Citation: Palmer, N.A.; Sarath, G.; Bowman, M.J.; Saathoff, A.J.; Edmé, S.J.; Mitchell, R.B.; Tobias, C.M.; Madhavan, S.; Scully, E.D.; Sattler, S.E. Divergent Metabolic Changes in Rhizomes of Lowland and Upland Switchgrass (Panicum virgatum) from Early Season through Dormancy Onset. Plants 2023, 12, 1732. https://doi.org/10.3390/ plants12081732 Academic Editor: Pengcheng Fu Received: 20 March 2023 Revised: 14 April 2023 Accepted: 18 April 2023 Published: 21 April 2023 Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). plants Article Divergent Metabolic Changes in Rhizomes of Lowland and Upland Switchgrass (Panicum virgatum) from Early Season through Dormancy Onset Nathan A. Palmer 1 , Gautam Sarath 1, *, Michael J. Bowman 2 , Aaron J. Saathoff 1,† , Serge J. Edmé 1 , Robert B. Mitchell 1 , Christian M. Tobias 3 , Soundararajan Madhavan 4 , Erin D. Scully 5 and Scott E. Sattler 1 1 Wheat, Sorghum, and Forage Research Unit, Agricultural Research Service, United States Department of Agriculture, Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; nathan.palmer@usda.gov (N.A.P.); ajsaathoff1@gmail.com (A.J.S.); serge.edme@usda.gov (S.J.E.); rob.mitchell@usda.gov (R.B.M.); scott.sattler@usda.gov (S.E.S.) 2 Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, 1815 North University St., Peoria, IL 61604, USA; michael.bowman@usda.gov 3 Division of Plant Systems-Production, National Institute of Food and Agriculture, United States Department of Agriculture, Beacon Complex, Kansas City, MO 64133, USA; christian.tobias@usda.gov 4 Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; msoundararajan1@unl.edu 5 Stored Products Insect and Engineering Research Unit, Agricultural Research Service, United States Department of Agriculture, Manhattan, KS 66502, USA; erin.scully@usda.gov * Correspondence: gautam.sarath@usda.gov; Tel.: +1-(402)-472-4204 † Current address: Zoetis Inc., Lincoln, NE 68521, USA. Abstract: High-biomass-yielding southerly adapted switchgrasses (Panicum virgatum L.) frequently suffer from unpredictable winter hardiness at more northerly sites arising from damage to rhizomes that prevent effective spring regrowth. Previously, changes occurring over the growing season in rhizomes sampled from a cold-adapted tetraploid upland cultivar, Summer, demonstrated a role for abscisic acid (ABA), starch accumulation, and transcriptional reprogramming as drivers of dormancy onset and potential keys to rhizome health during winter dormancy. Here, rhizome metabolism of a high-yielding southerly adapted tetraploid switchgrass cultivar, Kanlow—which is a significant source of genetics for yield improvement—was studied over a growing season at a northern site. Metabolite levels and transcript abundances were combined to develop physiological profiles accompanying greening through the onset of dormancy in Kanlow rhizomes. Next, comparisons of the data to rhizome metabolism occurring in the adapted upland cultivar Summer were performed. These data revealed both similarities as well as numerous differences in rhizome metabolism that were indicative of physiological adaptations unique to each cultivar. Similarities included elevated ABA levels and accumulation of starch in rhizomes during dormancy onset. Notable differences were observed in the accumulation of specific metabolites, the expression of genes encoding transcription factors, and several enzymes linked to primary metabolism. Keywords: abscisic acid; dormancy; metabolites; raffinose-family oligosaccharides (RFO); rhizomes; RNA-Seq; switchgrass (Panicum virgatum L.); transcriptomics 1. Introduction Switchgrass (Panicum virgatum L.) is a temperate, warm-season, perennial grass with good attributes as a forage, conservation, and bioenergy crop [1,2]. Switchgrass occurs as populations and synthetic cultivars that have distinct zones of adaptation [3,4]. The more northerly adapted upland types possess greater winter hardiness, but have lower biomass yields compared to the higher-yielding lowland southerly lines which have lower winter Plants 2023, 12, 1732. https://doi.org/10.3390/plants12081732 https://www.mdpi.com/journal/plants