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 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.

Differential Defense Responses of Upland and Lowland Switchgrass Cultivars to a Cereal Aphid Pest

“…Similar results were obtained in soybean lines infested with soybean aphids [ 86 ]. Collectively, these results suggested that elevated transcription of plant defense mechanisms could basally be higher in Kanlow relative to Summer, consistent with data reported for Kanlow and Summer plants raised under optimal greenhouse conditions [ 87 ]. A group of co-expressed genes comprising M4 were upregulated in YSA-uninfested and infested plants of Kanlow and downregulated in Summer.…”

Aphid-Responsive Defense Networks in Hybrid Switchgrass

“…As examples, four of the NAC TFs in M2 encoded ATNAP homologs [AT1G69490; (Guo and Gan, 2006)]. These four switchgrass NAC genes were also upregulated during the onset of leaf senescence in switchgrass (Palmer et al, 2015;Palmer et al, 2019b), indicating that certain senescence-related KEGG pathways such as 'peroxisomes' and 'fatty acid degradation' were induced by aphid herbivory, either due to loss of leaf functions or as a means to reallocate nutrients away from aphid-infested leaves to other sinks. More intriguingly, a grass specific WRKY (Pavir.5NG041300), related to Arabidopsis WRKY51 (AT5G64810), was strongly induced in M2.…”

Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species

“…DEGs were identified in the valine, leucine, and isoleucine biosynthesis pathways and their induction in response to osmoregulation under heat stress [ 83 ]. Several studies reported the differences between genotypes for differentially expressed transcripts in response to heat stress and other abiotic stresses as well as maintenance of different mechanisms to cope with the stress impacts [ 36 , 44 , 84 , 85 ]. These results suggest that the differential expression levels of genes involved in different biological pathways can help in understanding the variation in response to heat stress in the blueberry species.…”