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Journal of Zhejiang University SCIENCE B 2005 Vol.6 No.5 P.382~388

10.1631/jzus.2005.B0382


Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map


Author(s):  WANG Xu-sheng, ZHU Jun, MANSUETO Locedie, BRUSKIEWICH Richard

Affiliation(s):  Biometrics & Bioinformatics Unit, International Rice Research Institute DAPO 7777, Metro Manila, Philippines; more

Corresponding email(s):   r.Bruskiewich@cgiar.org

Key Words:  Rice genome sequence, Candidate genes, Drought stress, Quantitative Trait Loci (QTL)


WANG Xu-sheng, ZHU Jun, MANSUETO Locedie, BRUSKIEWICH Richard. Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map[J]. Journal of Zhejiang University Science B, 2005, 6(5): 382~388.

@article{title="Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map",
author="WANG Xu-sheng, ZHU Jun, MANSUETO Locedie, BRUSKIEWICH Richard",
journal="Journal of Zhejiang University Science B",
volume="6",
number="5",
pages="382~388",
year="2005",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.2005.B0382"
}

%0 Journal Article
%T Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map
%A WANG Xu-sheng
%A ZHU Jun
%A MANSUETO Locedie
%A BRUSKIEWICH Richard
%J Journal of Zhejiang University SCIENCE B
%V 6
%N 5
%P 382~388
%@ 1673-1581
%D 2005
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.2005.B0382

TY - JOUR
T1 - Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map
A1 - WANG Xu-sheng
A1 - ZHU Jun
A1 - MANSUETO Locedie
A1 - BRUSKIEWICH Richard
J0 - Journal of Zhejiang University Science B
VL - 6
IS - 5
SP - 382
EP - 388
%@ 1673-1581
Y1 - 2005
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.2005.B0382


Abstract: 
Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of Azucena×IR64 and Azucena×Bala. To find the candidate rice genes underlying quantitative Trait Loci (QTL) in these populations, we conducted in silico analysis of a candidate region flanked by the genetic markers RM212 and RM319 on chromosome 1, proximal to the semi-dwarf (sd1) locus. A total of 175 annotated genes were identified from this region. These included 48 genes annotated by functional homology to known genes, 23 pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST (Expressed sequence tag) of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among these, 16 candidate genes could potentially be involved in drought stress response.

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Reference

[1] Altschul, S.F., Warren, G., Webb, M., Eugene, W.M., David, J.L., 1990. Basic local alignment search tool. J Mol Biol, 215:403-410.

[2] Arisz, S.A., Valianpour, F., van Gennip, A.H., Munnik, T., 2003. Substrate preference of stress-activated phospholipase D in Chlamydomonas and its contribution to PA formation. Pant J, 34:595-604.

[3] Arumugam, K., Lafitte, R., Chen, J., Bennet, J., 2005. Expression microarrays and their application in drought stress research. Field Crops Research, in press.

[4] Bruskiewich, R.M., Cosico, A.B., Eusebio, W., Portugal, A.M., Ramos, L.M., Reyes, M.T., Sallan, M.A., Ulat, V.J., Wang, X., McNally, K.L., Sackville, H.R., McLaren, C.G., 2003. Linking genotype to phenotype: the International Rice Information System (IRIS). Bioinformatics, S1:I63-I65.

[5] Causse, M., Fulton, T.M., Cho, Y.G., Ahn, S.N., Chunwongse, J., Wu, K., Xiao, J., Yu, Z., Ronald, P.C., Harrington, S.B., et al., 1994. Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics, 138:1251-1274.

[6] Chen, M., Presting, G., Barbazuk, W.B., Goicoechea, J.L., Blackmon, B., Fang, G., Kim, H., Frisch, D., Yu, Y., Sun, S., 2002. An integrated physical and genetic map of the rice genome. Plant Cell, 14(3):537-545.

