title: Promises and Challenges of Eco-Physiological Genomics in the Field: Tests of Drought Responses in Switchgrass.
abstract: Identifying the physiological and genetic basis of stress tolerance in plants has proven to be critical to understanding adaptation in both agricultural and natural systems. However, many discoveries were initially made in the controlled conditions of greenhouses or laboratories, not in the field. To test the comparability of drought responses across field and greenhouse environments, we undertook three independent experiments using the switchgrass reference genotype Alamo AP13. We analyzed physiological and gene expression variation across four locations, two sampling times, and three years. Relatively similar physiological responses and expression coefficients of variation across experiments masked highly dissimilar gene expression responses to drought. Critically, a drought experiment utilizing small pots in the greenhouse elicited nearly identical physiological changes as an experiment conducted in the field, but an order of magnitude more differentially expressed genes. However, we were able to define a suite of several hundred genes that were differentially expressed across all experiments. This list was strongly enriched in photosynthesis, water status, and reactive oxygen species responsive genes. The strong across-experiment correlations between physiological plasticity-but not differential gene expression-highlight the complex and diverse genetic mechanisms that can produce phenotypically similar responses to various soil water deficits.
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.).
authors.forename: John T
authors.identifier: 0000-0002-8938-1166
authors.initials: JT
authors.lastname: Lovell
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.).
authors.forename: Eugene V
authors.identifier: 0000-0003-2689-7410
authors.initials: EV
authors.lastname: Shakirov
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.).
authors.forename: Scott
authors.initials: S
authors.lastname: Schwartz
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.).
authors.forename: David B
authors.initials: DB
authors.lastname: Lowry
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.).
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Aspinwall
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.).
authors.forename: Samuel H
authors.identifier: 0000-0001-9714-0656
authors.initials: SH
authors.lastname: Taylor
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.).
authors.forename: Jason
authors.identifier: 0000-0003-1835-8409
authors.initials: J
authors.lastname: Bonnette
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.).
authors.forename: Juan Diego
authors.initials: JD
authors.lastname: Palacio-Mejia
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.).
authors.forename: Christine V
authors.initials: CV
authors.lastname: Hawkes
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.).
authors.forename: Philip A
authors.initials: PA
authors.lastname: Fay
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas (J.T.L., E.V.S., S.S., J.B., J.D.P.-M., C.V.H., T.E.J.); Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia (E.V.S.); Department of Plant Biology, Michigan State University, East Lansing, Michigan (D.B.L.);Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia (M.J.A.); Departments of Environmental Studies and Biology, Keene State College, Keene, New Hampshire USA (S.H.T.); andUSDA-ARS Grassland Soil and Water Research Laboratory, Temple, Texas 76502 (P.A.F.) tjuenger@austin.utexas.edu.
authors.forename: Thomas E
authors.identifier: 0000-0001-9550-9288
authors.initials: TE
authors.lastname: Juenger
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D055864:Droughts; D017753:Ecosystem; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D023281:Genomics / Q000379:methods*; D008897:Panicum / Q000235:genetics*; D010788:Photosynthesis / Q000235:genetics; D018515:Plant Leaves / Q000235:genetics; D025341:Principal Component Analysis; D012987:Soil / Q000737:chemistry; D013312:Stress, Physiological; D014867:Water / Q000378:metabolism
chemical_list: D012987:Soil; D014867:Water