Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars

Authors: Palmer, Nathan - Nate; Rekalakunta Venka, Chowda Reddy; Muhle, Anthony; Tatineni, Satyanarayana - Ts; YUEN, GARY - University Of Nebraska; Edme, Serge; Mitchell, Robert - Rob; Sarath, Gautam

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/4/2019
Publication Date: 9/13/2019
Citation: Palmer, N.A., Rekalakunta Venka, C., Muhle, A., Tatineni, S., Yuen, G., Edme, S.J., Mitchell, R., Sarath, G. 2019. Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars. PLoS One. 14(9):e0222080. https://doi.org/10.1371/journal.pone.0222080.
DOI: https://doi.org/10.1371/journal.pone.0222080

Interpretive Summary: Switchgrass is a native perennial that can provide a sustainable supply of biomass on marginal lands. This biomass can have multiple end uses, including those as a feedstock for bioenergy. Upland and lowland cultivars of switchgrass can differ in their ability to withstand attack by plant pathogens. Possible molecular dynamics that drive these differences in non-infected plants have not been assessed. Here, the 4th emerging leaf from greenhouse grown Kanlow (lowland) and Summer (upland) switchgrass cultivars were collected from emergence through leaf senescence. RNA extracted from these leaves were subjected to high-throughput next generation sequencing. Data analyses indicated similar and cultivar-specific changes in gene expression. Overall development of leaf functions and transition to senescence were similar; however, Kanlow plants had a much greater number of expressed genes that could be involved in defense against pathogens. These data suggested that Kanlow plants could provide useful traits for the continued improvement of switchgrass germplasm with improved disease resistance.

Technical Abstract: Changes in basal and temporal expression of genes related to leaf function and defense could underlie the differences in the response of lowland (Kanlow) and upland (Summer) ecotypes of switchgrass (Panicum virgatum L.) to several biotic stressors. However not much is known about the similarities and differences in these gene expression profiles. To more fully elucidate these differences, three biological replicates of the 4th leaf pooled from 15 plants per replicate were harvested at weekly intervals from greenhouse grown Kanlow and Summer plants, beginning from leaf emergence through senescence. Harvested samples were analyzed for chlorophyll content to monitor leaf aging and by RNA-Seq using 3’-libraries to study gene-expression profiles. Increases and decreases in leaf chlorophyll content were similar for both ecotypes indicating no apparent differences in leaf developmental ontogeny. Likewise, non-metric multidimensional scaling (NMDS) analysis showed similar temporal changes in the leaf transcriptomes for both ecotypes indicating ecotype-independent gene expression, along with a clear population division, indicating ecotype-specific gene expression. Genes and gene-networks that were apparently ecotype-independent included those associated with leaf function, such as growth/senescence, carbon/nitrogen assimilation, photosynthesis, chlorophyll biosynthesis, and chlorophyll degradation. In contrast, many genes belonging to nucleotide-binding leucine rich repeat (NB-LRRs), wall-bound kinases, and gene classes such as WRKY transcription factors and others associated with detecting and responding to environmental signals were differentially expressed, and several belonged to co-expression networks unique to one or the other ecotype. 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 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.