Diversity in the Oryza genus

Current Opinion in Plant Biology

Volumn 6, Issue 2, 2003, Pages 139-146

  Vaughan, Duncan A ^a   Morishima, H ^b   Kadowaki, K ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b TOKYO UNIVERSITY OF AGRICULTURE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EMBRYOPHYTA; ORYZA;

EID: 0344511684     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5266(03)00009-8     Document Type: Review

References (73)

1. Kellogg EA: Evolutionary history of grasses. Plant Physiol 2001, 125:1198-1205.
2. Launert E: A survey of the genus Leersia in Africa. Senckenb Biol 1965, 46:129-153.
3. Tateoka T: Notes of some grasses. XVI. Embryo structure of the genus Oryza in relation to their systematics. Am J Bot 1964, 51:539-543.
4. Vaughan DA, Morishima H: Biosystematics of the genus Oryza. In Rice: Origin, History, Technology and Production. Edited by Wayne Smith C, Dilday RH. John Wiley and Sons, New York. 2003:27-65. Although this chapter was completed at the end of 1999, this is the most recent review of Oryza biosystematics and provides a comprehensive overview of information on all of the species in the genus as well as a discussion on weedy rice.
5. Tateoka T: Taxonomic studies of Oryza III. Key to the species and their enumeration. Bot Mag Tokyo 1963, 76:165-173.
6. Morishima H: Reports of the study-tours for investigation of wild and cultivated rice species. Parts I and II. 2002. This report provides the complete record of the reports from study trips undertaken up to 1998 by scientists from the Japanese National Institute of Genetics and their colleagues. This report is available from H Morishima.
7. Chang TT: Crop history and genetic conservation: rice a case study. Iowa State Uni J Res 1985, 59:425-455.
8. International Rice Research Institute (IRRI): Rice germplasm. Collecting, preservation, use. Los Banos, Philippines: IRRI; 1991.
9. Cai HW, Morishima H: QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet 2002, 104:1217-1228. This paper demonstrates the clustering of QTL that are associated with the domestication of rice and differentiation between the indica and japonica subspecies. The authors also show, however, that wild rice that has the AA genome does not have the same pattern of QTL clustering that is associated with ecotypic differentiation of cultivated genotypes.
10. 2 population of a cross between Oryza saliva and O. rufipogon. Theor Appl Genet 1999, 98:243-251.
11. de Wit JMJ: Species concepts and systematics of domesticated cereals. Kulturpflanze 1981, 29:177-198.
12. Oka HI: Origin of cultivated rice. Developments in Crop Science 14. Tokyo: Japan Scientific Societies Press; 1988.
13. Baki BB, Chin DV, Mortimer M (Eds): Wild and Weedy Rice in Rice Ecosystems in Asia - a Review. Limited Proceedings No. 2. Los Banos, Philippines: International Rice Research Institute. 2000.
14. Watanabe H, Vaughan DA, Tomooka N: Weedy rice complexes: case studies from Malaysia, Vietnam and Suriname. In Wild and Weedy Rice in Rice Ecosystems in Asia - a Review. Edited by Baki BB, Chin DV, Mortimer M. Limited proceedings No. 2. Los Banos, Philippines: International Rice Research Institute. 2000:25-34.
15. Bres-Patry C, Lorieux M, Clément G, Bangratz M, Ghesquière A: Heredity and genetic mapping of domestication-related traits in a temperate japonica weedy rice. Theor Appl Genet 2001, 102:118-126. The authors of this paper investigate the 'weed syndrome' and show that traits that are associated with weediness are located in a few chromosomal regions. They studied cultivated and weedy japonica rice from France, where wild Oryza species do not grow naturally, and found that the main weedy traits in the French germplasm had the same genes/QTL as the progeny of crosses between cultivated and wild rice.
16. Aggarawal RK, Brar DS, Khush GS: Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization. Mol Gen Genet 1997, 249:65-73.
