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Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

GEGC Publications listed alphabetically

Elizabeth A. Ainsworth (selected publications within last 5 years)

Yendrek CR, Koester RP, Ainsworth EA (2015) A comparative analysis of transcriptomic, biochemical and physiological responses to elevated ozone identifies species-specific mechanisms of resilience in legume crops. Journal of Experimental Botany, doi:10/1093/jxb/erv404.

Sanz-Saiz A, Heath KD, Burke PV, Ainsworth EA (2015) Inoculation with an enhanced N2-fixing Bradyrhizobium japonicum strain (USDA110) does not alter soybean (Glycine max Merr.) response to elevated CO2. Plant, Cell & Environment, DOI: 10.1111/pce.12577.

Siebers MH, Yendrek CR, Drag D, Locke AM, Acosta LR, Leakey ADB, Ainsworth EA, Bernacchi CJ, Ort DR (2015) Heat waves imposed during early pod development in soybean (Glycine max) cause significant yield loss despite a rapid recovery from oxidative stress. Global Change Biology, DOI: 10.1111/gcb.12935.

Leisner CP, Ming R, Ainsworth EA (2014) Distinct transcriptional profiles of ozone stress in soybean (Glycine max) flowers and pods. BMC Plant Biology 14: 335.

Koester RP, Skoneczka JA, Cary TR, Diers BW, Ainsworth EA (2014) Historical gains in soybean (Glycine max Merr.) seed yield are driven by linear increases in light interception, energy conversion and partitioning efficiencies. Journal of Experimental Botany 65: 3311-3321.

Ainsworth EA, Serbin SP, Skoneczka JA, Townsend PA (2014) Using leaf optical properties to detect ozone effects on foliar biochemistry. Photosynthesis Research 119: 65-76.

Slattery RA, Ainsworth EA, Ort DR (2013) A meta-analysis of responses of canopy photosynthetic conversion efficiency to environmental factors reveals major causes of yield gap. Journal of Experimental Botany 64: 3723-3733

Yendrek CR, Leisner CP, Ainsworth EA (2013) Chronic ozone exacerbates the reduction in photosynthesis and acceleration of senescence caused by limited N availability in Nicotiana sylvestris. Global Change Biology 19: 3155-3166

Betzelberger AM, Yendrek CR, Sun J, Leisner CP, Nelson RL, Ort DR, Ainsworth EA (2012) Ozone exposure response for U.S. soybean cultivars: linear reductions in photosynthetic potential, biomass and yield. Plant Physiology 160: 1827-1839.

Leakey ADB, Bishop KA, Ainsworth EA (2012) A multi-biome gap in understanding of crop and ecosystem responses to elevated CO2. Current Opinion in Plant Biology 15: 228-236

Ainsworth EA, Yendrek CR, Sitch S, Collins WJ, Emberson LD (2012) The effects of tropospheric ozone on net primary production and implications for climate change. Annual Review of Plant Biology 63: 637-661

Complete list of publications


May R. Berenbaum

Casteel CL, Segal LM, Niziolek OK, Berenbaum MR, DeLucia EH (2012) Elevated carbon dioxide increases salicyclic acid in Glycine max.  Environmental Entomology 41(6): 1435-1442

Hamilton J, Zangerl AR, Berenbaum MR, Sparks J, Elich L, Gattis A, Eisenstein A, and DeLucia EH (2012)  Elevated atmospheric CO2 alters arthropod community structure in a forest understory.  Acta Oecologica 43: 80-85

Niziolek O, Berenbaum MR, DeLucia EH (2012) Impact of elevated CO2 and increased temperature on Japanese beetle herbivory.  Insect Science,  DOI: 10.1111/j.1744-7917.2012.01515.x

Miresmailli S, Zeri M, Zangerl AR, Bernacchi CJ, Berenbaum MR, and DeLucia EH (2012) Impacts of biofuel crops on atmospheric volatile organic composition and potential consequences for global climate change.  Global Change Biology: Energy DOI: 10.1111/j/1757-1707.2012.01189.x

Casteel C, Berenbaum MR, DeLucia EH (2012) Effects of elevated CO2 and soil water content on phytohormone transcript induction in Glycine max after Popilla japonica feeding. Arthropod-Plant Interactions DOI:  10.1007/s11829-012-9195-2.

