as standard landmarkers in the rice genome. Theor Appl Genet 89: 728-734 (1994).
35. Ishii T, Brar DS, Multani DS, Khush GS: Molecular tagging of genes for brown plant hopper and earliness introgressed from Oryza australiensis into cultivated rice, O. sativa. Genome 37: 217-221 (1994).
36. Izawa T, Shimamoto K: Becoming a model plant: the importance of rice to plant science. Trends Plant Sci 1: 95-99 (1996).
37. Jena KK, Khush GS, Kochert G: Comparative RFLP mapping of a wild rice, Oryza officinalis, and cultivated rice, O. sativa. Genome 37: 382-389 (1988).
38. Kilian A, Kudrna DA, Kleinhofs A, Yano M, Kurata N, Steffenson B, Sasaki T: Rice-barley synteny and its application to saturation mapping of the barley Rpg1 region. Nucl Acids Res 23: 2729-2733 (1995).
39. Kinoshita T: Report of committee on gene symbolization. Rice Genet Newsl 12: 9-153 (1995).
40. Kishimoto N, Higo H, Abe K, Arai S, Saito A, Higo K: Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions. Theor Appl Genet 88: 722-726 (1994).
41. Kleinhofs A, Kilian A, Saghai Maroof MA, Biyashev RM, Hayes P, Chen FQ, Lapitan N, Fenwick A, Blake TK, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu B, Sorrells M, Heun M, Franckowiak JD, Hoffman D, Skadsen R, Steffenson BJ: A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86: 705-712 (1993).
42. Kurata N, Moore G, Nagamura Y, Foote T, Yano M, Minobe Y, Gale M: Conservation of genome structure between rice and wheat. Bio/technology 12: 276-278 (1994).
43. Kurata N, Nagamura Y, Yamamoto K, Harushima Y, Sue N, Wu J, Antonio BA, Shomura A, Shimizu T, Lin SY, Inoue T, Fukuda A, Shimano T, Kuboki Y, Toyama T, Miyamoto Y, Kirihara T, Hayasaka H, Miyao A, Monna L, Zhong HS, Tamura Y, Wang ZX, 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).
44. Landry BS, Michelmore RW: Selection of probes for restriction fragment length analysis from plant genomic clones. Plant Mol Biol Rep 3: 174-179 (1985).
45. Landry BS, Kesseli R, Leung H, Michelmore RW: Comparison of restriction endonucleases and sources of probes for their efficiency in detecting restriction fragment length polymorphism in lettuce (Lactuca sativa L.). Theor Appl Genet 74: 646-653 (1987).
46. Liu YG, Tsunewaki K: Restriction fragment length polymorphism (RFLP) analysis in wheat. II. Linkage maps of the RFLP sites in common wheat. Jpn J Genet 66: 617-633 (1991).
47. Mackill DJ, Salam MA, Wang ZY, Tanksley SD: A major photoperiod-sensitivity gene tagged with RFLP and isozyme markers in rice. Theor Appl Genet 85: 536-540 (1993).
48. Martin GB, Brommonschenke 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).
49. 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).
50. McCouch SR, Abenes ML, Angeles R, Khush GS, Tanksley SD: Molecular tagging of a recessive gene, xa-5, for resistance to bacterial blight of rice. Rice Genet Newsl 8: 143-145 (1991).
51. Mew TV, Parco AS, Hittalmani S, Inukai T, Nelson R, Zeigler S, Huang N: Fine-mapping of major genes for blast resistance in rice. Rice Genet Newsl 11: 126-128 (1994).
52. Mindrinos M, Katagiri F, Yu GL, Ausubel FM: The A. thaliana disease-resistant gene RPS2 encodes a protein containing a nucleotide-binding site and leucine-rich repeats. Cell 78: 1089-1099 (1994).
53. Miyamoto M, Ando I, Rybka K, Kodama O, Kawasaki S: High resolution mapping of the indica-derived rice blast resistance genes. I. Pi-b. Mol Plant-Microbe Interact 9: 6-13 (1996).
54. Mohan M, Nair S, Bentur RS, Rao UP, Bennett J: RFLP and RAPD mapping of the rice Gm2 gene that confers resistance to biotype 1 of gall midge (Orseolia oryzae). Theor Appl Genet 87: 782-788 (1994).
55. Moore G, Devos KM, Wang Z, Gale MD: Grasses, line up and form a circle. Curr Biol 5: 737-739 (1995).
56. Monna L, Miyao A, Inoue T, Fukuoka S, Yamazaki KM, Zhong HS, Sasaki T, Minobe Y: Determination of RAPD markers in rice and their conversion into sequence tagged sites (STSs) and STS-specific primers. DNA Res 1: 139-148 (1994).