17. Wu T, Wu R: A novel repetitive DNA sequence in the genus Oryza. Theor Appl Genet 1992, 84:136-144.
18. Yan HH, Min SK, Zhu LH: Visualization of Oryza eichingeri chromosomes in intergenomic hybrid plants from O. sativa x O. eichingeri via fluorescent in situ hybridization. Genome 1999, 42:48-51.
19. Dally AM, Second G: Chloroplast DNA diversity in wild and cultivated species in rice (Genus Oryza section Oryza). Cladistic-mutation and genetic distances analysis. Theor Appl Genet 1990, 80:209-222.
20. Kanno A, Hirai A: Comparative studies of the structure of chloroplast DNA from four species of Oryza: cloning and physical maps. Theor Appl Genet 1992, 83:791-798.
21. Li CB, Zhang DM, Ge S, Lu BR, Hong DY: Differentiation and intergenomic relationships among C, E and D genomes in the Oryza officinalis complex (Poaceae) as revealed by multicolor genomic in situ hybridization. Theor Appl Genet 2001, 103:197-203. The work described in this paper helps to clarify the distinctiveness of the DD genome, which has been questioned repeatedly.
22. Vaughan DA: Wild relatives of rice: genetic resources handbook. Los Banos, Philippines: International Rice Research Institute; 1994.
23. Shcherban AB, Vaughan DA, Tomooka N, Kaga A: Diversity in the integrase coding domain of a gypsy-like retrotransposon among wild relatives in the Oryza officinalis complex. Genetica 2001, 110:43-53. This paper describes the analysis of the sequence diversity of a new retrotransposon element, using a wider diversity of germplasm from the Oryza officinalis complex than has been studied previously. O. eichingeri is highlighted as a particularly diverse species, which is probably central to the evolution of the O. officinalis complex.
24. Ge S, Sang T, Lu BR, Hong DY: Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc Natl Acad Sci USA 1999, 96:14400-14405.
25. Jena KK, Kochert G: Restriction fragment length polymorphism analysis of CCDD genome species of the genus Oryza L.. Plant Mol Biol 1991, 16:831-839.
26. Nayar NM: Origin and cytogenetics of rice. Adv Genet 1973, 17:153-292.
27. Cordesse F, Grellet F, Reddy AS, Delseny M: Genome specificity of rDNA spacer fragments from Oryza saliva L.. Theor Appl Genet 1992, 83:864-870.
28. Zhao X, Wu T, Xie Y, Wu R: Genome-specific repetitive sequences in the genus Oryza. Theor Appl Genet 1989, 78:201-209.
29. Morishima H, Sano Y, Oka HI: Evolutionary studies in cultivated rice and its wild relatives. Oxford Surveys in Evolutionary Biology 1992, 8:135-184.
30. Lu BR, Zheng KL, Qian HR, Zhuang JY: Genetic differentiation of wild relatives of rice as assessed by RFLP analysis. Theor Appl Genet 2002, 106:101-106.
31. Ge S, Oliveira GCX, Schaal BA, Gao LZ, Hong DY: RAPD variation within and between natural populations of the wild rice Oryza rufipogon from China and Brazil. Heredity 1999, 82:638-644.
32. Sun CQ, Wang XK, Li ZC, Yoshimura A, Iwata N: Comparison of the genetic diversity of common wild rice (Oryza rufipogon Griff.) and cultivated rice (O. saliva L.) using RFLP markers. Theor Appl Genet 2001, 102:157-162. The authors measure parameters of genetic diversity for a large number of wild and cultivated rice accessions. As a group, Chinese wild rice (O. rufipogon, perennial AA genome) is shown to have wider genetic diversity than wild rice from South and Southeast Asia. Why this is the case remains to be determined.
33. Gao LZ, Ge S, Hong DY: Allozyme diversity and genetic structure of common wild rice Oryza rufipogon Griff. in China. Theor Appl Genet 2000, 101:494-502.
34. Gao LZ, Ge S, Hong DY: Low levels of genetic diversity within populations and high differentiation among populations of a wild rice, Oryza granulata Nees et Arn. ex Watt. from China. Int J Plant Sci 2000, 161:691-697.
