Research Paper

Comparative Analysis on Genomes from Oryza alta and Oryza latifolia by C0t-1 DNA

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  • Engineering Research Centre for the Protection and Utilization of Bioresource in Ethnic Area of Southern China, South-Central University for Nationalities, Wuhan 430074, China

Received date: 2009-12-04

  Revised date: 1900-01-01

  Online published: 2010-09-28

Supported by

the Science Foundation of South-Central University for Nationalities, China (Grant No. YZY10007).

Abstract

In order to reveal the origin and evolutionary relationship between two CCDD genome species, Oryza alta and Oryza latifolia, fluorescence in situ hybridization (FISH) was adopted to analyze the genomes of the two species with C0t-1 DNA from O. alta as a probe. Karyotype was also comparatively analyzed between O. alta and O. latifolia based on their similar band patterns of the hybridization signals. There were a high homology and close relationship between O. alta and O. latifolia, however, the distinction between the hybridization signals was also clear. C0t-1 DNA was proved to be species- and genome type-specific. It is suggested that C0t-1 DNA-FISH could be more efficient to analyze the genomic relationship between different species. According to the comparative analysis of highly and moderately repetitive DNA sequences between the two allotetraploidy species, O. alta and O. latifolia, the possible origin and evolutionary mechanism of allotetraploidy of Oryza were discussed.

Cite this article

WANG De-bin, WANG Yang, WU Qi, ZHAO Hou-ming, LI Gang, QIN Rui, WANG Chun-tai, LIU Hong . Comparative Analysis on Genomes from Oryza alta and Oryza latifolia by C0t-1 DNA[J]. Rice Science, 2010 , 17(3) : 185 -191 . DOI: 10.1016/S1672-6308(09)60016-0

