Population structure and conservation genetics of wild rice Oryza rufipogon (Poaceae): A region-wide perspective from microsatellite variation

Molecular Ecology

Volumn 13, Issue 5, 2004, Pages 1009-1024

  Gao, Lizhi ^a,b  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Conservation; Microsatellite; Population structure; Wild rice

Indexed keywords

MICROSATELLITE DNA;

CHINA; CLUSTER ANALYSIS; COMPARATIVE STUDY; ENVIRONMENTAL PROTECTION; GENE FREQUENCY; GENETIC VARIABILITY; GENETICS; INBREEDING; POPULATION GENETICS; REVIEW; RICE; SPECIES DIFFERENCE;

CHINA; CLUSTER ANALYSIS; CONSERVATION OF NATURAL RESOURCES; GENE FREQUENCY; GENETICS, POPULATION; INBREEDING; MICROSATELLITE REPEATS; ORYZA SATIVA; SPECIES SPECIFICITY; VARIATION (GENETICS);

EMBRYOPHYTA; ORYZA; ORYZA RUFIPOGON; POACEAE; TRANSPOSONS; ZIZANIA;

EID: 1942517957     PISSN: 09621083     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2004.02108.x     Document Type: Review

References (81)

1. Akagi H, Yokozeki Y, Inagaki A, Fujimura T (1996) Microsatellite DNA markers for rice chromosomes. Theoretical and Applied Genetics, 93, 1071-1077.
2. Akimoto M, Shimamoto Y, Morishima H (1998) Population genetic structure of wild rice Oryza glumaepatula distributed in the Amazon flood area influenced by its life-history traits. Molecular Ecology, 7, 1371-1382.
3. Aldrich P, Hamrick JL (1998) Reproductive dominance of pasture trees in a fragmented tropical mosaic. Science, 28, 103-105.
4. Barbier P (1989a) Genetic variation and ecotypic differentiation in the wild rice species Oryza rufipogon. I. Population differentiation in life-history traits and isozymic loci. Japanese Journal of Genetics, 64, 259-271.
5. Barbier P (1989b) Genetic variation and ecotypic differentiation in the wild rice species Oryza rufipogon. II. Influence of the mating system and life-history traits on the genetic structure of populations. Japanese Journal of Genetics, 64, 273-285.
6. Buso GSC, Rangel PH, Ferreira ME (1998) Analysis of genetic variability of South American wild rice populations (Oryza glumaepatula) with isozymes and RAPD markers. Molecular Ecology, 7, 107-117.
7. Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. American Journal of Human Genetics, 19, 233-257.
8. Chang TT (1984) Conservation of rice genetic resources: luxury or necessity? Science, 224, 251-256.
9. Chase MW, Hills HH (1991) Silica gel: an ideal material for field preservation of leaf samples for DNA studies. Taxon, 40, 215-220.
10. 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.). Theoretical and Applied Genetics, 95, 553-567.
11. Cho YG, Ishii T, Temnykh S et al. (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theoretical and Applied Genetics, 100, 713-722.
12. Doebley J (1989) Isozymic evidence and the evolution of crop plants. In: Isozymes in Plant Biology (eds Soltis DE, Soltis PS), pp. 165-191. Dioscorides Press, Portland, OR.
13. Edwards K, Johnstone C, Thompson C (1991) A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucleic Acids Research, 19, 1349.
14. El Mousadik A, Petit RJ (1996) Chloroplast DNA phylogeography of the argan tree of Morocco. Molecular Ecology, 5, 547-555.
15. Ellatrand NC, Prentice HC, Hancock JF (1999) Gene flow and introgression from domesticated plants into their wild relatives. Annual Review of Ecological Systems, 30, 539-563.
16. Friar EA, Boose DLLA, Doux T, Roalson EH, Robichaux RH (2001) Population structure in the endangered Mauna Loa silversword, Argyroxiphium kauense (Asteraceae), and its bearing on reintroduction. Molecular Ecology, 10, 1657-1663.
17. Gao LZ (1997) A study on genetic variation of three wild rices (Oryza spp.) in China and their conservation biology. PhD Dissertation, Institute of Botany, Chinese Academy of Sciences, Beijing.
18. Gao LZ (2002) The conservation of rice biodiversity in China: significance, genetic erosion, ethnobotany and prospect. Genetic Resources and Crop Evolution, 50 (1), 17-32.
19. Gao LZ, Ge S, Hong DY (2000a) Allozymic diversity and genetic structure of common wild rice Oryza rufipogon Griff, in China. Theoretical and Applied Genetics, 101, 494-502.
20. Gao LZ, Ge S, Hong DY (2000b) Low levels of genetic diversity within population and high differentiation among populations of a wild rice, Oryza granulata Nees et Arn Ex Watt from China. International Journal of Plant Sciences, 161, 691-697.
21. Gao LZ, Ge S, Hong DY (2000c) A preliminary study on ecological differentiation within common wild rice Oryza rufipogon Griff. Acta Agronomica Sinica, 26, 210-216 [in Chinese with English abstract].