35. Gao LZ, Ge S, Hong DY: High levels of genetic differentiation of Oryza officinalis Wall ex. Watt from China. J Hered 2001, 92:511-516. This is the first paper to describe population genetic variation in a CC genome Oryza species. The work revealed a high level of genetic differentiation between populations from different regions of China.
36. Qian W, Ge S, Hong DY: Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers. Theor Appl Genet 2001, 102:440-449.
37. Xie ZW, Lu YQ, Ge S, Hong DY, Li FZ: Clonality in wild rice (Oryza rufipogon, Poaceae) and its implications for conservation management. Am J Bot 2001, 88:1058-1064. The authors of this paper applied RAPD analysis to determine the extent of clones in populations of O. rufipogon in China. Variation appears to be largely a function of local environmental factors, particularly disturbance and soil moisture. The authors recommend sampling at intervals of more than 12 meters to prevent collection of the same genotype.
38. McIntyre CL, Winberg BC: A rapid means of identifying wild rice species DNA using dot blots and genome-specific rDNA probes. Genome 1998, 41:391-395.
39. Ge S, Sang T, Lu BR, Hong DY: Rapid and reliable identification of rice genomes by RFLP analysis of PCR-amplified Adh genes. Genome 2001, 44:1136-1142.
40. Martin C, Juliano A, Newbury HJ, Lu BR, Jackson MT, Ford-Lloyd BV: The use of RAPD markers to facilitate the identification of Oryza species within germplasm collections. Genet Res Crop Evol 1997, 44:175-183.
41. Morishima H: Conservation and genetic characterisation of plant genetic resources. In Plant Genetic Resources: Characterisation and Evaluation. Tsukuba, Japan: MAFF; 1998:31-42.
42. Ishii T, McCouch SR: Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight other Gramineae species. Theor Appl Genet 2000, 100:1257-1266.
43. Kanazawa A, Akimoto M, Morishima H, Shimamoto Y: The distribution of Stowaway transposable elements in AA genome species of wild rice. Theor Appl Genet 2000, 101:327-335.
44. Zhang Q, Kochert G: Independent amplification of two classes of Tourists in some Oryza species. Genetica 1998, 101:145-152.
45. Aggarwal RK, Brar DS, Nandi S, Huang N, Khush GS: Phylogenetic relationships among Oryza species revealed by AFLP markers. Theor Appl Genet 1999, 98:1320-1328.
46. Joshi SP, Gupta VS, Aggarwal RK, Ranjekar PK, Brar DS: Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor Appl Genet 2000, 100:1311-1320.
47. Iwamoto M, Nagashima H, Nagamine T, Higo H, Higo K: A Tourist element in the 5′-flanking region of the catalase gene CatA reveals evolutionary relationships among Oryza species with various genome types. Mol Gen Genet 1999, 262:493-500.
48. Heslop-Harrison JS: Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell 2000, 12:617-635.
49. Brar DS, Khush GS: Alien introgression in rice. Plant Mol Biol 1997, 35:35-47.
50. Xiao J, Li J, Grandillo S, Ahn SN, Yuan L, Tanksley SD, McCouch SR: Identification of trait-improving quantitative trait loci alleles from wild rice relative, Oryza rufipogon. Genet 1998, 150:899-909.
51. Brondani C, Pereira R, Brondani V, Rangel PHN, Ferreira ME: Development and mapping of Oryza glumaepatula-derived microsatellite markers in the interspecific cross Oryza glumaepatula x O. sativa. Hereditas 2001, 134:59-71.
52. Juliano AB, Naredo MEB, Jackson MT: Taxonomic status of Oryza glumaepatula Steud. I. Comparative morphological studies of New World diploids and Asian AA genome species. Genet Res Crop Evol 1998, 45:197-203.
53. Naredo EB, Juliano AB, Lu BR, Jackson MT: Taxonomic status of Oryza glumaepatula Steud. II. Hybridization between New World diploids and AA genome species from Asia and Australia. Genet Res Crop Evol 1998, 45:205-214.
