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This paper together with Sugio et al. [16] establishes that the bacterial pathogen has a battery of transcription activator-like effectors capable of taking over the transcriptional control of specific host genes, leading to susceptibility. At least two naturally occurring resistance genes xa5 and xa15 are results of mutations of host susceptibility genes. Can this phenomenon be exploited to generate more recessive resistance genes in the host by mutagenesis? Consideration of the fitness attributes of the host-susceptibility genes would be important.
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Yang B., Sugio A., and White F.F. Os8N3 is a host disease-susceptibility gene for bacterial blight of rice. Proc Natl Acad Sci U S A 103 (2006) 10503-10508. This paper together with Sugio et al. [16] establishes that the bacterial pathogen has a battery of transcription activator-like effectors capable of taking over the transcriptional control of specific host genes, leading to susceptibility. At least two naturally occurring resistance genes xa5 and xa15 are results of mutations of host susceptibility genes. Can this phenomenon be exploited to generate more recessive resistance genes in the host by mutagenesis? Consideration of the fitness attributes of the host-susceptibility genes would be important.
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Sugio A., Yang B., Zhu T., and White F.F. Two type III effector genes of Xanthomonas oryzae pv. oryzae control the induction of the host genes OsTFIIAγ1 and OsTFX1 during bacterial blight of rice. Proc Natl Acad Sci U S A 104 (2007) 10720-10725
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This is an excellent study illustrating the intricate molecular interactions between host and pathogen. The authors find that expression of the Xa27 resistance gene is determined by the sequence variation in the promoter region. The pathogen avrXa27 encodes a type III effector capable of activating specific eukaryotic promoter. It appears that over evolutionary time, the plant has evolved a mechanism to 'fool' the pathogen into activating the resistance gene to its own detriment.
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Gu K., Yang B., Tian D., Wu L., Wang D., Sreekala C., Yang F., Chu Z., Wang G.L., White F.F., and Yin Z. R gene expression induced by a type-III effector triggers disease resistance in rice. Nature 435 (2005) 1122-1125. This is an excellent study illustrating the intricate molecular interactions between host and pathogen. The authors find that expression of the Xa27 resistance gene is determined by the sequence variation in the promoter region. The pathogen avrXa27 encodes a type III effector capable of activating specific eukaryotic promoter. It appears that over evolutionary time, the plant has evolved a mechanism to 'fool' the pathogen into activating the resistance gene to its own detriment.
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Lee S.W., Han S.W., Bartley L.E., and Ronald P.C. Unique characteristics of Xanthomonas oryzae p.v. oryzae AvrXa21 and implications for plant innate immunity. Proc Natl Acad Sci U S A 103 (2006) 18395-18400
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The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice
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Qu S., Liu G., Zhou B., Bellizzi M., Zeng L., Dai L., Han B., and Wang G.L. The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice. Genetics 172 (2006) 1901-1914
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Zhou B., Qu S., Liu G., Dolan M., Sakai H., Lu G., Bellizzi M., and Wang G.L. The eight amino-acid differences within three leucine-rich repeats between Pi2 and Piz-t resistance proteins determine the resistance specificity to Magnaporthe grisea. Mol Plant Microbe Interact 19 (2006) 1216-1228
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A comprehensive review of recent progress in finding useful genes for addressing widespread soil problems, including salinity, phosphorus-deficiency, zinc-deficiency and iron-toxicity. The authors highlight the exciting possibilities in developing superior germplasm through the use of large-effect QTLs for the affected areas.
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Ismail A.M., Heuer S., Thomson M.J., and Wissuwa M. Genetic and genomic approaches to develop rice germplasm for problem soils. Plant Mol Biol 65 (2007) 547-570. A comprehensive review of recent progress in finding useful genes for addressing widespread soil problems, including salinity, phosphorus-deficiency, zinc-deficiency and iron-toxicity. The authors highlight the exciting possibilities in developing superior germplasm through the use of large-effect QTLs for the affected areas.
