Switchgrass Genetics and Breeding Challenges

Bartley, Laura E.; Wu, Yanqi; Saathoff, Aaron J.; Sarath, Gautam

doi:10.1002/9781118609477.ch2

Cited by 12 publications

(11 citation statements)

References 131 publications

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“…PC2 accounted for 19.2 % of the variation and separated the transcriptomes present in flag leaves harvested at the heading (7/3) and late seed fill stage (8/31) of plant development. Within each harvest date, the greatest variation between the biological replicates was observed in the transcriptomes for the earliest (7/3) and last (9/19) harvest, plausibly attributable to variation in plant development within switchgrass populations (Bartley et al 2013).…”

Section: Changes In Gene Expression Define Developmental Stagesmentioning

confidence: 99%

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

Palmer

Donze-Reiner

Horvath

et al. 2014

Funct Integr Genomics

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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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Section: Changes In Gene Expression Define Developmental Stagesmentioning

confidence: 99%

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

Palmer

Donze-Reiner

Horvath

et al. 2014

Funct Integr Genomics

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“…Switchgrass ( Panicum virgatum L.) is an economically important C4 grass and considered as an emerging model for bioenergy crops [1]. However, switchgrass is not immune to attack and damage caused by insect pests.…”

Section: Introductionmentioning

confidence: 99%

Fall armyworm (Spodoptera frugiperda Smith) feeding elicits differential defense responses in upland and lowland switchgrass

Palmer¹,

Basu

Heng-Moss

et al. 2019

PLoS ONE

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Switchgrass ( Panicum virgatum L.) is a low input, high biomass perennial grass being developed for the bioenergy sector. Upland and lowland cultivars can differ in their responses to insect herbivory. Fall armyworm [FAW; Spodoptera frugiperda JE Smith (Lepidoptera: Noctuidae)] is a generalist pest of many plant species and can feed on switchgrass as well. Here, in two different trials, FAW larval mass were significantly reduced when fed on lowland cultivar Kanlow relative to larvae fed on upland cultivar Summer plants after 10 days. Hormone content of plants indicated elevated levels of the plant defense hormone jasmonic acid (JA) and its bioactive conjugate JA-Ile although significant differences were not observed. Conversely, the precursor to JA, 12-oxo-phytodienoic acid (OPDA) levels were significantly different between FAW fed Summer and Kanlow plants raising the possibility of differential signaling by OPDA in the two cultivars. Global transcriptome analysis revealed a stronger response in Kanlow plant relative to Summer plants. Among these changes were a preferential upregulation of several branches of terpenoid and phenylpropanoid biosynthesis in Kanlow plants suggesting that enhanced biosynthesis or accumulation of antifeedants could have negatively impacted FAW larval mass gain on Kanlow plants relative to Summer plants. A comparison of the switchgrass-FAW RNA-Seq dataset to those from maize-FAW and switchgrass-aphid interactions revealed that key components of plant responses to herbivory, including induction of JA biosynthesis, key transcription factors and JA-inducible genes were apparently conserved in switchgrass and maize. In addition, these data affirm earlier studies with FAW and aphids that the cultivar Kanlow can provide useful genetics for the breeding of switchgrass germplasm with improved insect resistance.

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“…Tetraploid switchgrass populations and cultivars have higher yields as compared to octaploid populations [ 3 ]. Thus, most current breeding efforts are focused on improving biomass yields and quality in tetraploid lines [ 4 , 5 ]. Tetraploid populations can occur as upland and lowland ecotypes, with the lowland plants significantly out-yielding the upland lines across several locations [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

“…Thus, most current breeding efforts are focused on improving biomass yields and quality in tetraploid lines [ 4 , 5 ]. Tetraploid populations can occur as upland and lowland ecotypes, with the lowland plants significantly out-yielding the upland lines across several locations [ 5 ]. However, the latitudinal adaptation of these different ecotypes presents challenges, since most of southerly-adapted, high-yielding, lowland germplasm suffers from significant winter-kill at more northern sites of the USA [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

The WRKY transcription factor family and senescence in switchgrass

Rinerson¹,

Scully²,

Palmer³

et al. 2015

BMC Genomics

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BackgroundEarly aerial senescence in switchgrass (Panicum virgatum) can significantly limit biomass yields. WRKY transcription factors that can regulate senescence could be used to reprogram senescence and enhance biomass yields.MethodsAll potential WRKY genes present in the version 1.0 of the switchgrass genome were identified and curated using manual and bioinformatic methods. Expression profiles of WRKY genes in switchgrass flag leaf RNA-Seq datasets were analyzed using clustering and network analyses tools to identify both WRKY and WRKY-associated gene co-expression networks during leaf development and senescence onset.ResultsWe identified 240 switchgrass WRKY genes including members of the RW5 and RW6 families of resistance proteins. Weighted gene co-expression network analysis of the flag leaf transcriptomes across development readily separated clusters of co-expressed genes into thirteen modules. A visualization highlighted separation of modules associated with the early and senescence-onset phases of flag leaf growth. The senescence-associated module contained 3000 genes including 23 WRKYs. Putative promoter regions of senescence-associated WRKY genes contained several cis-element-like sequences suggestive of responsiveness to both senescence and stress signaling pathways. A phylogenetic comparison of senescence-associated WRKY genes from switchgrass flag leaf with senescence-associated WRKY genes from other plants revealed notable hotspots in Group I, IIb, and IIe of the phylogenetic tree.ConclusionsWe have identified and named 240 WRKY genes in the switchgrass genome. Twenty three of these genes show elevated mRNA levels during the onset of flag leaf senescence. Eleven of the WRKY genes were found in hotspots of related senescence-associated genes from multiple species and thus represent promising targets for future switchgrass genetic improvement. Overall, individual WRKY gene expression profiles could be readily linked to developmental stages of flag leaves.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2057-4) contains supplementary material, which is available to authorized users.

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Switchgrass Genetics and Breeding Challenges

Cited by 12 publications

References 131 publications

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

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

Fall armyworm (Spodoptera frugiperda Smith) feeding elicits differential defense responses in upland and lowland switchgrass

The WRKY transcription factor family and senescence in switchgrass

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