O'Neill BF, Zangerl AR, DeLucia EH, Casteel C, Zavala JA, Berenbaum M (2011) Leaf temperature of soybean growth under elevated CO2 increases Aphis glycines. (Hemiptera: Aphididae) population growth.  Insect Science DOI: 10.1111/j.1744-7917.2011.01420.x

O'Neill BF, Zangerl AR, DeLucia EH, Berenbaum MR (2010) Olfactory preferences of Popilla japonica, Vanessa cardui, and Aphis glycines for Glycine max grown under elevated CO2.  Environmental Entomology 39: 1291-1301

O'Neill BF, Zangerl AR, Bilgin DD, Casteel C, Zavala JA, Delucia EH, Berenbaum MR (2010) Impact of elevated levels of atmospheric CO2 and herbivory on flavonoids of soybean (Glycine max Linnaeus)  J. Chemical Ecol. 36: 35-45 (special issue on global climate change, January 2010)  10.1007/s10886-009-9727-0

Zavala JA, Casteel C, Nabity PD, Berenbaum MR, DeLucia EH (2009) Role of cysteine proteinase inhibitos in preference of Japanese beetles (Popilla japonica) for soybean (Glycine max) leaves of different ages and grown under elevated CO2.  Oecologia 161: 35-41

Dermody O, O'Neill BF, Berenbaum MR, DeLucia EH (2008)  Feeding behavior of invasive and mative insects in an agroecoystem modified by exposure to elevated carbon dioxide.  Arthropod Plant Interactions 2: 125-135

Zavala JA, Casteel C, DeLucia EH, Berenbaum MR (2008)  Anthropogenic increase in carbon dioxide compromises plant defense against invasive insects.  Proceedings of the National Academies of Sciences 105: 5129-5133

DeLucia EH, Nabity PD, Zavala JA, Berenbaum MR (2012) Climate change: resetting plant-insect interactions.  Plant Physiology DOI:

O'Neill BF, Zangerl AR, DeLucia EH, Berenbaum MR (2008) Longevity and fecundity of Japanese beetle (Popilla japonica Newman) on foliage grown under elevated CO2 or O3.  Enivironmental Entomology 37: 601-60

Complete list of publications


Carl J. Bernacchi

Toomey M., Friedl, M.A., Frolking, S., Hufkens, K, Klosterman S., Sonnentag, O,. Baldocchi, D.D., Bernacchi, C.J., Bohrer, G., Brzostek, E., Burns, S.P., Coursolle, C., Hollinger, D.Y., Margolis, H.A., McCaughey, H., Monson R.K., Munger, J.W., Pallardy, S., Phillips, R.P., Torn, M., Wharton, S., Zeri, M., Richardson, A.D., Greenness indices from digital cameras predict the timing and seasonal dynamics of canopy-scale photosynthesis. Ecological Applications, 25, 99–115. 2015.

Bagley, J., Rosenthal, D.M., Ruiz-Vera, U.M., Siebers, M., Kumar P., Ort, D.R., and Bernacchi, C.J.  The influence of photosynthetic acclimation to rising CO2 and warmer temperatures on leaf and canopy photosynthesis models. Global Biogeochemical Cycles, 29, 194-206. 2015.

Bernacchi, C.J. and VanLoocke, A.  Terrestrial Ecosystems in a Changing Environment: A Dominant Role for Water.  Annual Review of Plant Biology, 66, 18.1–18.24.  2015.

Kimball, B.A., White, J.W., Ottman, M.J., Wall, G.W., Bernacchi, C.J., Morgan, J., and Smith, D.P.  Predicting Canopy Temperatures and Infrared Heater Energy Requirements for Warming Field Plots.  Agronomy Journal, 107, 129-141. 2015.

