Molecular Evolution of the TAC1 Gene from Rice (Oryza sativa L.)

a.
State Key Laboratory of Plant Physiology and Biochemistry, National Centre for Evaluation of Agricultural Wild Plants (Rice), Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
b.
Rice Research Institute, Fujian Academy of Agricultural Science, Fuzhou 350018, China

More Information

Corresponding author: E-mail address: suncq@cau.edu.cn (Chuanqing Sun)

摘要

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Abstract: Tiller angle is a key feature of the architecture of cultivated rice (Oryza sativa), since it determines planting density and influences rice yield. Our previous work identified Tiller Angle Control 1 (TAC1) as a major quantitative trait locus that controls rice tiller angle. To further clarify the evolutionary characterization of the TAC1 gene, we compared a TAC1-containing 3164-bp genomic region among 113 cultivated varieties and 48 accessions of wild rice, including 43 accessions of O. rufipogon and five accessions of O. nivara. Only one single nucleotide polymorphism (SNP), a synonymous substitution, was detected in TAC1 coding regions of the cultivated rice varieties, whereas one synonymous and one nonsynonymous SNP were detected among the TAC1 coding regions of wild rice accessions. These data indicate that little natural mutation and modification in the TAC1 coding region occurred within the cultivated rice and its progenitor during evolution. Nucleotide diversities in the TAC1 gene regions of O. sativa and O. rufipogon of 0.00116 and 0.00112, respectively, further indicate that TAC1 has been highly conserved during the course of rice domestication. A functional nucleotide polymorphism (FNP) of TAC1 was only found in the japonica rice group. A neutrality test revealed strong selection, especially in the 3′-flanking region of the TAC1 coding region containing the FNP in the japonica rice group. However, no selection occurred in the indica and wild-rice groups. A phylogenetic tree derived from TAC1 sequence analysis suggests that the indica and japonica subspecies arose independently during the domestication of wild rice.
- Diversity /
- Evolution /
- Rice /
- Sequence

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参考文献(47)