22. Gao LZ, Ge S, Hong DY (2001) High levels of genetic differentiation of Oryza officinalis Wall et Watt from China. Journal of Heredity, 92, 511-516.
23. Gao LZ, Ge S, Hong DY (2002b) Low levels of allozyme diversity and conservation genetics of common wild rice Oryza rufipogon Griff, from Yunnan, China. Euphytica, 124, 273-281.
24. Gao LZ, Ge S, Hong DY, Chen W, Jiang WZ, Wang XK (2000d) Genetic erosion in northern marginal population of common wild rice Oryza rufipogon Griff, and its conservation, revealed by allozyme analysis. Hereditas, 133 (1), 47-53.
25. Gao LZ, Hong DY (1999) Advances in the studies on the genus Oryza in China. Scientia Agricultura Sinica, 32 (6), 40-46 [in Chinese with English abstract].
26. Gao LZ, Schaal BA, Zhang CH, Jia JZ, Dong YS (2002a) Assessment of population genetic structure of common wild rice Oryza rufipogon Griff, detected by microsatellite DNA and allozyme loci. Theoretical and Applied Genetics, 106, 173-180.
27. Gao LZ, Zhang SZ, Zhou Y, Ge S, Hong DY (1996) A survey of the current status of wild rice in China. Chinese Biodiversity, 4, 160-166 [in Chinese with English abstract].
28. Gao LZ, Zhou Y, Ge S et al. (1998) Germplasm resources of common wild rice Oryza rufipogon Griff. and its conservation strategies in Guangxi Province, China. Acta Agricultura Sinica, 31 (1), 32-39 [in Chinese with English abstract].
29. Ge S, Oliveira GCX, Schaal BA, Gao LZ, Hong DY (1999b) RAPD variation within and between natural populations of the wild rice Oryza rufipogon Griff. from China and Brazil. Heredity, 82, 638-644.
30. Ge S, Sang T, Lu BR, Hong DY (1999a) Phylogeny of rice genomes with emphasis on the origins of allotetraploid species. Proceedings of the National Academy of Sciences of the USA, 96, 14400-14405.
31. Goudet J (2001) ESTAT, A Program for Windows (95 and Above) to Estimate and Test Gene Diversities and Fixation Indices Version 2.9.3. http://www.unil.ch/izea/sofrwares/fstat.html.
32. Goudet J, Raymond M, de Meeüs T, Rousset F (1996) Testing differentiation in diploid populations. Genetics, 144, 1933-1940.
33. Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics, 48, 361-372.
34. Hall P, Walker S, Bawa K (1996) Effect of forest fragmentation on genetic diversity and mating system in a tropical tree, Pithecellobium elegans. Conservation Biology, 10, 757-768.
35. Hamrick JL, Godt MJ (1996) Conservation genetics of endangered plant species. In: Conservation Genetics: Case Histories from Nature (eds Avise JC, Hamrick JL), pp. 281-304. Chapman & Hall, New York.
36. Hartl DL, Clark AG (1997) Principles of Population Genetics, 3rd edn. Sinauer Associates, Sunderland, MA.
37. Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theoretical and Applied Genetics, 38, 226-231.
38. Innan H, Terauchi R, Miyashita NT (1997) Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics, 146, 1441-1452.
39. Jackson MT (1994) Preservation of rice strains. Nature (London), 371, 470.
40. King TL, Kalinowski ST, Schill WB, Spidle AP, Lubinski BA (2001) Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variation. Molecular Ecology, 10, 807-821.
41. Knapp EE, Dyer AR (1998) When do genetic considerations require special approaches to ecological restoration? In: Conservation Biology (eds Fiedler PL, Kareiva PM), pp. 345-363. Chapman & Hall, New York.
42. Liang N, Wu WR (1993) Wild rice resources in Guangdong and Hainan provinces. In: Rice Germplasm Resources in China (ed. Ying CS), pp. 285-301. Chinese Agricultural Technology and Science Press, Beijing [in Chinese].
43. Liao ZM (1975) The origin and evolution of cultivated rice in China. Acta Genetica Sinica, 2 (1), 21-29.
44. Liu KJ (2001) POWERSSR: New Genetic Data Analysis Software, Version 12. http://www.stat.ncsu.edu/-panzea/powerssr
45. McCouch SR, Chen X, Panaud O et al. (1997) Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Molecular Biology, 35, 89-99.
46. Mills LS, Smouse PE (1994) Demographic consequences of inbreeding in remnant populations. American Naturalist, 144, 412-431.
47. Morishima H (1985) Habitat, genetic structure and dynamics of perennial and annual populations of the Asian wild rice Oryza perennis. In: Genetic Differentiation and Dispersal in Plants NATO ASI Series, Vol. G5, pp. 179-190. Springer-Verlag, Berlin.
48. Morishima H, Barbier P (1990) Mating system and genetic structure of natural populations in wild rice Oryza rufipogon. Plant Species Biology, 5, 31-39.
49. Moritz C (1994) Defining 'Evolutionarily Significant Units' for conservation. Trends in Ecology and Evolution, 9, 373-375.
50. Nason JD, Hamrick JL (1997) Reproductive and genetic consequences of forest fragmentation: two case studies of Neotropical canopy trees. Journal of Heredity, 88, 264-276.