Woo, D.K., Quijano, J., Kumar, P., Chaoka, S., and Bernacchi, C.J.  Threshold Dynamics in Soil Carbon Storage for Bioenergy Crops. Environmental Science and Technology, 48, 12090–12098. 2014.

Bagley, J.E., Davis, S.C., Georgescu, M., Hussain, M.Z., Miller, J., Nesbitt, S.W., VanLoocke, A., Bernacchi, C.J. The biophysical link between climate, water, and vegetation in bioenergy agro-ecosystems. Biomass & Bioenergy, 71, 187–201. 2014.

Rosenthal D.M., Ruiz-Vera, U.M., Siebers M.H., Gray, S.B., Bernacchi, C.J., and Ort, D.R. Biochemical acclimation, stomatal limitation and precipitation patterns underlie decreases in photosynthetic stimulation of Soybean (Glycine max) at elevated [CO2] and temperatures under fully open air field conditions.  Plant Science, 226, 136-146. 2014.

Sun, J., Feng Z., Leakey A.D.B., Zhu, X.-G., Bernacchi, C.J., and Ort, D.R.  Inconsistency of mesophyll conductance estimate causes the inconsistency for the estimates of maximum rate of Rubisco carboxylation among the linear, rectangular and non-rectangular hyperbola biochemical models of leaf photosynthesis – A case study of CO2 enrichment and leaf aging effects in soybean.  Plant Science, 226, 49-60. 2014.

Gilmanov, T. G., Baker, J. M., Bernacchi, C. J., Billesbach, D. P., Burba, G. G., Castro, S., et al. Productivity and Carbon Dioxide Exchange of Leguminous Crops: Estimates from Flux Tower Measurements. Agronomy Journal, 106(2), 545-559. 2014.

Locke, A.M., Sack, L., Bernacchi, C.J., and Ort, D.R. Soybean leaf hydraulic conductance does not acclimate to growth at elevated [CO2] or temperature in growth chambers or in the field.  Annals of Botany, 112: 911–918. 2013.

Complete list of publications


Patrick J. Brown 

Arruda MA, Brown PJ, Lipka AE, Krill AM, Thurber C, Kolb FL. (2015) Genomic Selection for Predicting Fusarium Head Blight Resistance in a Wheat Breeding Program. The Plant Genome 8(3): 1-12.

Burks P, Kaiser C, Hawkins EM, Brown PJ. (2015) Genomewide association for sugar yield in sweet sorghum. Crop Science 55: 2138-48

Hayes CM, Burow GB, Brown PJ, Thurber C, Xin Z, Burke JJ. (2015) Natural variation in synthesis and catabolism genes influences dhurrin content in sorghum (Sorghum bicolor L. Moench). The Plant Genome 8(2): 1-9.

Higgins RH, Thurber CS, Assaranurak I, Brown PJ (2014) Multi-parental mapping of height and flowering QTL in partially-isogenic sorghum populations. Genes, Genomes, Genetics 4:1681-1687: 1593-1602

Thurber CS, Ma JM, Higgins RH, Brown PJ (2013) Retrospective genomic analysis of sorghum adaptation to temperate zone grain production. Genome Biology 14(6): R68.

Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J, Glaubitz JC, Buckler ES, Kresovich S (2013) Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci USA 110: 453-458.

Poland J, Brown PJ, Sorrells M, Jannink J-L. (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7: e32253.

Brown PJ, Upadyayula N, Mahone GS, Tian F, Bradbury PJ, Myles S, Holland JB, Flint-Garcia S, McMullen MD, Buckler ES, Rocheford TR. (2011) Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genetics 7: e1002383.

Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford T, McMullen MD, Holland JB, Buckler ES. (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43: 159-162.


