Molecular constitution of weedy rice (Oryza sativa L.) found in Okayama prefecture, Japan
Weedy rice (Oryza sativa L.) plants found in Okayama, Japan, exhibit various morphophysiological characteristics, and are roughly classified into japonica-type and indica-type. We characterized the weedy strains collected from nine sites with molecular markers in flanking regions of two diagnostic i...
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| Published in | Breeding Science Vol. 59; no. 3; pp. 229 - 236 |
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| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
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Tokyo
Japanese Society of Breeding
2009
Japan Science and Technology Agency |
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| Online Access | Get full text |
| ISSN | 1344-7610 1347-3735 |
| DOI | 10.1270/jsbbs.59.229 |
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| Abstract | Weedy rice (Oryza sativa L.) plants found in Okayama, Japan, exhibit various morphophysiological characteristics, and are roughly classified into japonica-type and indica-type. We characterized the weedy strains collected from nine sites with molecular markers in flanking regions of two diagnostic isozyme loci, Acp1 and Sdh1. Haplotype analysis for closely-linked SSR markers flanking Acp1 revealed that 1) japonica-type weedy strains shared the same haplotypes with local varieties, and 2) indica-type weedy strains carrying an indica-specific isozyme allele possessed two haplotypes. One of the two haplotypes was common to a forage variety, ‘Moretsu’. PCR analysis revealed that the dwarf weedy strains carried the deletion inside OsGA20ox2 as the semi-dwarf allele (sd1). The deletion was also found in ‘Moretsu’. The other haplotype was shared with indica forage variety, ‘Tetep’, which showed the same sequence haplotype for Sdh1 with the indica-type weedy strains. The results obtained from this study suggested that the weedy strains in Okayama have multiple origins and semi-dwarfness possibly derived from ‘Moretsu’ or indica modern varieties. |
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| AbstractList | Weedy rice (Oryza sativa L.) plants found in Okayama, Japan, exhibit various morphophysiological characteristics, and are roughly classified into japonica-type and indica-type. We characterized the weedy strains collected from nine sites with molecular markers in flanking regions of two diagnostic isozyme loci, Acp1 and Sdh1. Haplotype analysis for closely-linked SSR markers flanking Acp1 revealed that 1) japonica-type weedy strains shared the same haplotypes with local varieties, and 2) indica-type weedy strains carrying an indica-specific isozyme allele possessed two haplotypes. One of the two haplotypes was common to a forage variety, ‘Moretsu’. PCR analysis revealed that the dwarf weedy strains carried the deletion inside OsGA20ox2 as the semi-dwarf allele (sd1). The deletion was also found in ‘Moretsu’. The other haplotype was shared with indica forage variety, ‘Tetep’, which showed the same sequence haplotype for Sdh1 with the indica-type weedy strains. The results obtained from this study suggested that the weedy strains in Okayama have multiple origins and semi-dwarfness possibly derived from ‘Moretsu’ or indica modern varieties. |
| Author | Kawasaki, Akiko Imai, Katsunori Ushiki, Jun Ishikawa, Ryuji Ishii, Toshio |
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| Cites_doi | 10.1270/jsbbs1951.42.235 10.7312/nei-92038 10.1270/jsbbs.50.1 10.1270/jsbbr.07.179 10.1126/science.1126410 10.1007/s10722-004-6132-y 10.1007/s001220050417 10.1007/s00122-002-0898-0 10.1007/s00122-001-0807-y 10.1007/s10722-005-2257-x 10.1073/pnas.132266399 10.1270/jsbbs1951.41.605 |
