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Switchgrass (Panicum virgatum L) flag leaf transcriptomes reveal molecular signatures of leaf development, senescence, and mineral dynamics

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Abstract

Switchgrass flag leaves can be expected to be a source of carbon to the plant, and its senescence is likely to impact the remobilization of nutrients from the shoots to the rhizomes. However, many genes have not been assigned a function in specific stages of leaf development. Here, we characterized gene expression in flag leaves over their development. By merging changes in leaf chlorophyll and the expression of genes for chlorophyll biosynthesis and degradation, a four-phase molecular roadmap for switchgrass flag leaf ontogeny was developed. Genes associated with early leaf development were up-regulated in phase 1. Phase 2 leaves had increased expression of genes for chlorophyll biosynthesis and those needed for full leaf function. Phase 3 coincided with the most active phase for leaf C and N assimilation. Phase 4 was associated with the onset of senescence, as observed by declining leaf chlorophyll content, a significant up-regulation in transcripts coding for enzymes involved with chlorophyll degradation, and in a large number of senescence-associated genes. Of considerable interest were switchgrass NAC transcription factors with significantly higher expression in senescing flag leaves. Two of these transcription factors were closely related to a wheat NAC gene that impacts mineral remobilization. The third switchgrass NAC factor was orthologous to an Arabidopsis gene with a known role in leaf senescence. Other genes coding for nitrogen and mineral utilization, including ureide, ammonium, nitrate, and molybdenum transporters, shared expression profiles that were significantly co-regulated with the expression profiles of the three NAC transcription factors. These data provide a good starting point to link shoot senescence to the onset of dormancy in field-grown switchgrass.

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Acknowledgments

We thank Drs. James D. Eudy and Alok Dhar for sample preparation and analysis on the Illumina Hi-Seq 2,000 instrument. We thank Dr. Aaron J. Saathoff for help with leaf collection. This work was supported in part by the Office of Science (BER), US Department of Energy Grant Number DE-AI02-09ER64829, USDA-NIFA Grant Number 2011-67009-30096, and by the USDA-ARS CRIS project 5440-21000-030-00D. The US Department of Agriculture, Agricultural Research Service, is an equal opportunity/affirmative action employer and all agency services are available without discrimination. Mention of commercial products and organizations in this manuscript is solely to provide specific information. It does not constitute endorsement by USDA-ARS over other products and organizations not mentioned.

The University of Nebraska DNA Sequencing Core receives partial support from the NCRR (1S10RR027754-01, 5P20RR016469, RR018788-08) and the National Institute for General Medical Science (NIGMS) (8P20GM103427, GM103471-09). This publication’s contents are the sole responsibility of the authors and do not necessarily represent the official views of the NIH or NIGMS.

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  1. Grain, Forage and Bioenergy Research Unit, USDA-ARS, Lincoln, NE, 68583-0937, USA

    Nathan A. Palmer & Gautam Sarath

  2. Grain, Forage and Bioenergy Research Unit, USDA-ARS, and Department of Agronomy and Horticulture, University of Nebraska, 137 Keim Hall, Lincoln, NE, 68583-0937, USA

    Gautam Sarath

  3. Department of Entomology, University of Nebraska, Lincoln, NE, 68583-0816, USA

    Teresa Donze-Reiner & Tiffany Heng-Moss

  4. Sunflower and Plant Biology Research Unit, USDA-ARS, Fargo, ND, 58102-2765, USA

    David Horvath

  5. Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583-0915, USA

    Brian Waters

  6. Genomics and Gene Discovery Research Unit, USDA-ARS, Albany, CA, 94710, USA

    Christian Tobias

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  1. Nathan A. Palmer
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Palmer, N.A., Donze-Reiner, T., Horvath, D. et al. Switchgrass (Panicum virgatum L) flag leaf transcriptomes reveal molecular signatures of leaf development, senescence, and mineral dynamics. Funct Integr Genomics 15, 1–16 (2015). https://doi.org/10.1007/s10142-014-0393-0

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