Genetic diversity and phylogeny of Japanese sake-brewing rice as revealed by AFLP and nuclear and chloroplast SSR markers

Theoretical and Applied Genetics

Volumn 109, Issue 8, 2004, Pages 1586-1596

  Hashimoto, Z ^a   Mori, N ^a   Kawamura, M ^a   Ishii, T ^a   Yoshida, S ^b   Ikegami, M ^b   Takumi, S ^a   Nakamura, C ^a  

^a KOBE UNIVERSITY   (Japan)

^b Hyogo Institute of Agriculture Forestry and Fishery   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BREWERIES; CROPS; CULTIVATION; GRAIN SIZE AND SHAPE; PROTEINS;

COOKING CULTIVARS; GENETIC DIVERSITY; PHYLOGENY; POLYMORPHISMS;

GENETIC ENGINEERING;

CHLOROPLAST DNA;

ANALYSIS OF VARIANCE; ARTICLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; CROP; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; JAPAN; NUCLEIC ACID AMPLIFICATION; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RICE; SPECIES DIFFERENCE; VARIABLE NUMBER OF TANDEM REPEAT;

ANALYSIS OF VARIANCE; CLUSTER ANALYSIS; CROPS, AGRICULTURAL; DNA, CHLOROPLAST; GEOGRAPHY; HAPLOTYPES; JAPAN; MINISATELLITE REPEATS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; ORYZA SATIVA; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SPECIES SPECIFICITY; VARIATION (GENETICS);

CHLOROPHYLLS; CLUMPS; CULTIVATION; GENETIC ENGINEERING; GRAIN; HEATING; PLASTIDS; PROTEINS; RICE; VARIANCE;

ORYZA SATIVA; ORYZA SATIVA (JAPONICA CULTIVAR-GROUP); PIERIS BRASSICAE;

EID: 11144325062     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-004-1794-6     Document Type: Article

References (34)

1. Aggarwal RK, Brar DS, Nandi S, Huang N, Khush GS (1999) Phylogenetic relationships among Oryza species revealed by AFLP markers. Theor Appl Genet 98:1320-1328
2. Akagi H, Yokozeki Y, Inagaki A, Fujimura T (1997) Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theor Appl Genet 94:61-67
3. Ashikawa I, Fukuta Y, Tamura K, Yagi T (1999) Application of AFLP technique that uses non-radioactive fluorescent primers to the detection of genetic diversity in Japanese rice cultivars and cloning of DNA sequences derived from an Indica genome. Breed Sci 49:225-231
4. Botstein D, White RL, Sholnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314-331
5. Chang T (1976) The origin, evolution, cultivation, dissemination, and diversification of Asian and African rices. Euphytica 25:425-441
6. Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553-567
7. Innan H, Terauchi R, Kahl G, Tajima F (1999) A method for estimating nucleotide diversity from AFLP data. Genetics 151:1157-1164
8. Ishii T, McCouch SR (2000) Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight other Gramineae species. Theor Appl Genet 100:1257-1266
9. Ishii T, Xu Y, McCouch SR (2001) Nuclear- and chloroplast-microsatellite variation in A-genome species of rice. Genome 44:658-666
10. Kato T (1989) Diallel analysis of grain size of rice (Oryza sativa L.). Jpn J Breed 39:39-45
11. Kubo TA, Yoshimura A, Iwata N (1998) Trial construction of molecular linkage map of Japonica rice. J Fac Agric Kyushu Univ 43:95-101
12. Mackill DJ, Zhang Z, Redona ED, Colowit PM (1996) Level of polymorphism and genetic mapping of AFLP markers in rice. Genome 39:969-977
13. Maheswaran M, Subudhi PK, Nandi S, Xu JC, Parco A, Yang DC, Huang N (1997) Polymorphism, distribution, and segregation of AFLP markers in a doubled haploid rice population. Theor Appl Genet 94:39-45
14. Mano Y, Kawasaki S, Takaiwa F, Komatsuda T (2001) Construction of a genetic map of barely (Hordeum vulgare L.) cross 'Azumamugi' x 'Kanto Nakate Gold' using a simple and efficient amplified fragment length polymorphism system. Genome 44:284-292
15. Miyashita NT, Kawabe A, Innan H (1999) DNA variation in the wild plant Arabidopsis thariana revealed by amplified fragment length polymorphism analysis. Genetics 152:1723-1731
16. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321-4325
17. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
18. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5296-5273
19. Okamoto M (1994) Studies on effect of chemical components on stickiness of cooked rice and their selection method for breeding. Bull Chugoku Agric Exp Stn 14:1-68
20. Olufowote JO, Xu Y, Chen X, Park WD, Beachell HM, Dilday RH, Goto M, McCouch SR (1997) Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome 40:370-378
21. Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597-607
22. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
23. Sneath PHA, Sokal RR (1973) Numerical taxonomy. WH Freeman, San Francisco
24. Takeda K (1990) Inheritance of grain size and its implications for rice breeding. In: Proceedings of the Second International Rice Genetics Symposium. IRRI, Manila, pp 181-189
25. Takita T (1985) Inheritance of grain size and the relationship between grain size and other characters in rice. Bull Natl Agric Res Center 3:55-71
26. Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063-1066
27. Tauz D (1989) Hypervariability of simple sequences as a general source of polymorphic DNA markers. Nucleic Acids Res 17:6463-6471
28. Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697-712
29. Vos P, Hogers R, Bleeker M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414
30. Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241:225-235
31. Yang GP, Saghai Maroof MA, Xu CG, Zhang Q, Biyashev RM (1994) Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol Gen Genet 245:187-194
32. Yoshida S, Ikegami M, Kuze J, Sawada K, Hashimoto Z, Ishii T, Nakamura C, Kamijima O (2002) QTL analysis for plant and grain characters of sake-brewing rice using a doubled haploid population. Breed Sci 52:309-317
33. Yu SB, Xu WJ, Vijayakumar CHM, Ali J, Fu BY, Xu JL, Jiang YZ, Marghirang R, Domingo J, Aquino C, Virmani SS, Li ZK (2003) Molecular diversity and multilocus organization of the parental lines used in the international rice molecular breeding program. Theor Appl Genet 108:131-140
34. Zhu J, Gale MD, Quarrie S, Jackson MT, Bryan GJ (1998) AFLP markers for the study of rice biodiversity. Theor Appl Genet 96:602-611