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| References | Ishikawa, R., Y.-I. Sato, T. Tang and I. Nakamura (2002a) Different maternal origins of Japanese and upland rice populations. Theor. Appl. Genet. 104: 976–980. Ishikawa, R., K. Maeda, T. Harada, M. Niizeki and K. Saito (1991) Classification of Japanese rice varieties into indica and japonica types by using isozyme genotypes. Jpn. J. Breed. 41: 605–622. Sadakane (1952) Study on cultivation techniques of rice. Agr. Study 40: 179–190. Ishikawa, R., I. Nakamura, T. Nishihara, M. Kikuchi, M. Senda, S. Akada, T. Harada and M. Niizeki (2002b) Origin of cytoplasm substituted rice cultivars found in Japan. Theor. Appl. Genet. 105: 608–613. Ishii, T. and M. Akazawa (2003) Direct seeding in dry field and weedy rice in Okayama prefecture. Proceeding of the 18th symposium in Japanese Weedy Association, pp. 7–16. Konishi, S., T. Izawa, S.Y. Lin, K. Ebana, Y. Fukuta, T. Sasaki and M. Yano (2006) An SNP caused loss of seed shattering during rice domestication. Science 312: 1392–1396. Uehara, Y., Y. Koga, H. Uchiyamada, S. Samoto, S. Ishizaka, U.Y. Fujita, K. Okuno, M. Nakagahra, H. Horiuchi, K. Miura, K. Maruyama, T. Yamada, T. Yagi and K. Mori (1999) Extension and parental utilities of the rice variety “Kinuhikari” with superior eating quality and tolerance to lodging. The Hokuriku Crop Science 34: 1–3. Nei, M. (1987) Molecular evolutionary genetics. Columbia University Press, New York, p. 512. Tang, L.H. and H. Morishima (1997) Genetic characterization of weedy rices and the inference on their origins. Breed. Sci. 47: 153–160. Miyajima, Y. and N. Takahashi (1974) ‘Toukon’ as red rice in Nagano Prefecture. J. Agric. Sci. 29: 453–455. Ushiki, J., T. Ishii and R. Ishikawa (2005) Morpho-physiological characters and geographical distribution of japonica and indica weedy rice (Oryza sativa) in Okayama prefecture, Japan. Breed. Res. 7: 179–187. Ishikawa, R., N. Toki, K. Imai, Y.-I. Sato, H. Yamagishi, Y. Shimamoto, K. Ueno, H. Morishima and T. Sato (2005) Origin of weedy rice grown in Bhutan and the force of genetic diversity. Genet. Resour. Crop. Evol. 52: 395–403. Ishikawa, R., T. Harada, M. Niizeki and K. Saito (1992) Reconstruction of linkage map with isozyme, morphological and physiological markers in rice Chromosome 12. Jpn. J. Breed. 42: 235–244. Sakai, N. and M. Saito (2003) Observation of weedy rice in Nagano prefecture and a method to protect weedy rice. In: Proceedings of the 18th Symposium, Weed Science Society of Japan, pp. 1–6. Spielmeyer, W., M.H. Ellis and P.M. Chandler (2002) Semidwarf (sd-1), “green evolution” rice, contains a defective gibberellin 20-oxidase. Proc. Natl. Acad. Sci. USA 99: 9043–9048. Suh, H.S., Y.-I. Sato and H. Morishima (1997) Genetic characterization of weedy rice (Oryza sativa L.) based on morpho-physiology, isozymes and RAPD markers. Theor. Appl. Genet. 94: 316–321. Tabuchi, H., N. Hashimoto, A. Takeuchi, T. Terao and Y. Fukuta (2000) Genetic analysis of semidwarfism of the japonica rice cultivar Kinuhikari. Breed. Sci. 50: 1–7. Ishii, T. (2001) Weedy rice observed after direct seeding in flooded paddy fields in Okayama prefecture. J. Agri. Sci. 40: 179–190. Ishikawa, R., S. Yamanaka, Y. Fukuta, S. Chitrakon, C. Bounphanousay, K. Kanyavong, L.-H. Tang, I. Nakamura, T. Sato and Y.-I. Sato (2006) Genetic erosion from modern varieties into traditional upland rice cultivars (Oryza sativa L.) in northern Thailand. Genet. Resour. Crop Evol. 53: 245–252. 11 12 13 14 15 17 18 19 ISHIKAWA R (4) 1992; 42 1 2 3 5 6 7 8 9 TABUCHI H (16) 2000; 50 10 |
| References_xml | – reference: Tang, L.H. and H. Morishima (1997) Genetic characterization of weedy rices and the inference on their origins. Breed. Sci. 47: 153–160. – reference: Ushiki, J., T. Ishii and R. Ishikawa (2005) Morpho-physiological characters and geographical distribution of japonica and indica weedy rice (Oryza sativa) in Okayama prefecture, Japan. Breed. Res. 7: 179–187. – reference: Suh, H.S., Y.-I. Sato and H. Morishima (1997) Genetic characterization of weedy rice (Oryza sativa L.) based on morpho-physiology, isozymes and RAPD markers. Theor. Appl. Genet. 