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Genome-wide identification and analysis of genes associated with lysigenous aerenchyma formation in rice roots

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Abstract

Plants develop lysigenous aerenchyma to improve their survival in soils that are low in oxygen, such as in paddy fields. To investigate the genes involved in this formation in rice, we sampled the lysigenous aerenchyma formed part (LAFP) and lysigenous aerenchyma unformed part (LAUP) from seminal roots and conducted transcriptome analysis with a whole-genome microarray platform, i.e., Agilent 4X44K arrays. In all, 268 genes were highly upregulated in LAFP and 259 genes in LAUP, showing fold-changes of at least 1.5 (log2) and p-values <0.01. The MapMan toolkit was used for functional characterization of differentially expressed genes. As expected, genes associated with ethylene signaling and the redox response, heat shock proteins, and secondary metabolite metabolism (e.g., flavonoids and phenylpropanoids) were prominent in LAFP. By contrast, genes related to auxins, peroxidase, glucosidase, and proteins active in pathogen responses were expressed more highly in LAUP. Previous research has shown that genes detected in LAFP, such as our candidates, are important for conferring tolerance to multiple abiotic stresses while genes expressed in LAUP are necessary for root development and soil stress (i.e., drought and nutrient deficiencies) tolerance. This genome-wide examination of the formation of lysigenous aerenchyma in rice roots presents potential candidate genes involved in the molecular mechanism that supports this production.

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Authors and Affiliations

  1. Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea

    Yo-Han Yoo & Ki-Hong Jung

  2. Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Korea

    Yo-Han Yoo & Ki-Hong Jung

  3. Department of Biological Science, Ajou University, Suwon, 443-749, Korea

    Hong-Keun Choi

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  1. Yo-Han Yoo
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Correspondence to Ki-Hong Jung.

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Yoo, YH., Choi, HK. & Jung, KH. Genome-wide identification and analysis of genes associated with lysigenous aerenchyma formation in rice roots. J. Plant Biol. 58, 117–127 (2015). https://doi.org/10.1007/s12374-014-0486-2

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