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Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array

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Abstract

Plants alter their gene expression patterns in response to drought. Sometimes these transcriptional changes are successful adaptations leading to tolerance, while in other instances the plant ultimately fails to adapt to the stress and is labeled as sensitive to that condition. We measured the expression of approximately half of the genes in rice (∼21,000) in phenotypically divergent accessions and their transgressive segregants to associate stress-regulated gene expression changes with quantitative trait loci (QTLs) for osmotic adjustment (OA, a trait associated with drought tolerance). Among the parental lines, a total of 662 transcripts were differentially expressed. Only 12 genes were induced in the low OA parent, CT9993, at moderate dehydration stress levels while over 200 genes were induced in the high OA parent, IR62266. The high and low OA parents had almost entirely different transcriptional responses to dehydration stress suggesting a complete absence of an appropriate response rather than a slower response in CT9993. Sixty-nine genes were up-regulated in all the high OA lines and nine of those genes were not induced in any of the low OA lines. The annotation of four of those genes, sucrose synthase, a pore protein, a heat shock and an LEA protein, suggests a role in maintaining high OA and membrane stability. Of the 3,954-probe sets that correspond to the QTL intervals, very few had a differential expression pattern between the high OA and low OA lines that suggest a role leading to the phenotypic variation. However, several promising candidates were identified for each of the five QTL including a snRNP auxiliary factor, a LEA protein, a protein phosphatase 2C and a Sar1 homolog.

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Author notes

  1. Samuel P. Hazen

    Present address: The Scripps Research Institute, 10550 North Torrey Pines, La Jolla, CA 92037, USA

  2. M. Safiullah Pathan & Henry T. Nguyen

    Present address: Department of Agronomy, University of Missouri, Columbia, MO 65211, USA

  3. Molly Dunn, Bram Estes & Tong Zhu

    Present address: Syngenta Biotechnology Inc., 3054 Cornwallis Road, Research Triangle Park, NC 27709, USA

  4. Hur-Song Chang & Joel A. Kreps

    Present address: Diversa Corporation, 4955 Directors Place, San Diego, CA 92121, USA

Authors and Affiliations

  1. Torrey Mesa Research Institute, Syngenta, 3115 Merryfield Row, San Diego, CA 92121, USA

    Samuel P. Hazen, Molly Dunn, Bram Estes, Hur-Song Chang, Tong Zhu & Joel A. Kreps

  2. The Scripps Research Institute, 10550 North Torrey Pines, La Jolla, CA 92037, USA

    Ivan Baxter

  3. Department of Plant and Soil Sciences, Texas Tech University, Lubbock, TX 79409, USA

    M. Safiullah Pathan, Alma Sanchez & Henry T. Nguyen

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  1. Samuel P. Hazen
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Correspondence to Henry T. Nguyen.

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Hazen, S.P., Pathan, M.S., Sanchez, A. et al. Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array. Funct Integr Genomics 5, 104–116 (2005). https://doi.org/10.1007/s10142-004-0126-x

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  • DOI: https://doi.org/10.1007/s10142-004-0126-x

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