57. Nagamura Y, Inoue T, Antonio BA, Shimano T, Kajiya H, Shomura A, Lin SY, Kuboki Y, Harushima Y, Kurata N, Minobe Y, Yano M, Sasaki T: Conservation of duplicated segments between rice chromosomes 11 and 12. Breed Sci 45: 373-376 (1995).
58. Nair S, Bentur JS, Prasada Rao U, Mohan M: DNA markers tightly linked to a gall midge resistance gene (Gm2) are potentially useful for marker-aided selection in rice breeding. Theor Appl Genet 91: 68-73 (1995).
59. Nair S, Kumar A, Srivastava MN, Mohan M: PCR-based DNA markers linked to a gall midge resistance gene, Gm4t, has potential for marker-aided selection in rice. Theor Appl Genet 92: 660-665 (1996).
60. O'Donoughue LS, Kianian SF, Rayapati PJ, Penner GA, Sorrells ME, Tanksley SD, Phillips RL, Rines HW, Lee M, Fedak G, Molnar SJ, Hoffmann D, Salas CA, Wu B, Autrique E, van Deynze A: A molecular map of cultivated oats. Genome 38: 368-380 (1995).
61. 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).
62. Powell W, Machray GC, Provan J: Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1: 215-222 (1996).
63. Qian HR, Zhuang JY, Lin HX, Lu J, Zheng KL: Identification of a set of RFLP probes for subspecies differentiation on Oryza saliva L.. Theor Appl Genet 90: 878-884 (1995).
64. Redona ED, Mackill DJ: Molecular mapping of quantitative trait loci in japonica rice. Genome 39: 395-403 (1996).
65. Ronald P, Albano B, Tabien R, Abenes L, Wu K, McCouch SR, Tanksley SD: Genetic and physical analysis of rice bacterial blight resistance locus, Xa21. Mol Gen Genet 236: 113-120 (1992).
66. Saghai Maroof MA, Yang GP, Biyashev, Maughan PJ, Zhang Q: Analysis of the barley and rice genomes by comparative RFLP linkage mapping. Theor Appl Genet 92: 541-551 (1996).
67. Saito A, Yano M, Kishimoto N, Nakagahra M, Yoshimura A, Saito K, Kuhara S, Ukai Y, Kawase M, Nagamine T, Yoshimura S, Ideta O, Ohsawa R, Hayano Y, Iwata N, Sugiura M: Linkage map of restriction fragment length polymorphism loci in rice. Jpn J Breed. 41: 665-670 (1991).
68. Sasaki T, Song J, Koga-Ban Y, Matsui E, Fang F, Higo H, Nagasaki H, Hori M, MiyaM, Murayama-Kayano E, Takiguchi T, Takasuga A, Niki T, Ishimaru K, Ikeda H, Yamamoto Y, Mukai Y, Ohta I, Miyadera N, Havukkala I, Minobe Y: Toward cataloguing all rice genes: large-scale sequencing of randomly chosen rice cDNAs from a callus cDNA library. Plant J 6: 615-624 (1994).
69. Singh K, Ishii T, Parco A, Huang N, Brar D, Khush GS: Centromere mapping and orientation of the molecular linkage map of rice (Oryza sativa L.). Proc Natl Acad Sci USA 93: 6163-6168 (1996).
70. Song WY, Wang GL, Chen LL, Kim HS, Holsten T, Wang B, Zhai WX, Zhu LH, Fauquet C, Ronald P: The rice disease resistance gene, Xa21, encodes a receptor kinase-like protein. Science 270: 1804-1806 (1995).
71. Tanksley SD: Molecular markers in plant breeding. Plant Mol Biol Rep 1:3-8 (1983).
72. Tanksley SD, Young ND, Paterson AH, Bonierbale MW: RFLP mapping in plant breeding: New tools for an old science. Bio/technology 7: 257-264 (1989).
73. Tanksley SD, Ganal NW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB, Messeguer R, Miller JC, Miller L, Paterson AH, Pineda O, Röder MS, Wing RA, Wu W, Young ND: High density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141-1160 (1992).
74. Tsunematsu H, Yoshimura A, Harushima Y, Nagamura Y, Kurata N, Yano M, Sasaki T, Iwata N: RFLP framework map using recombinant inbred lines in rice. Breed Sci 46: 279-284 (1996).
75. Umehara Y, Inagaki A, Tanoue H, Yasukouchi 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).
76. Van Deynze AE, Nelson JC, Yglesias ES, Harrington SE, Braga DP, McCouch SR, Sorrells ME: Comparative mapping in grasses. Wheat relationships. Mol Gen Genet 248: 744-754 (1995).
