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Acta Agron Sin ›› 2009, Vol. 35 ›› Issue (11): 2122-2126.doi: 10.3724/SP.J.1006.2009.02122

• RESEARCH ACTIVITIES • Previous Articles     Next Articles

Nucleotide Polymorphism in the Adh2 of Oryza rufipogon Griff. from Hainan Island

DONG Yi-Bo1,PEI Xin-Wu2,Yuan Qin-Hua3,PENG Yu-Fa1,*   

  1. 1 State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100094, China; 2 Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing 100081, China; 3 College of Life Science and Agriculture, MOE Key Lab of Tropic Biological Resources, Hainan University, Haikou, 570228, China
  • Received:2009-03-31 Revised:2009-06-25 Online:2009-11-12 Published:2009-08-07
  • Contact: PENG Yu-Fa,E-mail:yfpeng@ippcaas.cn;Tel:010-62815936

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Abstract:

The sequence polymorphism of Adh2 in six populations of Oryza rufipogon (WN, WA, WC, DZ, QH, and LD) from Hainan and two Oryza sativa (Nipponbare, 9311) was analyzed. The result showed that there were nine singleton variable sites, four parsimony informative sites, eight synonymous sites and five replacement sites at coding region. There were 21 singleton variable sites, 29 parsimony informative sites and 161 indels sites at intron region. Adh2 polymorphism (pR, qR) at entire region was 0.011. The polymorphism at intron was higher than that at coding region. At coding region, the polymorphism of synonymous sites was higher than that at replacement sites. Neutrality tests showed that there was more purified selection at coding region than at intron region, although no significant difference was found. Cluster analysis showed O. rufipogon from Hainan could be divided into two groups. One group (QH, LD) was clustered with O. rufipogon from China mainland and O. sativa. The other group was clustered with some O. rufipogon from southeast Asia.

Key words: Oryza rufipogon, Adh2, Sequence polymorphism


[1] Oka H I. Experimental studies on the origin of cultivated rice. Genetics, 1974, 974: 475-486

[2] Xiao J, Grandillo S, Ahn S N, Mccouch S R, Tanksley S D, Li J, Yuan L. Genes from wild rice improve yield. Nature, 1996, 384: 223-224

[3] Gao L Z, Chen W, Jiang W Z, Ge S, Hong D Y, Wang X K. Genetic erosion in the Northern marginal population of the common wild rice Oryza rufipogon Griff. and its conservation, revealed by the change of population genetic structure. Hereditas, 2000, 133: 47-53

[4] Wang M X, Zhang H L, Zhang D L, Qi Y W, Fan Z L, Li D Y, Pan D J, Cao Y S, Qiu Z E, Yu P, Yang Q W, Wang X K, Li Z C. Genetic structure of Oryza rufipogon Griff. in China. Heredity, 2008, 101: 527-535

[5] Menegus F, Cattaruzza L, Mattana M, Beffagna N, Ragg E. Response to anoxia in rice and wheat seedlings: Changes in the pH of intracellular compartments, glucose-6-phosphate level, and metabolic rate. Plant Physiol, 1991, 95: 760-767


[6] Xie Y, Wu R. Rice alcohol dehydrogenase genes: anaerobic induction, organ-specific expression and characterization of cDNA clones. Plant Mol Biol, 1989, 13: 53-68

[7] Gaut B S, Clegg M T. Molecular evolution of alcohol dehydrogenase 1 in members of the grass family. Proc Natl Acad Sci USA, 1991, 88: 2060-2064

[8] Zhu Q, Zheng X, Luo J, Gaut B, Ge S. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol, 2007, 24: 875-888

[9] Xu X, Ke W, Yu X, Wen J, Ge S. A preliminary study on population genetic structure and phylogeography of the wild and cultivated Zizania latifolia (Poaceae) based on Adh1a sequences. Theor Appl Genet, 2008, 116: 835-843

[10] Yoshida K, Miyashita N T. Nucleotide polymorphism in the Adh2 region of the wild rice Oryza rufipogon. Theor Appl Genet, 2005, 111: 1215-1228

[11] Weising K, Kaemmer D, Weigand F, Epplen J T, Kahl G. Oligonucleotide fingerprinting reveals various prove-dependent levels of informativeness in chickpea (Cicer arietinum). Genome, 1991, 35: 436-442

[12] Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123: 585-595

[13] Fu Y X, Li W H. Statistical tests of neutrality of mutations. Genetics, 1993, 133: 693-709

[14] Gao L Z, Hong D Y, Ge S. Allozyme variation and population genetic structure of common wild rice Oryza rufipogon Griff. in China. Theor Appl Genet, 2000, 101: 494-502

[15] Zhou H F, Xie Z W, Ge S. Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China. Theor Appl Genet, 2003, 107: 332-339

[16] Londo J P, Chiang Y C, Hung K H, Chiang T Y, Schaal B A. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivatedrice, Oryza sativa. Proc Natl Acad Sci USA, 2006, 103: 9578-9583


[17] Kovach M J, Sweeney M T, McCouch S R. New insights into the history of rice domestication. Trends Genet, 2007, 23: 578-587

[18] Song Z P, Zhu W Y, Rong J, Xu X, Chen J, Lu B R. Evidences of introgression from cultivated rice to Oryza rufipogon (Poaecae) populations based on SSR fingerprinting: implications for wild rice differentiation and conservation. Evol Ecol, 2006, 20: 501-522

[19] Lu B R, Song Z P, Chen J K. Crop to wild gene flow in rice and its ecological consequences. In: Nijs H C M, Bartsch D, Sweet J, eds. Introgression from Genetically Modified Plants into Wild Relatives. UK: CAB International, 2004. pp 139-150

[20] Ellstrand N C, Prentice H C, Hancock J F. Gene flow and introgression from domesticated plants into their wild relatives. Annu Rev Ecol Syst, 1999, 30: 539-563

[21] Chen L-L(陈玲玲), Peng G-Z(彭贵子), Zhang W-L(张伟丽), Tian D-C(田大成). The significance of mutations in genomic evolution. Hereditas (遗传), 2006, 28(5): 631-638 (in Chinese with English abstract)

[22] Tang P(唐萍), Wang Q(王强), Chen J-Q(陈建群). The patterns and influences of insertions, deletions and nucleotide substitutions in Solanaceae chloroplast genome. Hereditas (遗传), 2008, 30(11): 1506-1512 (in Chinese with English abstract)

[23] Cartwright R A. Problems and solutions for estimating indel rates and length distributions. Mol Biol Evol, 2009, 26: 473-480

[24] Kawakita A, Sota T, Ascher J, Ito M, Tanaka H, Kato M. Evolution and phylogenetic utility of alignment gaps within intron sequences of three nuclear genes in Bumble Bees (Bombus). Mol Biol Evol, 2003, 20: 87-92
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