Elevated CO2differentially affects gene expression and metabolite profiles in Arabidopsis thalianaecotypes and in Thellungiella halophilaPinghua Li1, Shrinivasrao Mane2, Alexander Ulanov3, Allan Sioson4, Gregory Grothaus4, Andrew Leakey1, Elizabeth Ainsworth1,Lenwood HeathLenwood Heath4, T. M. Murali4, Hans J Bohnert, Hans J Bohnert1,3, Ruth Grene, Ruth Grene21Department of Plant Biology, and Department of Plant Biology, and 3Department of Crop Sciences, University of Illinois, 1201 W Gregory Drive, Urbana, Il 61801, USA2Department of Plant Pathology, Physiology, and Weed Science, andDepartment of Plant Pathology, Physiology, and Weed Science, and4Department of Computer Science, Virginia Tech, Blacksburg, VA 24Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA061, USAGlobal atmospheric CO2 concentration [CO2] has increased to its highest level in recent history and is expected to nearly double during this century. Insight into how plants respond and adapt to the projected increase in [CO2] is important, and understanding will also help to better comprehend the biochemistry of carbon assimilation in general and the consequences for plant performance in a shifting global scenario to which plants must adapt. The UIUC SoyFACE (Free-Air Concentration Enrichment) facility, which simulates atmospheric conditions expected by 2050, provides great advantage to gauge plant responses to elevated CO2.In this study, we grew ArabidopsisthalianaCol-0, Cvi-0, WS and Thellungiella halophilain the field within SoyFACE, harvested them after a 10-14d exposure to elevated CO2, used Arabidopsis long oligo microarrays combined with metabolite profiles by GC-MS to monitor effects of elevated CO2on transcript and metabolite abundance. The results indicated that a core set of signature processes and genes reporting atmospheric CO2 response pathways united Thellungiellaand the three Arabidopsisecotypes, while different behavior in several metabolic pathways distinguished ecotypes among each other and with respect to Thellungiella.IntroductionExperiment and analysis flow chartShoots RNA extraction Microarray hybridizationReal-time PCR verificationSynthesis & labeling of cDNAWolfinger two-stages statistical analysisMapman pathway analysisAmbient CO2materialElevated CO2materialSegments from the Arabidopsisoligo-array slide(total 26,000 elements, control elements are boxed)Wolfingertwotwo-stages statistical analysisFirst – Normalization Model Fittingygijkln= μ+ Ti+ Dj+ Ak+ (T×A)ik+ Bl(k)+ εgijklny: Log intensity values μ: Overall means T: Treatment D: Dye A: ArrayT×A:Treat-array interaction B: Block within arraySecond - Gene Model Fittingεgijkln= Gg+ (G×T)gi+ (G×D)gj+ (G×A)gk+(G×S)gn+ λgijklnε: Residuals from normalization G: Gene specific mean λ: ResidualsG×T: Gene treatment interaction G×D: Gene Dye interaction G×A: Gene array interaction G×S: Gene spot interactionAssessment of significantly differential expressed genesResultsCvi-0 grew best in elevated CO2
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