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Systematic analysis of NPK1-like genes in rice reveals a stress-inducible gene cluster co-localized with a quantitative trait locus of drought resistance

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Abstract

Phosphorylation by protein kinase is a ubiquitous key mechanism in translating external stimuli such as drought stress. NPK1 is a mitogen-activated protein kinase kinase kinase identified in Nicotiana tabacum and plays important roles in cytokinesis and auxin signaling transduction and responses to multiple stresses. Here we report the evolution, structure, and comprehensive expression profile of 21 NPK1-like genes in rice (Oryza sativa L.). Phylogenetic analysis of NPK1-like sequences in rice (OsNPKL), Arabidopsis, and other plants reveals that NPK1-like genes could be classified into three subgroups. Three OsNPKL gene clusters, located on chromosome 1 (OsNPKL1, 2, 3, and 4), 5 (OsNPKL14 and 15), and 10 (OsNPKL19 and 20), respectively, were identified in the rice genome. These clustered genes, which most likely evolved by tandem gene duplication, belong to the same phylogenetic subgroup, with similar genomic structures and conserved motifs in the kinase domain, which is unique to this subgroup. Expression analysis of OsNPKL genes under abiotic stresses suggests that the stress-responsive genes are mainly from the same subgroup. Especially interesting is that all the clustered genes are induced by drought, salt, or cold stress, and a few members are very strongly induced by drought. Some of the clustered genes are also induced by abscisic acid. The gene cluster on chromosome 1 is co-located with a quantitative trait locus (QTL) related to drought resistance. Although the drought-induced expression levels of the four genes in the cluster show no difference between the two parents used for QTL mapping, sequence variation in coding regions of the genes between the parents has provided some clues for further functional characterization of this gene cluster in abiotic stress tolerance in rice.

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Acknowledgments

This work was supported by grants from the National Special Key Project of China on Functional Genomics of Major Plants and Animals, the National Program on the Development of Basic Research, the National Natural Science Foundation of China, the Ministry of Education of China (NO 707045), EU FP6 INCO-MPC2 project (INCOCT-2005-015468), and the Rockefeller Foundation.

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  1. National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China

    Jing Ning, Siyuan Liu, Honghong Hu & Lizhong Xiong

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  1. Jing Ning
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  2. Siyuan Liu
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  3. Honghong Hu
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  4. Lizhong Xiong
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Correspondence to Lizhong Xiong.

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Communicated by A. Tyagi.

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Ning, J., Liu, S., Hu, H. et al. Systematic analysis of NPK1-like genes in rice reveals a stress-inducible gene cluster co-localized with a quantitative trait locus of drought resistance. Mol Genet Genomics 280, 535–546 (2008). https://doi.org/10.1007/s00438-008-0385-7

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