Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars
Abstract
The genetics and responses to biotic stressors of tetraploid switchgrass (Panicum virgatum L.) lowland cultivar ‘Kanlow’ and upland cultivar Summer are distinct and can be exploited for trait improvement. In general, there is a paucity of data on the basal differences in transcription across tissue developmental times for switchgrass cultivars. Here, the changes in basal and temporal expression of genes related to leaf functions were evaluated for greenhouse grown ‘Kanlow’, and ‘Summer’ plants. Three biological replicates of the 4th leaf pooled from 15 plants per replicate were harvested at regular intervals beginning from leaf emergence through senescence. Increases and decreases in leaf chlorophyll and N content were similar for both cultivars. Likewise, multidimensional scaling (MDS) analysis indicated both cultivar-independent and cultivar-specific gene expression. Cultivar-independent genes and gene-networks included those associated with leaf function, such as growth/senescence, carbon/nitrogen assimilation, photosynthesis, chlorophyll biosynthesis, and chlorophyll degradation. However, many genes encoding nucleotide-binding leucine rich repeat (NB-LRRs) proteins and wall-bound kinases associated with detecting and responding to environmental signals were differentially expressed. Several of these belonged to unique cultivar-specific gene co-expression networks. Analysis of genomic resequencing data provided several examples of NB-LRRs genes that were not expressed and/or apparently absent in the genomes ofmore »
- Authors:
-
[3];
[1]
- US Dept. of Agriculture (USDA), Lincoln, NE (United States). Agricultural Research Service (ARS)
- Univ. of Nebraska, Lincoln, NE (United States)
- US Dept. of Agriculture (USDA), Lincoln, NE (United States). Agricultural Research Service (ARS); Univ. of Nebraska, Lincoln, NE (United States)
- Publication Date:
- Research Org.:
- Univ. of Nebraska, Lincoln, NE (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Institute for General Medical Science (NIGMS)
- OSTI Identifier:
- 1783155
- Grant/Contract Number:
- SC0016483; SC0016108
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Volume: 14; Journal Issue: 9; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Palmer, Nathan A., Chowda-Reddy, R. V., Muhle, Anthony A., Tatineni, Satyanarayana, Yuen, Gary, Edmé, Serge J., Mitchell, Robert B., and Sarath, Gautam. Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars. United States: N. p., 2019.
Web. doi:10.1371/journal.pone.0222080.
Palmer, Nathan A., Chowda-Reddy, R. V., Muhle, Anthony A., Tatineni, Satyanarayana, Yuen, Gary, Edmé, Serge J., Mitchell, Robert B., & Sarath, Gautam. Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars. United States. https://doi.org/10.1371/journal.pone.0222080
Palmer, Nathan A., Chowda-Reddy, R. V., Muhle, Anthony A., Tatineni, Satyanarayana, Yuen, Gary, Edmé, Serge J., Mitchell, Robert B., and Sarath, Gautam. Thu .
"Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars". United States. https://doi.org/10.1371/journal.pone.0222080. https://www.osti.gov/servlets/purl/1783155.
@article{osti_1783155,
title = {Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars},
author = {Palmer, Nathan A. and Chowda-Reddy, R. V. and Muhle, Anthony A. and Tatineni, Satyanarayana and Yuen, Gary and Edmé, Serge J. and Mitchell, Robert B. and Sarath, Gautam},
abstractNote = {The genetics and responses to biotic stressors of tetraploid switchgrass (Panicum virgatum L.) lowland cultivar ‘Kanlow’ and upland cultivar Summer are distinct and can be exploited for trait improvement. In general, there is a paucity of data on the basal differences in transcription across tissue developmental times for switchgrass cultivars. Here, the changes in basal and temporal expression of genes related to leaf functions were evaluated for greenhouse grown ‘Kanlow’, and ‘Summer’ plants. Three biological replicates of the 4th leaf pooled from 15 plants per replicate were harvested at regular intervals beginning from leaf emergence through senescence. Increases and decreases in leaf chlorophyll and N content were similar for both cultivars. Likewise, multidimensional scaling (MDS) analysis indicated both cultivar-independent and cultivar-specific gene expression. Cultivar-independent genes and gene-networks included those associated with leaf function, such as growth/senescence, carbon/nitrogen assimilation, photosynthesis, chlorophyll biosynthesis, and chlorophyll degradation. However, many genes encoding nucleotide-binding leucine rich repeat (NB-LRRs) proteins and wall-bound kinases associated with detecting and responding to environmental signals were differentially expressed. Several of these belonged to unique cultivar-specific gene co-expression networks. Analysis of genomic resequencing data provided several examples of NB-LRRs genes that were not expressed and/or apparently absent in the genomes of Summer plants. It is plausible that cultivar (ecotype)-specific genes and gene-networks could be one of the drivers for the documented differences in responses to leaf-borne pathogens between these two cultivars. Incorporating broad resistance to plant pathogens in elite switchgrass germplasm could improve sustainability of biomass production under low-input conditions.},
doi = {10.1371/journal.pone.0222080},
journal = {PLoS ONE},
number = 9,
volume = 14,
place = {United States},
year = {Thu Sep 12 00:00:00 EDT 2019},
month = {Thu Sep 12 00:00:00 EDT 2019}
}
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SNP Discovery with EST and NextGen Sequencing in Switchgrass (Panicum virgatum L.)
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Heterosis in Switchgrass: Biomass Yield in Swards
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journal, January 2014
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Biomass Yield of Switchgrass Cultivars under High- versus Low-Input Conditions
journal, January 2017
- Casler, Michael D.; Sosa, Sergio; Hoffman, Lindsey
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Registration of ‘Liberty’ Switchgrass
journal, January 2014
- Vogel, K. P.; Mitchell, R. B.; Casler, M. D.
- Journal of Plant Registrations, Vol. 8, Issue 3
Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis
journal, January 2015
- Serba, Desalegn D.; Uppalapati, Srinivasa Rao; Mukherjee, Shreyartha
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