94: 316–321. – reference: Sadakane (1952) Study on cultivation techniques of rice. Agr. Study 40: 179–190. – reference: Ishikawa, R., S. Yamanaka, Y. Fukuta, S. Chitrakon, C. Bounphanousay, K. Kanyavong, L.-H. Tang, I. Nakamura, T. Sato and Y.-I. Sato (2006) Genetic erosion from modern varieties into traditional upland rice cultivars (Oryza sativa L.) in northern Thailand. Genet. Resour. Crop Evol. 53: 245–252. – reference: Ishikawa, R., K. Maeda, T. Harada, M. Niizeki and K. Saito (1991) Classification of Japanese rice varieties into indica and japonica types by using isozyme genotypes. Jpn. J. Breed. 41: 605–622. – reference: Nei, M. (1987) Molecular evolutionary genetics. Columbia University Press, New York, p. 512. – reference: Miyajima, Y. and N. Takahashi (1974) ‘Toukon’ as red rice in Nagano Prefecture. J. Agric. Sci. 29: 453–455. – reference: Spielmeyer, W., M.H. Ellis and P.M. Chandler (2002) Semidwarf (sd-1), “green evolution” rice, contains a defective gibberellin 20-oxidase. Proc. Natl. Acad. Sci. USA 99: 9043–9048. – reference: Ishikawa, R., T. Harada, M. Niizeki and K. Saito (1992) Reconstruction of linkage map with isozyme, morphological and physiological markers in rice Chromosome 12. Jpn. J. Breed. 42: 235–244. – reference: Konishi, S., T. Izawa, S.Y. Lin, K. Ebana, Y. Fukuta, T. Sasaki and M. Yano (2006) An SNP caused loss of seed shattering during rice domestication. Science 312: 1392–1396. – reference: Ishii, T. and M. Akazawa (2003) Direct seeding in dry field and weedy rice in Okayama prefecture. Proceeding of the 18th symposium in Japanese Weedy Association, pp. 7–16. – reference: Uehara, Y., Y. Koga, H. Uchiyamada, S. Samoto, S. Ishizaka, U.Y. Fujita, K. Okuno, M. Nakagahra, H. Horiuchi, K. Miura, K. Maruyama, T. Yamada, T. Yagi and K. Mori (1999) Extension and parental utilities of the rice variety “Kinuhikari” with superior eating quality and tolerance to lodging. The Hokuriku Crop Science 34: 1–3. – reference: Ishii, T. (2001) Weedy rice observed after direct seeding in flooded paddy fields in Okayama prefecture. J. Agri. Sci. 40: 179–190. – reference: Ishikawa, R., N. Toki, K. Imai, Y.-I. Sato, H. Yamagishi, Y. Shimamoto, K. Ueno, H. Morishima and T. Sato (2005) Origin of weedy rice grown in Bhutan and the force of genetic diversity. Genet. Resour. Crop. Evol. 52: 395–403. – reference: Tabuchi, H., N. Hashimoto, A. Takeuchi, T. Terao and Y. Fukuta (2000) Genetic analysis of semidwarfism of the japonica rice cultivar Kinuhikari. Breed. Sci. 50: 1–7. – reference: Sakai, N. and M. Saito (2003) Observation of weedy rice in Nagano prefecture and a method to protect weedy rice. In: Proceedings of the 18th Symposium, Weed Science Society of Japan, pp. 1–6. – reference: Ishikawa, R., Y.-I. Sato, T. Tang and I. Nakamura (2002a) Different maternal origins of Japanese and upland rice populations. Theor. Appl. Genet. 104: 976–980. – reference: Ishikawa, R., I. Nakamura, T. Nishihara, M. Kikuchi, M. Senda, S. Akada, T. Harada and M. Niizeki (2002b) Origin of cytoplasm substituted rice cultivars found in Japan. Theor. Appl. Genet. 105: 608–613. – ident: 2 – volume: 42 start-page: 235 issn: 0536-3683 issue: 2 year: 1992 ident: 4 doi: 10.1270/jsbbs1951.42.235 – ident: 17 – ident: 11 doi: 10.7312/nei-92038 – ident: 18 – volume: 50 start-page: 1 issn: 1344-7610 issue: 1 year: 2000 ident: 16 doi: 10.1270/jsbbs.50.1 – ident: 1 – ident: 19 doi: 10.1270/jsbbr.07.179 – ident: 12 – ident: 9 doi: 10.1126/science.1126410 – ident: 8 doi: 10.1007/s10722-004-6132-y – ident: 10 – ident: 13 – ident: 15 doi: 10.1007/s001220050417 – ident: 6 doi: 10.1007/s00122-002-0898-0 – ident: 5 doi: 10.1007/s00122-001-0807-y – ident: 7 doi: 10.1007/s10722-005-2257-x – ident: 14 doi: 10.1073/pnas.132266399 – ident: 3 doi: 10.1270/jsbbs1951.41.605 |
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| Title | Molecular constitution of weedy rice (Oryza sativa L.) found in Okayama prefecture, Japan |
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