Evan H. DeLucia

Dwivedi P, Wang W, Hudiburg T, Deepak J, Parton W, Long S, DeLucia E, and Khanna M (2015) Cost of Abating Greenhouse Gas Emissions with Cellulosic Ethanol. Environmental Science Technology. Volume 49: 2512-2522 (see Larson article)

DeLucia EH, Gomez-Casanovas N, Greenberg JA, Hudiburg TW, Kantola IB, Long SP, Miller AD, Ort DR, and Parton WJ (2014) The Theoretical Limit to Plant Productivity. Environmental Science and Technology. Vol. 48: 9471−9477

Nabity PD, Haus MJ, Berenbaum MR, and DeLucia EH (2013) Leaf-galling phylloxera on grapes reprograms host metabolism and morphology. PNAS Early Edition (

Duval BD, Anderson-teixeira KJ, Davis SC, Keogh C, Long, SP, Parton WJ, DeLucia EH (2013) Predicting Greenhouse Gas Emissions and Soil Carbon from Changing Pasture to an Energy Crop. PLOS One Volume 8 (8) E72019.

Anderson-Teixeira KJ, Miller AD, Mohan JE, Hudiburg TW, Duval BD, DeLucia EH (2013) Altered dynamics of forest recovery under a changing climate. Global Change Biology (doi: 10.1111/gcb.12194)

Zavala JA, Nabity PD, DeLucia EH (2013) An Emerging Understanding of Mechanisms Governing Insect Herbivory Under Elevated CO2. Annual Review of Entomology, (58):79-97

Smith CM, David MB, Mitchell CA, Masters MM, Anderson-Teixeira KJ, Bernacchi CJ, DeLucia EH (2013) Reduced Nitrogen Losses after Conversion of Row Crop Agriculture to Perennial Biofuel Crops. Journal of Environmental Quality. Volume 42:219-228[News Coverage]

Delucia EH, Nabity PD, Zavala JA, Berenbaum MR (2012) Climate Change: Resetting Plant-Insect Interactions. Plant Physiology. Volume 160: 1677-1685

Anderson-Teixeira KJ, Snyder PK, Twine TE, Cuadra SV, Costa MH, DeLucia EH (2012) Climate-regulation services of natural and agricultural ecoregions of the Americas. Nature Climate Change Letters (online publication) DOI 10.1038/NClimate1346 (News&Views, Hungate & Hampton)

Davis SC, Parton WJ, Del Grosso SJ, Keough C, Marx E, Adler PR, and DeLucia EH (2011) Impact of second-generational biofuel agriculture on greenhouse-gas emissions in the corn-growing regions of the US. Frontiers in Ecology and the Environment (doi:10.1890/110003)

Complete list of publications


Andrew D.B. Leakey

Gray SB, Strellner RS, Puthuva KK, Shulman R, Siebers MH, Rogers A, Leakey ADB (accepted for publication) Minirhizotron imaging reveals nodulation of field-grown soybean is enhanced by Free-Air CO2 Enrichment only when combined with drought stress. Functional Plant Biology    

Gillespie KM, Xu F, Richter KT, McGrath JM, Markelz RJC, Ort DR, Leakey ADB, Ainsworth EA (2012) Greater antioxidant and respiratory metabolism in field-grown soybean exposed to elevated O3 under both ambient and elevated CO2 concentrations. Plant, Cell & Environment 35: 169-184    

Leakey ADB, Lau JA(2012) Evolutionary context for understanding and manipulating plant responses to past, present and future atmospheric [CO2]. Philosophical Transactions of the Royal Society B 367: 613-629

Markelz RJC, Strellner RS, Leakey ADB (2011) Impairment of C4 photosynthesis by drought is exacerbated by limiting nitrogen and ameliorated by elevated [CO2] in maize. Journal of Experimental Botany 62:3235-3246

Edwards EJ, Osborne CP, Stromberg CAE, Smith SA, Bond WJ, Christin PA, Cousins AB, Duvall MR, Fox DL, Freckleton RP, Ghannoum O, Hartwell J, Huang Y, Janis CM, Keeley JE, Kellogg EA, Knapp AK, Leakey ADB, Nelson DM, Passey BH, Saarela JM, Sage RF, Sala OE, Salamin N, Still CJ, Tipple B (2010) The Origins of C4 Grasslands: Integrating Evolutionary and Ecosystem Science. Science 328: 587-591

