title: Contrasting metabolism in perenniating structures of upland and lowland switchgrass plants late in the growing season.
abstract: BACKGROUND
  Switchgrass (Panicum virgatum L.) is being developed as a bioenergy crop for many temperate regions of the world. One way to increase biomass yields is to move southern adapted lowland cultivars to more northern latitudes. However, many southerly adapted switchgrass germplasm can suffer significant winter kill in northerly climes.
  
  
  METHODS
  Here, we have applied next-generation sequencing in combination with biochemical analyses to query the metabolism of crowns and rhizomes obtained from two contrasting switchgrass cultivars. Crowns and rhizomes from field-grown lowland (cv Kanlow) and upland (cv Summer) switchgrass cultivars were collected from three randomly selected post-flowering plants. Summer plants were senescing, whereas Kanlow plants were not at this harvest date.
  
  
  RESULTS
  Principal component analysis (PCA) differentiated between both the Summer and Kanlow transcriptomes and metabolomes. Significant differences in transcript abundances were detected for 8,050 genes, including transcription factors such as WRKYs and those associated with phenylpropanoid biosynthesis. Gene-set enrichment analyses showed that a number of pathways were differentially up-regulated in the two populations. For both populations, protein levels and enzyme activities agreed well with transcript abundances for genes involved in the phenylpropanoid pathway that were up-regulated in Kanlow crowns and rhizomes. The combination of these datasets suggests that dormancy-related mechanisms had been triggered in the crowns and rhizomes of the Summer plants, whereas the crowns and rhizomes of Kanlow plants had yet to enter dormancy.
  
  
  CONCLUSIONS
  Delayed establishment of dormancy at more northerly latitudes could be one factor that reduces winter-survival in the high-yielding Kanlow plants. Understanding the cellular signatures that accompany the transition to dormancy can be used in the future to select plants with improved winter hardiness.
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Grain, Forage and Bioenergy Research Unit and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, United States of America.
authors.forename: Nathan A
authors.initials: NA
authors.lastname: Palmer
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Grain, Forage and Bioenergy Research Unit and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, United States of America.
authors.forename: Aaron J
authors.initials: AJ
authors.lastname: Saathoff
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Genomics and Gene Discovery Research Unit, Western Regional Research Center, Albany, California, United States of America.
authors.forename: Christian M
authors.initials: CM
authors.lastname: Tobias
authors.affiliation: Biology Department, University of Nebraska, Kearney, Nebraska, United States of America.
authors.forename: Paul
authors.initials: P
authors.lastname: Twigg
authors.affiliation: Center for Biotechnology, University of Nebraska, Lincoln, Nebraska, United States of America.
authors.forename: Yuannan
authors.initials: Y
authors.lastname: Xia
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Retired, Lincoln, Nebraska, United States of America.
authors.forename: Kenneth P
authors.initials: KP
authors.lastname: Vogel
authors.affiliation: Department of Biochemistry, University of Nebraska, Lincoln, Nebraska, United States of America.
authors.forename: Soundararajan
authors.initials: S
authors.lastname: Madhavan
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Grain, Forage and Bioenergy Research Unit and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, United States of America.
authors.forename: Scott E
authors.initials: SE
authors.lastname: Sattler
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Grain, Forage and Bioenergy Research Unit and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, United States of America.
authors.forename: Gautam
authors.initials: G
authors.lastname: Sarath
mesh_terms: D018533:Biomass; D008897:Panicum / Q000235:genetics / Q000254:growth & development*; D025341:Principal Component Analysis; D012621:Seasons; D059467:Transcriptome / Q000235:genetics