[7] Choi, D.W., Rodriguez, E.M., Close, T.J., 2002. Barley Cbf3 gene identification, expression pattern, and map location. Plant Physiol, 129:1781-1787.

[8] Dey, M.M., Upadhyaya, H.K., 1996. Yield Loss Due to Drought, Cold and Submergence Tolerance. In: Evenson, R.E., Herdt, R.W., Hossain, M. (Eds.), Rice Research in Asia: Progress and Priorities. International Rice Research Institute in Collaboration with CAB International, UK.

[9] Feng, Q., Zhang, Y., Hao, P., Wang, S., Fu, G., Huang, Y., Li, Y., Zhu, J., Liu, Y., Hu, X., et al., 2002. Sequence and analysis of rice chromosome 4. Nature, 420:316-320.

[10] Fujimoto, S.Y., Ohta, M., Usui, A., Shinshi, H., Ohme-Takagi, M., 2000. Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell, 12:393-404.

[11] Gaxiola, R.A., Li, J., Undurraga, S., Dang, L.M., Allen, G.J., Alper, S.L., Fink, G.R., 2001. Drought- and salt-tolerant plants result from overexpression of the AVP1 H+-pump. Proc Natl Acad Sci USA, 98:11444-11449.

[12] Gilmour, S.J., Zarka, D.G., Stockinger, E.J., Salazar, M.P., Houghton, J.M., Thomashow, M.F., 1998. Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J, 16:433-442.

[13] Goff, S.A., Ricke, D., Lan, T.H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., et al., 2002. A draft sequence of the rice Genome (Oryza sativa L. ssp. japonica). Science, 296:92-100.

[14] Harushima, Y.M., Yano, A., Shomura, M., Sato, T., Shimano, Y., Kuboki, T., Yamamoto, S.Y., Lin, B.A., Antonio, A., Parco, H., et al., 1998. A High-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics, 148:479-494.

[15] Ingram, J., Bartels, D., 1996. The molecular basis of dehydration tolerance in plants. Annu Rev Plant Physiol Plant Mol Biol, 47:377-403.

[16] Jennings, P.R., 1964. Plant type as a rice breeding objective. Crop Sci, 4:13-15.

[17] Kim, J.S., Kim, Y.O., Ryu, H.J., Kwak, Y.S., Lee, J.Y., Kang, H., 2003. Isolation of stress-related genes of rubber particles and latex in fig tree (Ficus carica) and their expressions by abiotic stress or plant hormone treatments. Plant Cell Physiol, 44:412-414.

[18] Kovtun, Y., Chiu, W.L., Tena, G., Sheen, J., 2000. Functional analysis of oxidative stress-activated mitogen-activated protein kinase cascade in plants. Proc Natl Acad Sci USA, 97:2940-2945.

[19] Lafitte, H.R., Courtois, B., Arraudeau, M., 2002. Genetic improvement of rice in aerobic systems: progress from yield to genes. Field Crops Res, 75:171-190.

[20] Lewis, S.E., Searle, S.M.J., Harris, N., Gibson, M., Iyer, V., Ricter, J., Wiel, C., Bayraktaroglu, L., Birney, E., Crosby, M.A., et al., 2002. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol, 3:1-22.

[21] Li, Z.K., Yu, S.B., Lafitte, H.R., Huang, N., Courtois, B., Hittalmani, S., Vijayakumar, C.H.M., Liu, G.F., Wang, G.C., Shashidhar, H.E., et al., 2003. QTL x environment interactions in rice. I. Heading date and plant height. Theor Appl Genet, 108(1):141-153.

[22] Price, A.H., Cairns, J.E., Horton, P., Jones, H.G., Griffiths, H., 2002a. Linking drought-resistance mechanisms to drought avoidance in upland rice using a QTL approach: progress and new opportunities to integrate stomatal and mesophyll responses. J Exp Bot, 53:989-1004.

