Molecular mapping of quantitative trait loci in japonica rice

Genome

Volumn 39, Issue 2, 1996, Pages 395-403

  Redoña, Edilberto D ^a,b   Mackill, David J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b PHILIPPINE RICE RESEARCH INSTITUTE   (Philippines)

Author keywords

Japonica; Oryza sativa; Qtl mapping; RAPD; RFLP; Seedling vigor

Indexed keywords

JAPONICA; ORYZA SATIVA;

EID: 0000739022     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/g96-050     Document Type: Article

References (53)

1. Allard, R.W. 1956. Formulas and tables to facilitate the calculation of recombination values in heredity. Hilgardia, 24: 235-278.
2. Asins, M.J., Mestre, P., García, J.E., Dicenta, F., and Carbonell, E.A. 1994. Genotype X environment interaction in QTL analysis of an intervarietal almond cross by means of genetic markers. Theor. Appl. Genet. 89: 358-364.
3. Breto, M.P., Asins, M.J., and Carbonell, E.A. 1994. Salt tolerance in Lycopersicon species. 3. Detection of quantitative trait loci by means of molecular markers. Theor. Appl. Genet. 88: 395-401.
4. Causse, M.A., Fulton, T.M., Cho, Y.G., Ahn, S.N., Chunwongse, J., Wu, K.S., Xiao, J.H., Yu, Z.H., Ronald, P.C., Harrington, S.E., Second, G., McCouch, S.R., and Tanksley, S.D. 1994. Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics, 138: 1251-1274.
5. Champoux, M., Wang, G., Sarkarung, S., Huang, N., Mackill, D.J., O'Toole, J.C., and McCouch, S.R. 1995. Locating genes associated with root morphology and drought avoidance in rice via linkage to molecular markers. Theor. Appl. Genet. 90: 969-981.
6. Chang, T.T., and Bardenas, E.A. 1965. The morphology and varietal characteristics of the rice plant. Int. Rice Res. Inst. Tech. Bull. No. 4.
7. de Vicente, M.C., and Tanksley, S.D. 1993. QTL analysis of transgressive segregation in an interspecific tomato cross. Genetics, 134: 585-596.
8. Dilday, R.H., Mgonja, M.A., Amonsilpa, S.A., Collins, F.C., and Wells, B.R. 1990. Plant height vs. mesocotyl and coleoptile elongation in rice: linkage or pleiotropism? Crop Sci. 30: 815-818.
9. Edwards, M. 1992. Use of molecular markers in the evaluation and introgression of genetic diversity for quantitative traits. Field Crops Res. 29: 241-260.
10. Foolad, M.R., and Jones, R.A. 1993. Mapping salt-tolerance genes in tomato (Lycopersicon esculentum) using trait-based marker analysis. Theor. Appl. Genet. 87: 184-192.
11. Glaszmann, J.C. 1987. Isozymes and classification of Asian rice varieties. Theor. Appl. Genet. 74: 21-30.
12. Haldane, J.B.S. 1919. The combination of linkage values, and the calculation of distance between the loci of linked factors. J. Genet. 8: 299-309.
13. Jones, D.B., and Peterson, M.L. 1976. Rice seedling vigor at sub-optimal temperatures. Crop Sci. 16: 102-105.
14. Kosambi, D.D. 1944. The estimation of map distances from recombination values. Ann. Eugen. 12: 172-175.
15. Kurata, N., Nagamura, Y., Yamamoto, K., Harushima, Y., Sue, N., Wu, J., Antonio, B.A., Shomura, A., Shimizu, T., Lin, S.Y., Inoue, T., Fukuda, A., Shimano, T., Kuboki, Y., Toyama, T., Miyamoto, Y., Kirihara, T., Hayasaka, K., Miyao, A., Monna, L., Zhong, H.S., Tamura, Y., Wang, Z.X., Momma, T., Umehara, Y., Yano, M., Sasaki, T., and Minobe, Y. 1994. A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nature Genet. 8: 365-372.
16. Lander, E.S., and Botstein, D. 1989. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics, 121: 185-199.
17. Lander, E.S., Green, P., Abrahamson, J., Barlow, A., Daly, M., Lincoln, S.E., and Newburg, L. 1987. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 1: 174-181.
18. Li, C.C., and Rutger, J.N. 1980. Inheritance of cool temperature seedling vigor in rice and its relationship with other agronomic characters. Crop Sci. 20: 295-298.
19. Lin, S.Y., Ikehashi, H., Yanagihara, S., and Kawashima, A. 1992. Segregation distortion via male gametes in hybrids between indica and japonica or wide-compatibility varieties of rice (Oryza sativa L.). Theor. Appl. Genet. 84: 812-818.
20. Litt, M., and Luty, J.A. 1989. A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am. J. Hum. Genet. 44: 397-401.
21. Mackill, D.J. 1995. Classifying japonica rice cultivars with RAPD markers. Crop Sci. 35: 889-894.
22. McCouch, S.R., Kochert, G., Yu, Z.H., Wang, Z.Y., Khush, G.S., Coffman, W.R., and Tanksley, S.D. 1988. Molecular mapping of rice chromosomes. Theor. Appl. Genet. 76: 815-829.
23. McKenzie, K.S., Johnson, C.W., Tseng, S.T., Oster, J.J., and Brandon, D.M. 1994. Breeding improved rice cultivars for temperate regions - a case study. Aust. J. Exp. Agric. 34: 897-905.