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Ismail, A.M.1
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Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice
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This work together with that of Fukao et al. [28] provide a fine example of integrating key ingredients in translating results from germplasm characterization, molecular and physiological studies to field applications on a large scale. The submergence tolerance gene was identified years ago in traditional germplasm FR13A, and then isolated by positional cloning, validated by transformation analysis and analysis of allelic variation in germplasm conserved in the public gene bank. The rapid incorporation of Sub1 into popular local varieties through marker-assisted backcrossing demonstrated the utility of genome-wide marker resource in breeding.
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Xu K., Xu X., Fukao T., Canlas P., Maghirang-Rodriguez R., Heuer S., Ismail A.M., Bailey-Serres J., Ronald P.C., and Mackill D.J. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442 (2006) 705-708. This work together with that of Fukao et al. [28] provide a fine example of integrating key ingredients in translating results from germplasm characterization, molecular and physiological studies to field applications on a large scale. The submergence tolerance gene was identified years ago in traditional germplasm FR13A, and then isolated by positional cloning, validated by transformation analysis and analysis of allelic variation in germplasm conserved in the public gene bank. The rapid incorporation of Sub1 into popular local varieties through marker-assisted backcrossing demonstrated the utility of genome-wide marker resource in breeding.
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Nature
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Xu, K.1
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A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice
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Fukao T., Xu K., Ronald P.C., and Bailey-Serres J. A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell 18 (2006) 2021-2034
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+ uptake of the shoots and roots controlling rice salt tolerance. Theor Appl Genet 108 (2004) 253-260
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Ren Z.H., Gao J.P., Li L.G., Cai X.L., Huang W., Chao D.Y., Zhu M.Z., Wang Z.Y., Luan S., and Lin H.X. A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37 (2005) 1141-1146
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This work presents for the first time strong evidence of a major QTL for grain yield under drought stress. The results argue that there is sufficient heritable variation to make selection gain for a complex trait such as drought tolerance. Although the resolution of the mapping is still low, it provides a candidate region to look for genes of large effect. The genes or chromosomal regions understudied are expected to be relevant to realistic agronomic conditions because all the phenotypes and experimental parameters are done under field conditions.
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Bernier J., Kumar A., Ramaiah V., Spaner D., and Atlin G. A large-effect QTL for grain yield under reproductive-stage drought stress in upland rice. Crop Sci 47 (2007) 505-516. This work presents for the first time strong evidence of a major QTL for grain yield under drought stress. The results argue that there is sufficient heritable variation to make selection gain for a complex trait such as drought tolerance. Although the resolution of the mapping is still low, it provides a candidate region to look for genes of large effect. The genes or chromosomal regions understudied are expected to be relevant to realistic agronomic conditions because all the phenotypes and experimental parameters are done under field conditions.
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Kumar R., Venuprasad R., and Atlin G.N. Genetic analysis of rainfed lowland rice drought tolerance under naturally-occurring stress in eastern India: heritability and QTL effects. Field Crops Res 103 (2007) 42-52
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Sakuma Y., Maruyama K., Qin F., Osakabe Y., Shinozaki K., and Yamaguchi-Shinozaki K. Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression. Proc Natl Acad Sci U S A 103 (2006) 18822-18827
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Hu H., Dai M., Yao J., Xiao B., Li X., Zhang Q., and Xiong L. Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc Natl Acad Sci U S A 103 (2006) 12987-12992
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Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice
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Nakashima K., Tran L.S., Van Nguyen D., Fujita M., Maruyama K., Todaka D., Ito Y., Hayashi N., Shinozaki K., and Yamaguchi-Shinozaki K. Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J 51 (2007) 617-630
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Improvement of water use efficiency in rice by expression of HARDY, an Arabidopsis drought and salt tolerance gene
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A good example of comparative functional genetic analysis in Arabidopsis and rice. The HARDY gene was first identified in Arabidopsis as a gain-of-function mutation through activation tagging. The gene confers greater water use efficiency as well as tolerance to salinity in Arabidopsis. In rice, constitutive expression of the gene also improves water use efficiency. It is interesting to note that the rice transgene has a high number of bundle sheath cells, an anatomy often associated with C4 plants. It may be of interest to use it as a 'starter' line to introduce C4 biochemistry.