[23] Price, A.H., Steele, K.A., Moore, B.J., Jones, R.G.W., 2002b. Upland rice grown in soil-filled chambers and exposed to contrasting water-deficit regimes: II. Mapping QTL for root morphology and distribution. Field Crops Res, 76:25-43.

[24] Price, A.H., Townend, J., Jones, M.P., Audebert, A., Courtois, B., 2002c. Mapping QTLs associated with drought avoidance in upland rice grown in the Philippines and West Africa. Plant Mol Biol, 48:683-695.

[25] Sasaki, T., 2001. The Rice Genome Project in Japan. In: Wilson, R.F., Hou, C.T., Hildebrand, D.F. (Eds.), Dealing with Genetically Modified Crops. AOCS Press, Champaign Illinois, p.102-109.

[26] Sasaki, T., Matsumoto, T., Yamamoto, K., Sakata, K., Baba, T., Katayose, Y., Wu, J., Niimura, Y., Cheng, Z., Nagamura, Y., et al., 2002. The genome sequence and structure of rice chromosome 1. Nature, 420:312-316.

[27] Schuler, G.D., 1997. Sequence mapping by electronic PCR. Genome Res, 7:541-550.

[28] Seki, M., Narusaka, M., Ishida, J., Nanjo, T., Fujita, M., Oono, Y., Kamiya, A., Nakajima, M., Enju, A., Sakurai, T., et al., 2002. Monitoring the expression pattern of around 7000 Arabidopsisgenes under ABA treatments using a full-length cDNA microarray. Funct Integr Genomics, 2:282-291.

[29] Shinozaki, K., Yamaguchi-Shinozaki, K., 1996. Molecular responses to drought and cold stress. Curr Opin Biotech, 7:161-167.

[30] Shinozaki, K., Yamaguchi-Shinozaki, K., 1997. Gene expression and signal transduction in water-stress response. Plant Physiol, 115:327-334.

[31] Siepel, A., Farmer, A., Tolopko, A., Zhuang, M., Mendes, P., Beavis, W., Sobral, B., 2001. ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics, 17:83-94.

[32] Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., Lewis, S., 2002. The generic genome browser: a building block for a model organism system database. Genome Res, 12:1599-1610.

[33] Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cartinhour, S., McCouch, S., 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res, 11:1441-1452.

[34] Urao, T., Katagiri, T., Mizoguchi, T., Yamaguchi-Shinozaki, K., Hayashida, N., Shinozaki, K., 1994. Two genes that encode Ca2+-dependent protein kinases are induced by drought and high-salt stresses in Arabidopsis thaliana. Mol Gen Genet, 244:331-340.

[35] Ware, D., Jaiswal, P., Ni, J., Pan, X., Chang, K., Clark, K., Teytelman, L., Schmidt, S., Zhao, W., Cartinhour, S., et al., 2002. Gramene: a resource for comparative grass genomics. Nucleic Acids Res, 30:103-105.

[36] Xiong, L., Zhu, J.K., 2001. Abiotic stress signal transduction in plants: Molecular and genetic perspectives. Physiol Plant, 112:152-166.

[37] Xiong, L., Schumaker, K.S., Zhu, J.K., 2002. Cell signaling during cold, drought, and salt stress. The Plant Cell, 14 (Suppl):S165-183.

[38] Yamaguchi-Shinozaki, K., Kasuga, M., Liu, Q., Nakashima, K., Sakuma, Y., Abe, H., Shinwari, Z.K., Seki, M., Shinozaki, K., 2002. Biological mechanisms of drought stress response. JIRCAS Working Report, 23:1-8.

[39] Yu, J., Hu, S., Wang, J., Wong, G.K., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., et al., 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296:79-92.

[40] Zhang, J., Kirkham, M.B., 1994. Drought-stress-induced changes in activities of superoxide dismutase, catalase, and peroxidase in wheate species. Plant Cell Physiol, 35:758-791.

[41] Zhu, J.K., 2002. Salt and drought stress signal transduction in plants. Annu Rev Plant Biol, 53:247-273.

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