Leakey ADB, Xu F, Gillespie K, McGrath J, AinsworthEA, Ort DR (2009) Genomic basis for stimulated respiration by plants growing under elevated carbon dioxide. Proceedings of the National Academy of Sciences 106: 3597-3602 *** This paper was highlighted on F1000***

Leakey ADB, Ainsworth EA, Bernard SM, Markelz RJC, Ort DR, Placella S, Rogers A, Smith MD, Sudderth E, Weston DJ, Wullschleger SD, Yuan S (2009) Gene expression profiling – opening the black box of plant ecosystem responses to global change Global Change Biology 15: 1201-1213

Leakey ADB (2009) Rising atmospheric carbon dioxide concentration and the future of C4 crops for food and fuel. Proceedings of the Royal Society B: Biological Sciences 276: 2333-2343

Leakey ADB, Ainsworth EA, Bernacchi CJ, Rogers A , Long SP, Ort DR (2009) Elevated CO2 effects on plant carbon, nitrogen and water relations: six important lessons from FACE. Journal of Experimental Botany 60: 2859-2876

Rogers A, Ainsworth EA, Leakey ADB (2009) Will elevated carbon dioxide concentration amplify the benefits of nitrogen fixation by legumes? Plant Physiology 151: 1009-1016.

Ainsworth EA, Leakey ADB, Ort DR, Long SP. (2008) FACE-ing the facts: Inconsistencies and interdependence among field, chamber and modeling studies of elevated [CO2] impacts on crop yield and food supply. New Phytologist 179: 1-5.

Ainsworth EA, Rogers A, Leakey ADB (2008) Targets for crop biotechnology in a future high-CO2 and high-O3 world. Plant Physiology 147: 13-19.** these authors contributed equally to this work. *** This paper was amongst the top 10 “most read” articles in Plant Physiology in November and December 2008 ***

Ainsworth EA, Beier C, Calfapietra C, Ceuleman R, Durand-Tardif M, Farquhar GD, Godbold DL, Hendrey GR, Hickler T, Kaduk J, Karnosky DR, Kimball BA, Korner C, Koornneef M, Larfarge T, Leakey ADB, Lewin KF, Long SP, Manderscheid R, McNeil DL, Mies TA, Miglietta F, Morgan JA, Nagy J, Norby RJ, Norton RM, Percy KE, Rogers A, JSoussana J-F, Stitt M, Weigel H-J and White JW (2008) Next Generation of elevated [CO2] experiments with crops: a critical investment for feeding the future world. Plant, Cell and Environment 31: 1317-1324

Leakey ADB, Uribelarrea M, Ainsworth EA , Naidu SL, Rogers A, Ort DR, Long SP (2006) Photosynthesis, productivity and yield of Zea mays are not affected by open-air elevation of CO2 concentration in the absence of drought. Plant Physiology 140: 779-790

Long SP, Ainsworth EA, Leakey ADB, Nosberger J, Ort DR (2006) Food for thought: Lower than expected crop yield stimulation with rising carbon dioxide concentrations. Science 312: 1918-1921


Stephen P. Long     

McGrath JM, Betzelberger AM, Wang S, Shook E, Zhue X-G, Long SP and Ainsworth EA. Analysis of ozone damage to historical maize and soybean yields in the United States Proceeding of the National Academy of Sciences doi:10.1073/pnas.1509777112

Glocacka K, Ahmed A, Sharma S, Abbott T, Comstock JC, Long SP (2015) Can chilling tolerance of C4 photosynthesis in Miscanthus be transferred to Sugarcane? GCB Bioenergy