51. National Exploration Group of Wild Rices (1984) An investigation of genetic resources of wild rices in China. Acta Agricultura Sinica, 6, 3-10.
52. Nei M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the USA, 70, 3321-3323.
53. Nei M, Koehn RK, eds. (1983) Evolution of Genes and Proteins. Sinauer Associates, Sunderland, MA.
54. Nevo E (1998) Genetic diversity in wild cereals: regional and local studies and their bearing on conservation ex situ and in situ. Genetic Resources and Crop Evolution, 45, 355-370.
55. Nevo E (2001) Evolution of genome-phenome diversity under environmental stress. Proceedings of the National Academy of Sciences of the USA, 98, 6233-6240.
56. O'Brien SJ (1994) A role for molecular genetics in biological conservation. Proceedings of the National Academy of Sciences of the USA, 91, 5748-5755.
57. Ohta T, Kimura M (1969) Linkage disequilibrium due to random genetic drift. Genetic Research, 13, 47-55.
58. Oka HI, Chang WT (1961) Hybrid swarms between wild and cultivated rice species, Oryza perennis and O. sativa. Evolution, 15, 418-430.
59. Olsen KM, Schaal BA (2001) Microsatellite variation in cassava (Manihot esculenta, Euphorbiaceae) and its wild relatives: further evidence for a southern Amazonian origin of domestication. American Journal of Botany, 88 (1), 131-142.
60. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences, 12, 357-358.
61. Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSR) in rice (Oryza sativa L.). Molecular and General Genetics, 252, 597-607.
62. Qian W, Ge S, Hong DY (2001) Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers. Theoretical and Applied Genetics, 102, 440-449.
63. Quesada T, Lobo J, Espinoza AM (2002) Isozyme diversity and analysis of the mating system of the wild rice Oryza latifolia Desv. in Costa Rica. Genetics Resources and Crop Evolution, 49, 633-643.
64. Raymond M, Rousset F (1995) GENEPOP: population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248-249.
65. Rice WR (1989) Analyzing tables of statistical tests. Evolution, 43, 223-225.
66. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular and Biological Evolution, 4, 406-425.
67. Schaal BA, Leverich WJ, Rogstad SH (1991) Comparison of methods for assessing genetic variation in plant conservation biology. In: Genetics and Conservation of Rare Plants (eds Falk DA, Holsinger KE), pp. 123-134. Oxford University Press, New York.
68. Slatkin M (1989) Rane alleles as indicators of gene flow. Evolution, 39, 53-65.
69. Song ZP, Lu BR, Zhu YG, Chen JK (2003) Gene flow from cultivated rice to the wild species Oryza rufipogon under experimental field conditions. New Phytologist, 157, 657-665.
70. Temnykh S, Park WD, Ayres N et al. (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theoretical and Applied Genetics, 100, 697-712.
71. Ting Y (1949) Origin of cultivated rice in China. Special Journal of Agriculture and Horticulture (Agricultural College, Zhongshan University), 7, 11-24 [in Chinese].
72. Vaughan DA (1994) The Wild Relatives of Rice: A Genetic Resources Handbook. International Rice Research Institute, Manila, Philippines.
73. Weir BS, Cockerhan CC (1984) Estimating F-statistics for the analysis of population structre. Evolution, 38, 1358-1370.
74. Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Molecular and General Genetics, 241, 225-235.
75. Xiao J, Li J, Grandillo S et al. (1996) A wild species contains genes that may significantly increase the yield of rice. Nature (London), 384, 223-224.
76. Xie ZW (1999) Population genetics and conservation strategies of Oryza rufipogon Griff. in China. PhD Dissertation, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
77. Xie ZW, Lu YQ, Ge S, Hong DY, Li FZ (2001) Clonality in wild rice (Oryza rufipogon, Poaceae) and its implications for conservation management. American Journal of Botany, 88, 1058-1064.
78. Yeh FC, Yang RC, Mao JYeZ, Boyle TJB (1996) POPGENE the Microsoft Windows-Based User-Friendly Software for Population Genetics Analysis of Co-Dominant and Dominant Markers and Quantitative Traits. Department of Renewable Resources, University of Alberta, Edmonton.
79. You XL (1995) The History of Rice Cultivation in China. Chinese Agricultural Press, Beijing.
80. Young A, Boyle T, Brown T (1996) The population genetic consequences of habitat fragmentation for plants. Trends in Ecology and Evolution, 11, 413-418.
81. Yuan LP, Virmani SS, Mao CX (1989) Hybrid Rice - Achievement and Outlook. Progress in Irrigated Rice Research. International Rice Research Institute, Manila, Philippines.