References

Aggarwal R K, Brar D S, Khush G S. 1997. Two new genomes in the Oryza complex identified on the basic of molecular divergence analysis using total genomic DNA hybridization. Mol Gen Genet, 254: 1–12.
Aggarwal R K, Brar D S, Nandi S, Huang N, Khush G S. 1999. Phylogenetic relationships among Oryza species revealed by AFLP markers. Theor Appl Genet, 98: 1320–1328.
Bao Y, Ge S. 2003. Identification of Oryza species with the CD genome based on RFLP analysis of nuclear ribosomal ITS sequences. Acta Bot Sin, 45(7): 762–765.
Bao Y, Ge S. 2004. Origin and phylogeny of Oryza species with the CD genome based on multiple-gene sequence data. Plant Syst, 249: 55–66.
Bennetzen J L, Jianxin M A, Devos K M. 2005. Mechanisms of recent genome size variation in flowering plants. Ann Bot, 95: 127–132.
Cheng Z K, Dong F G, Langdon T, Ouyang S, Buell R, Gu M, Blattner F R, Jiang J. 2002. Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell, 14: 1691–1704.
Dong Z W, Liu Z S, Wang D B, Lan W Z, Qin R. 2007. Comparative analysis of O. punctata and O. brachyantha genome with Cot-1 DNA and genomic DNA. J Plant Genet Res, 8(3): 343–346.
Flavell R B. 1986. Repetitive DNA and chromosome evolution in plants. Philos Trans R Soc Lond B: Biol Sci, 312: 227–242.
Fukui K, Shishido R, Kinoshita T. 1997. Identification of the rice D-genome chromosomes by genomic in situ hybridization. Theor Appl Genet, 95: 1239–1245.
Ge S, Sang T, Lu B R, Hong D Y. 1999. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc Natl Acad Sci USA, 96: 14400–14405.
Gopalakrishnan R, Sampath S. 1976. Taxonomic status and the origin of American tetraploid species of the series Latifoliae Tateoka in the genus Oryza. Ind J Agric Sci, 37: 465–475.
Han F, Fedak G, Guo W, Liu B. 2005. Rapid and repeatable elimination of a parental genome-specific DNA repeat (pGc1R-1a) in newly synthesized wheat allopolyploids. Genetics, 170: 1239–1245.
Jena K K, Kochert G. 1991. Restriction fragment length polymorphism analysis of CCDD-genome species of the genus Oryza L. Plant Mol Biol, 16: 831–839.
Lan W Z, He G C, Wu S J, Qin R. 2006a. Comparative analysis of Oryza sativa, O. officinalis and O. meyeriana genomes with Cot-1 DNA and genomic DNA. Sci Agric Sin, 39(6): 1083–1090. (in Chinese with English abstract)
Lan W Z, Qin R, Li G, He G C. 2006b. Comparative analysis of A, B, C and D genomes in the genus Oryza with C0t-1 DNA of C genome. Chin Sci Bull, 5(14): 1710–1720. (in Chinese)
Li C B, Zhang D M, Ge S, Lu B R, Hong D Y. 2001. Differentiation and inter-genomic relationships among C, E and D genomes in the Oryza officinalis complex (Poaceae) as revealed by multicolor genomic in situ hybridization. Theor Appl Genet, 103: 197–203.
Liu L, Lafitte R, Guan D. 2004. Wild Oryza species as potential sources of drought-adaptive traits. Euphytica, 138: 149–161.
Lu B R. 1999. Taxonomy of the genus Oryza (Poaceae): A historical perspective and current status. Intl Rice Res Notes, 24: 4–8.
Ma X F, Gustafson J P. 2006. Timing and rate of genome variation in triticale following allopolyploidization. Genome, 49: 950– 958.
Matyasek R, Gazdova B, Fajkus J, Bezde M. 1997. NTRS, a new family of highly repetitive DNAs specific for the T1 chromosome of tobacco. Chromosoma, 106: 369–379.
Nobuko O, Kijima K, Akiyama Y, de Jong J H, Fukui K. 2000. Quantification of total genomic DNA and selected repetitive sequences reveals concurrent changes in different DNA families in indica and japonica rice. Mol Gen Genet, 263: 388–394.
Ren N, Song Y C, Bi X Z, Ding Y, Liu L H. 1997. The physical location of genes cdc2 and prh1 in maize (Zea mays L.). Hereditas, 126(3): 211–217.
Ren F G, Lu B R, Li S Q, Huang J Y, Zhu Y G. 2003. A comparative study of genetic relationships among the AA- genome Oryza species using RAPD and SSR markers. Theor Appl Genet, 108: 113–120.
Sakurako U, Hiroshi I, Nobuko O, Ohtsubo H, Ohtsubo E, Fukui K. 1997. Repetitive sequences: Cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Mol Biol, 35: 791–799.
Schwarzacher T, Leitch A R, Bennett M D, Harrison J S H. 1989. In situ localization of parental genomes in a wide hybrid. Ann Bot, 64: 315–324.
Second G, Rouhan G. 2008. Human-mediated emergence as a weed and invasive radiation in the wild of the CD genome allotetraploid rice species (Oryza, Poaceae) in the Neotropics. PLoS ONE, 3(7): e2613.
Toshie M, Ken L N, Hiroko M, Nori K. 2007. Genome size of twenty wild species of Oryza determined by flow cytometric and chromosome analyses. Breeding Sci, 57: 73–78.
Vaughan D A. 1989. The genus Oryza L.: Current status of taxonomy. In: IRRI Research Paper Series No. 138. Manila: IRRI: 1–21.
Vaughan D A, Morishima H, Kadowaki K. 2003. Diversity in the Oryza genus. Curr Opin Plant Biol, 6: 139–146.
Yan H M, Song Y C, Li L J, Bi X Z, Fu B Y. 1998. Physical location of the rice Pi-5(t), Glh and RTSV genes by ISH of BAC clones. Wuhan Univ J: Nat Sci, 3(2): 226–230. (in Chinese with English abstract)
Yin P, Hartemink A J. 2005. Theoretical and practical advances in genome halving. Bioinformatics, 21: 869–879.
Yogeeswaran K, Frary A, York T L, Amenta A, Lesser A H, Nasrallah J B, Thanksly S D, Nasrallah M E. 2005. Comparative genome analyses of Arabidopsis spp.: Inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. Genome Res, 15: 505–515.
Zwick M S, Hanson R E, Faridi M N, Stelly D M, Wing R A, Price H J, McKnight T D. 1997. A rapid procedure for the isolation of COt-1 DNA from plants. Genome, 40: 138–142.
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