[1]	Caicedo, A.L., Williamson, S.H., Hernandez, R.D. et al. Genome-wide patterns of nucleotide polymorphism in domesticated rice PLoS Genet., 3 (2007),pp. 1745-1756
[2]	Chen, W.B., Nakamura, I., Sato, Y.I. et al. Distribution of deletion type in cpDNA of cultivated and wild rice Jpn. J. Genet., 68 (1993),pp. 597-603
[3]	Cheng, C., Motohashi, R., Tsuchimoto, S. et al. Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs Mol. Bio. Evol., 20 (2003),pp. 67-75
[4]	Chou, S.L. China is the place of origin of rice J. Rice Soc. China, 7 (1948),pp. 53-54
[5]	Dally, A.M., Second, G. Theor. Appl. Genet., 80 (1990),pp. 209-222
[6]	Doebley, J.B., Gaut, B.S., Smith, B.D. The molecular genetics of crop domestication Cell, 127 (2006),pp. 1309-1321
[7]	Dong, Y., Lin, D., Kamiunten, H. et al. Jpn. J. Trop. Agricul., 48 (2004),pp. 228-234
[8]	Gaut, B.S., Morton, B.R., McCaig, B.C. et al. Proc. Natl. Acad. Sci. USA, 93 (1996),pp. 10274-10297
[9]	Ge, S., Sang, T., Lu, B.R. et al. Phylogeny of rice genomes with emphasis on origins of allotetraploid species Proc. Natl. Acad. Sci. USA, 96 (1999),pp. 14400-14405
[10]	Glaszmann, J.C. Isozymes and classification of Asian rice varieties Theor. Appl. Genet., 74 (1987),pp. 21-30
[11]	Garris, A.J., Tai, T.H., Coburn, J. et al. Genetics, 169 (2005),pp. 1631-1638
[12]	Ishii, T., Terachi, T., Tsunewaki, K. Restriction endonuclease analysis of chloroplast DNA from A-genome diploid species of rice Jpn. J. Genet., 63 (1988),pp. 523-536
[13]	Izawa, T., Konishi, S., Shomura, A. et al. DNA changes tell us about rice domestication Curr. Opin. Plant Biol., 12 (2009),pp. 1-8
[14]	Jin, J., Huang, W., Gao, J.P. et al. Genetic control of rice plant architecture under domestication Nat. Genet., 40 (2008),pp. 1365-1369
[15]	Khush, G.S. Origin, dispersal, cultivation and variation of rice Plant Mol. Biol., 35 (1997),pp. 25-34
[16]	Kovach, M.J., Sweeney, M.T., McCouch, S.R. New insights into the history of rice domestication Trends Genet., 23 (2007),pp. 578-587
[17]	Li, P.J., Wang, Y.H., Qian, Q. et al. Cell Res., 17 (2007),pp. 402-410
[18]	Londo, J.P., Chiang, Y.C., Hung, K.H. et al. Proc. Natl. Acad. Sci. USA, 103 (2006),pp. 9578-9583
[19]	Murray, M.G., Thompson, W.F. The isolation of high molecular weight plant DNA Nucleic Acids Res., 8 (1980),pp. 4321-4325
[20]	Nakano, M., Yoshimura, A., Iwata, N. Phylogenetic study of cultivated rice and its wild relatives by RFLP Rice Genet. Newsl., 9 (1992),pp. 132-134
[21]	Oka, H.I.
[22]	Peng, J., Richards, D.E., Hartley, N.M. et al. Green revolution genes encode mutant gibberellin response modulators Nature, 400 (1999),pp. 256-261
[23]	Rakshit, S., Rakshit, A., Matsumura, H. et al. Theor. Appl. Genet., 114 (2007),pp. 731-743
[24]	Rozas, J., Rozas, R. DnaSP, DNA sequence polymorphism: an interactive program for estimating population genetics parameters from DNA sequence data Comput. Appl. Biosci., 11 (1995),pp. 621-625
[25]	Saitoh, K., Onishi, K., Mikami, I. et al. Genetics, 168 (2004),pp. 997-1007
[26]	Sang, T., Ge, S. Genetics and phylogenetics of rice domestication Curr. Opin. Genet. Dev., 17 (2007),pp. 533-538
[27]	Sweeney, M., McCouch, S. The complex history of the domestication of rice Ann. Bot., 100 (2007),pp. 951-957
[28]	Second, G. Jpn. J. Genet., 57 (1982),pp. 25-57
[29]	Sun, C.Q., Wang, X.K., Yoshimur, A. et al. Theor. Appl. Genet., 104 (2002),pp. 1335-1345
[30]	Tamura, K., Nei, M., Kumar, S. Prospects for inferring very large phylogenies by using the neighbor-joining method Proc. Natl. Acad. Sci. USA, 101 (2004),pp. 11030-11035
[31]	Tamura, K., Dudley, J., Nei, M. et al. MEGA4: Molecular Evolutionary Genetics Analysis. MEGA software version 4.0 Mol. Bio. Evol., 24 (2007),pp. 1596-1599
[32]	Tan, L.B., Li, X.R., Liu, F.X. et al. Control of a key transition from prostrate to erect growth in rice domestication Nat. Genet., 40 (2008),pp. 1360-1364
[33]	Ting, Y. The origin and evolution of cultivated rice in China Acta. Agron. Sin., 8 (1957),pp. 243-260
[34]	Ting, Y.
[35]	Thompson, J.D., Higgins, D.G., Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res., 22 (1994),pp. 4673-4680
[36]	Vitte, C., Ishii, T., Lamy, F. et al. Mol. Genet. Genomics, 272 (2004),pp. 504-511
[37]	Wang, X.K., Cheng, K.S., Lu, Y.X. et al. Coordinated studies on genetic resources of rice in Yunnan. III. Glabrous hull rice (guangkedao) in Yunnan Res. Bull. Beijing Agri. Univ., 10 (1984),pp. 333-344
[38]	Wang, X.K., Cai, H.W., Sun, C.Q. et al. Chinese J. Rice Sci., 8 (1994),pp. 205-210
[39]	Wang, Z.Y., Tanksley, S.D. Genome, 32 (1989),pp. 1113-1118
[40]	Xu, Y.B., Shen, Z.T. Genetic analysis of tiller angles for early season indica rice Acta Agricul. Zhejiang, 5 (1993),pp. 1-5
[41]	Xu, Y.B., McCouch, S.R., Shen, Z.T. Transgressive segregation of tiller angle in rice caused by complementary gene action Crop Sci., 38 (1998),pp. 12-19
[42]	Yamane, H., Ito, T., Ishikubo, H. et al. Rice, 2 (2009),pp. 56-66
[43]	Yu, B.S., Lin, Z.W., Li, H.X. et al. Plant J., 52 (2007),pp. 891-898
[44]	Yu, C., Liu, Y., Jiang, L. et al. Acta Genet. Sin., 32 (2005),pp. 948-954
[45]	Yoshida, K., Miyashita, N.T., Ishii, T. Theor. Appl. Genet., 109 (2004),pp. 1406-1416
[46]	Yoshihara, T., Lino, M. Plant Cell Physiol., 48 (2007),pp. 678-688
[47]	Zhu, Q., Zheng, X., Luo, J. et al. Mol. Bio. Evol., 24 (2007),pp. 875-888