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Karaba A., Dixit S., Greco R., Aharoni A., Trijatmiko K.R., Marsch-Martinez N., Krishnan A., Nataraja K.N., Udayakumar M., and Pereira A. Improvement of water use efficiency in rice by expression of HARDY, an Arabidopsis drought and salt tolerance gene. Proc Natl Acad Sci U S A 104 (2007) 15270-15275. A good example of comparative functional genetic analysis in Arabidopsis and rice. The HARDY gene was first identified in Arabidopsis as a gain-of-function mutation through activation tagging. The gene confers greater water use efficiency as well as tolerance to salinity in Arabidopsis. In rice, constitutive expression of the gene also improves water use efficiency. It is interesting to note that the rice transgene has a high number of bundle sheath cells, an anatomy often associated with C4 plants. It may be of interest to use it as a 'starter' line to introduce C4 biochemistry.
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Thomson M.J., Edwards J.D., Septiningsih E.M., Harrington S.E., and McCouch S.R. Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL. Genetics 172 (2006) 2501-2514
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An old reference but worthy of reading. It articulates the original concept of examining gene expression in a chromosomal context, providing the methodology for subsequent studies of correlation gene expression in fully sequenced organisms.
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Spellman P.T., and Rubin G.M. Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol 1 (2002) 5.1-5.8. An old reference but worthy of reading. It articulates the original concept of examining gene expression in a chromosomal context, providing the methodology for subsequent studies of correlation gene expression in fully sequenced organisms.
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Hurst L.D., Pál C., and Lercher M.J. The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 5 (2004) 299-310. A comprehensive review of gene expression data from organisms with near-genome wide sequence information. The emerging picture is that gene orders in eukaryotes are not 'random' but organized in such a way that presumably enable coordinated expression of neighboring genes. It poses the interesting possibility that quantitative traits are governed by coordinated expression of groups of neighboring genes. As more sequenced genomes are available, this question can be experimentally tested using specialized genetic stocks such as near-isogenic lines as was done in Juenger et al. (2006).
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Zhan S., Horrocks J., and Lukens L.N. Islands of co-expressed neighboring genes in Arabidopsis thaliana suggest higher-order chromosome domains. Plant J 45 (2006) 347-357
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Jiao Y., Jia P., Wang X., Su N., Yu S., Zhang D., Ma L., Feng Q., Jin Z., Li L., et al. A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. Plant Cell 7 (2005) 1641-1657
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The authors demonstrate the value of using near-isogenic lines to define narrow regions of chromosome enriched with differentially expressed genes. Though not explicitly discussed, the observation is consistent with the presence of chromosomal domains unique to a genotype. Compared to expression analysis of a large population of recombinant inbred lines, the use of NIL may be an appealing 'short-cut' to understand the relationship between expression patterns and phenotypes.
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Juenger T.E., Wayne T., Boles S., Vaughan S., Mckay J., and Coughlan S.J. Natural genetic variation in whole-genome expression in Arabidopsis thaliana: the impact of physiological QTL introgression. Mol Ecol 15 (2006) 1351-1365. The authors demonstrate the value of using near-isogenic lines to define narrow regions of chromosome enriched with differentially expressed genes. Though not explicitly discussed, the observation is consistent with the presence of chromosomal domains unique to a genotype. Compared to expression analysis of a large population of recombinant inbred lines, the use of NIL may be an appealing 'short-cut' to understand the relationship between expression patterns and phenotypes.
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