54. Morishima H: Phenetic similarity and phylogenetic relationships among strains of Oryza perennis, estimated by methods of numerical taxonomy. Evolution 1969, 23:429-443.
55. International Rice Research Institute (IRRI): Safeguarding and Preservation of the Biodiversity of Rice Genepool [CD Rom]. Los Banos, Philippines: IRRI; 2000.
56. Akimoto M, Shimamoto Y, Morishima H: Population genetic structure of rice O. glumaepatula distributed in the Amazon flood area influenced by its life-history traits. Mol Ecol 1998, 7:1371-1381.
57. Buso GSC, Rangel PHN, Ferreira ME: Analysis of genetic variability of South American wild rice populations (Oryza glumaepatula) using isozymes and RAPD markers. Mol Ecol 1998, 7:107-117.
58. Sobrizal, Ikeda K, Sanchez PL, Doi K, Angeles ER, Khush GS, Yoshimura A: Development of Oryza glumaepatula introgression lines in rice, O. sativa L. Rice Genet Newsl 1999, 16:107-108.
59. Sobrizal, Matsuzaki Y, Sanchez PL, Ikeda K, Yoshimura A: Identification of a gene for male abortion in backcross progeny of Oryza sativa and Oryza glumaepatula. Rice Genet Newsl 2000, 17:59-61.
60. Ikeda K, Sobrizal, Sanchez PL, Yasui H, Yoshimura A: Hybrid weakness restoration gene (Rhw) for Oryza glumaepatula cytoplasm. Rice Genet Newsl 1999, 16:62-64.
61. 1 population.
62. Akimoto M: Biolsystematics in the AA genome wild taxa of genus Oryza (O. sativa complex): a comparative study of morpho-physiological traits, isozymes and RFLPs of nuclear and organelle. 1999 Ph.D. Thesis, Hokkaido University.
63. Doi K, Nonomura MN, Yoshimura A, Iwata N, Vaughan DA: RFLP relationships of A-genome species in the genus Oryza. J Fac Agric Kyushu Univ 2000, 45:83-98.
64. Shcherban AB, Vaughan DA, Tomooka N: Isolation of a new retrotransposon-like DNA sequence and its use in analysis of diversity within the Oryza officinalis complex. Genetica 2000, 108:145-154.
65. Yan HH, Xiong ZM, Min SK, Hu Y, Zhang ZT, Tian SL, Tang SX: The transfer of brown plant hopper resistance from O. eichingeri to O. sativa. Chin J Genet 1997, 24:277-284.
66. th Stadler Genetics Symposium. Edited by Gustafson JP. New York: Plenum Press; 1990:77-93.
67. Yan HH, Liu GQ, Cheng ZK, Min SK, Zhu LH: Characterization of euploid backcross progenies derived from interspecific hybrids between Oryza sativa and O. eichingeri by RFLP analysis and genomic in situ hybridization. Genome 2001, 44:86-95. A detailed analysis of a successful intergenomic (AA x CC) cross. The authors provide information about what occurs in such wide crosses at the chromosome level. In addition, they present an RFLP map that reveals the location of six O. eichingeri (CC genome) introgression segments.
68. Jena KK, Khush GS, Kochert G: RFLP analysis of rice (Oryza sativa L.) introgression lines. Theor Appl Genet 1992, 84:608-616.
69. Couzin J: NSF's ark draws alligators, algae, and wasps. Science 2002, 297:1638-1639.
70. Jena KK, Khush GS, Kochert G: Comparative RFLP mapping of a wild rice, Oryza officinalis, and cultivated rice, O. sativa. Genome 1994, 37:382-389.
71. Uozu S, Ikehashi H, Ohmido N, Ohtsubo H, Ohtsubo E, Fukui K: Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Mol Biol 1997, 37:791-799.
72. Martinez CP, Arumuganathan K, Kikuchi H, Earle ED: Nuclear DNA content of ten rice species as determined by flow cytometry. Jpn J Genet 1994, 69:513-523.
73. Tateoka T: Taxonomy and chromosome numbers of African representatives of the Oryza officinalis complex. Bot Mag Tokyo 1965, 78:198-201.