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Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice

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Abstract

The control of seed germination under environmental conditions, where plants will be grown, is important for the adaptability of plants. Low-temperature is one of the most common environmental stress factors that affect plant growth and development and places a major limit on crop productivity in cultivated areas. Previously, qLTG3-1, a major quantitative trait locus controlling low-temperature tolerance at the germination stage in rice (called low-temperature germinability) was identified, which encodes a protein of unknown function. To identify genes targeted by qLTG3-1, a genome-wide expression profiling analysis using the 44 K Rice Oligo microarray was performed. Because the expression of qLTG3-1 was dramatically increased at 1 day after incubation, the expression profiles at this time were compared between Hayamasari, which has a loss-of-function qLTG3-1 allele, and a near isogenic line with a functional allele. A total of 4,587 genes showed significant differences between their expression levels in the two lines. Most of these genes might be involved in the process of seed germination itself, and then a focus was made on qLTG3-1 dependently induced or suppressed genes, defined as ‘qLTG3-1 dependent’ genes. Twenty-nine ‘qLTG3-1 dependent’ genes with diverse functions were categorized, implying that disruption of cellular homeostasis leads to a wide range of metabolic alterations and diverse cross-talk between various signaling pathways. In particular, genes involved in defense responses were up-regulated by qLTG3-1, indicating that qLTG3-1 expression is required for the expression of defense response genes in low-temperature germinability in rice.

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Acknowledgments

We thank Nagamura (National Institute of Agrobiological Sciences, Japan) for support with the 44 K oligo microarray analysis. This work was supported in part by grants from the Ministry of Agriculture, Forestry and Fisheries of Japan (Integrated research project for plant, insect and animal using genome technology QT-3007 and Genomics for Agricultural Innovation QTL-1005).

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  1. Plant Breeding & Production Division, Agricultural Research Institute, Hokuren Federation of Agricultural Cooperatives, Naganuma, Hokkaido, 0691317, Japan

    Kenji Fujino & Yasuyuki Matsuda

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  1. Kenji Fujino
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  2. Yasuyuki Matsuda
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Correspondence to Kenji Fujino.

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Fujino, K., Matsuda, Y. Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice. Plant Mol Biol 72, 137–152 (2010). https://doi.org/10.1007/s11103-009-9559-x

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