77. Van Deynze AE, Nelson JC, O'Donoughue, Ahn SN, Siripoonwiat W, Harrington SE, Yglesias ES, Braga DP, McCouch SR, Sorrells ME: Comparative mapping in grasses. Oat relationships. Mol Gen Genet 249: 349-356 (1995).
78. Van Deynze AE, Doubcovsky J, Gill KS, Nelson JC, Sorrells ME, Dvorak J, Gill BS, Lagudah ES, McCouch SR, Apples R: Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oats. Genome 38: 45-59 (1995).
79. Vos P, Hogers R, Bleeker M, Reijians M, Lee T, Homes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M: AFLP: a new technique for DNA fingerprinting. Nucl Acids Res 23: 4407-4414 (1995).
80. Wang GL, Mackill DJ, Bonman JM, McCouch SR, Champoux MC, Nelson RJ: RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. Genetics 136: 1421-1434 (1994).
81. Wang ZY, Tanksley SD: Restriction fragment length poly-morphism in Oryza sativa L.. Genome 32: 1113-1118 (1989).
82. Whitkus R, Doebley J, Lee M: Comparative genome mapping of sorghum and maize. Genetics 132: 1119-1130 (1992).
83. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV: DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acids Res 18: 6531-6535 (1990).
84. Wu J, Matsui E, Yamamoto K, Nagamura Y, Kurata N, Sasaki T, Minobe Y: Genomic organization of 57 ribosomal protein genes in rice (Oryza sativa L.) through RFLP mapping. Genome 38: 1189-1200 (1995).
85. Wu KS, Tanksley SD: Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241: 225-235 (1993).
86. Xu GW, Magill CW, Schertz KF, Hart GE: A RFLP linkage map of Sorghum bicolor (L.) Moench. Theor Appl Genet 89: 139-145 (1994).
87. 1 hybrid of rice. Genes Genet Syst 71: 37-41 (1996).
88. Yano M, Harushima Y, Nagamura Y, Kurata N, Minobe Y, Sasaki T: Fine scale mapping of quantitative trait loci conferring heading date in rice, Oryza sativa L.. submitted.
89. Yoshimura S, Nelson R, Yoshimura A, Mew TW, Iwata N: RFLP mapping of the bacterial blight resistance genes Xa-3 and Xa-4. Rice Genet Newsl 9: 136-138 (1992).
90. Yoshimura S, Yoshimura A, Saito A, Kishimoto N, Kawase M, Yano M, Nakagahra M, Ogawa T, Iwata N: RFLP analysis of introgressed chromosomal segments in three near-isogenic lines of rice for bacterial blight resistance genes, Xa-I, Xa-3 and Xa-4. Jpn J Genet 67: 29-37 (1992).
91. Yoshimura S, Yoshimura A, Nelson RJ, Mew TW, Iwata N: Tagging Xa-1, the bacterial blight resistance gene in rice, by using RAPD markers. Breed Sci 45: 81-85 (1995).
92. Yoshimura S, Umehara Y, Kurata N, Nagamura Y, Sasaki T, Minobe Y, Iwata N: Identification of a YAC clone carrying the Xa-1 allele, a bacterial blight resistance gene in rice. Theor Appl Genet 93: 117-122 (1996).
93. Young ND, Tanksley SD: Restriction fragment length polymorphism maps and the concept of graphical genotypes. Theor Appl Genet 77: 95-101 (1989).
94. Yu ZH, Mackill DJ, Bonman JM, Tanksley SD: Tagging genes for blast resistance in rice via linkage to RFLP markers. Theor Appl Genet 81: 471-476 (1991).
95. Yu ZH, McCouch SR, KinoshitaT, Sato S, Tanksley SD: Association of morphological and RFLP markers in rice (Oryza saliva L.). Genome 38: 566-574 (1995).
96. Zhao X, Kochert G: Phylogenetic distribution and genetic mapping of a (GGC)n microsatellite from rice (Oryza sativa L.). Plant Mol Biol 21: 607-614 (1993).
97. Zhang G, Angeles ER, Abenes MLP, Khush GS, Huang N: RAPD and RFLP mapping of the bacterial blight resistance gene xa-13 in rice. Theor Appl Genet 93: 65-67 (1966).
98. Zhu LH, Chen Y, Xu YB, Xu JC, Cai HW, Ling ZZ: Construction of a molecular map of rice and gene mapping using a doubled haploid population of a cross between indica and japonica varieties. Rice Genet Newsl 10: 132-135 (1993).