24. Michelmore, R.W., Paran, I., and Kesseli, R.V. 1991. Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc. Natl. Acad. Sci. U.S.A. 88: 9828-9832.
25. Oka, H.I. 1988. Origin of cultivated rice. Elsevier, Tokyo.
26. Panaud, O., Chen, X., and McCouch, S.R. 1995. Frequency of microsatellite sequences n rice (Oryza sativa L.). Genome, 38: 1170-1176.
27. Paterson, A.H., Lander, E.S., Hewitt, J.D., Peterson, S., Lincoln, S.E., and Tanksley, S.D. 1988. Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature (London), 335: 721-726.
28. Peterson, M.L., Jones, D.B., and Rutger, J.N. 1978. Cool temperature screening of rice lines for seedling vigor. Il Riso, Vol. 27. Ente Nazionale Risi, Milan, Italy, pp. 269-274.
29. Pham, J.L., and Bougerol, B. 1993. Abnormal segregations in crosses between two cultivated rice species. Heredity, 70: 466-471.
30. Pham, J.L., Glaszmann, J.C., Sano, R., Barbier, P., Ghesquière, A., and Second, G. 1990. Isozyme markers in rice: genetic analysis and linkage relationships. Genome, 33: 348-359.
31. Raney, F. 1963. Rice water temperature. Calif. Agric. 17: 6-7.
32. Redoña, E.D., and Mackill, D.J. 1996a. Genetic variation for seedling vigor traits in rice. Crop Sci. In press.
33. Redoña, E.D., and Mackill, D.J. 1996b. Mapping quantitative trait loci for seedling vigor in rice using RFLPs. Theor. Appl. Genet. In press.
34. Reiter, R.S., Williams, J.G.K., Feldmann, K.A., Rafalski, J.A., Tingey, S.V., and Scolnik, P.A. 1992. Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAs. Proc. Natl. Acad. Sci. U.S.A. 89: 1477-1481.
35. 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., and Sugiura, M. 1991. Linkage map of restriction fragment length polymorphism loci in rice. Jpn. J. Breed. 41: 665-670.
36. SAS Institute Inc. 1989. SAS/STAT® user's guide, version 6, 4th ed., vol. 1. SAS Institute Inc. Cary, N.C.
37. Schön, C.C., Lee, M., Melchinger, A.E., Guthrie, W.D., and Woodman, W.L. 1993. Mapping and characterization of quantitative trait loci affecting resistance against second-generation European corn borer in maize with the aid of RFLPs. Heredity, 70: 648-659.
38. Stuber, C.W. 1995. Mapping and manipulating quantitative traits in maize. Trends Genet. 11: 477-481.
39. Stuber, C.W., Edwards, M.D., and Wendel, J.F. 1987. Molecular marker-facilitated investigations of quantitative trait loci in maize. II. Factors influencing yield and its component traits. Crop Sci. 27: 639-648.
40. Tanksley, S., Young, N., Paterson, A., and Bonierbale, M. 1989. RFLP mapping in plant breeding: new tools for an old science. Bio/Technology, 7: 257-264.
41. Tanksley, S.D. 1983. Molecular markers in plant breeding. Plant Mol. Biol. Rep. 1: 3-8.
42. Tautz, D. 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 17: 6463-6471.
43. Tingey, S.V., and del Tufo, J.P. 1993. Genetic analysis with random amplified polymorphic DNA markers. Plant Physiol. 101: 349-352.
44. Turner, F.T., Chen, C.C., and Bollich, C.N. 1982. Coleoptile and mesocotyl length in semi-dwarf rice seedlings. Crop Sci. 22: 43-46.
45. Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Homes, M., Fritjers, A., Pot, J., Peleman, J., Kuiper, M., and Zabeau, M. 1995. AFLP: a new concept for DNA fingerprinting. Nucleic Acids Res. 23: 4407-4414.
46. Wang, G.L., Mackill, D.J., Bonman, J.M., McCouch, S.R., Champoux, M.C., and Nelson, R.J. 1994. RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. Genetics, 136: 1421-1434.
47. Waugh, R., and Powell, W. 1992. Using RAPD markers for crop improvement. Trends Biotechnol. 10: 186-191.
48. Williams, J.G., Hanafey, M.K., Rafalski, J.A., and Tingey, S.V. 1993. Genetic analysis using random amplified polymorphic DNA markers. Methods Enzymol. 218: 704-740.
49. Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A., and Tingey, S.V. 1990. DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18: 6531-6535.
50. Xiao, J.H., Li, J.M., Yuan, L.P., and Tanksley, S.D. 1995. Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers. Genetics, 140: 745-754.
51. Yang, X., and Quiros, C.F. 1995. Construction of a genetic linkage map in celery using DNA-based markers. Genome, 38: 36-44.
52. Yu, L.X., and Nguyen, H.T. 1994. Genetic variation detected with RAPD markers among upland and lowland rice cultivars (Oryza sativa L.). Theor. Appl. Genet. 87: 668-672.
53. Zhang, Q.F., Maroof, M.A.S., Lu, T.Y., and Shen, B.Z. 1992. Genetic diversity and differentiation of indica and japonica rice detected by RFLP analysis. Theor. Appl. Genet. 83: 495-499.