D. Wang, D. Jaiswal, D.S. LeBauer, T.M. Wertin, G.A. Bollero, A.D.B. Leakey, S.P. Long (2015) A physiological and biophysical model of coppice willow (Salix spp.) production yields for the contiguous USA in current and future climate scenarios. Plant, cell & Environment 

Long SP, Marshall-Colon A, Zhu XG (2015) Meeting the Global Food Demand of the Future by Engineering Crop Photosynthesis and Yield Potential. Cell 161 (1) 56-66

Drewry DT, P. Kumar P, Long SP (2014) Simultaneous improvement in productivity, water use, and albedo throught crop structural modification. Global Change Biology 20, 1955-1967

Ort DR and Long SP (2014) Limits on yields in the corn belt. Science 344 (6183), 484-485

McGrath JM and Long SP (2014) Can the Cyanobacterial Carbon-Concentrating Mechanism Increase Photosynthesis in Crop Species? A theoretical analysis. Plant Physiology 164 (4), 2247-2261

Spence AK, Boddu J, Wang D, James B, Swaminathan K,  Moose SP and Long SP (2014)
Transcriptional responses indicate maintenance of photosynthetic proteins as key to the exceptional chilling tolerance of C4 photosynthesis in Miscanthus X giganteus. Journal of Experimental Botany  65 (13), 3737-3747

Clark LV, Bummer JE, Glowacka K, Hall MC, Heo K, Peng J, Yamada T, Yoo JH, Yu CY, Zhao H, Long SP and Sacks EJ (2014) A footprint of past climate change on the diversity and population structure of Miscanthus sinensis. Annals of Botany (2014)  114 (1) 97-107

Bishop KA, Betzelberger AM, Long SP, Ainsworth EA  (2014) Is there potential to adapt soybean (Glycine max Merr.) to  future [CO2]? An analysis of the yield response of 18 genotypes in free-air CO2 enrichment. Plant, Cell & Environment (2014)


Donald R. Ort

Betzelberger AM, Yendrek CR, Sun J, Leisner CP, Nelson RL, Ort DR, and Ainsworth EA (2012) Ozone exposure response for U.S. soybean cultivars:  Linear reductions in photosynthetic potential, biomass, and yield.  Plant Physiology 160:  1827-1839

Zhu XG, Song Q, and Ort DR, (2012) Elements of a dynamic systems model of canopy photosynthesis. Curr Opin Plant Biol 15: 237-244

Rosenthal DM, Slattery R, Miller R, Gleadow R, Grennan AK, Cavagnaro T, Fauquet C, and Ort DR (2012) Cassava about-FACE: greater than expected yield stimulation of cassava (Manihot esculenta) by future CO2 levels.  Global Change Biology 18: 2661-2675

Rosenthal DM and Ort DR (2012) Examining cassava's potential to enhance food security under climate change.  Tropical Plant Biology 5: 30-38

Gillespie KM, Xu F, Richter KR, McGrath JM, Markelz RJC, Ort DR, Leakey ADB, and Ainsworth EA (2011) Greater antioxidant and respiratory metabolism in field-grown soybean exposed to elevated 03 under both ambient and elevated CO2 concentrations.  Plant Cell and Environment 35: 169-184

Rosenthal DM, Locke AM, Khozaei M, Raines CA, Long SP, and Ort DR (2011)  Over-expressing the C3 photosynthesis cycle enzyme Sedoheptulose-1-7 Bisphosphatase improves photosynthetic carbon gain and yield under fully open air CO2 fumigation (FACE).  BMC Plant Biology 11: 123
DOI:  10.1186/1471-2229-11-123

Bernacchi CJ, Leakey ADB, Kimbal B, and Ort Dr (2011)  Growth of soybean at midcentury tropospheric ozone concentrations decreases canopy evapotranspiration and soil water depletion.  Environmental Pollution 159:  1464-1472

Ort DR, Zhu XG, and Melis A (2011) Optimizing antenna size to maximize photosynthetic efficiency.  Plant Physiology  155: 79-85

Feng Z, Pang J, Kabayashi K, Zhu J, and Ort DR (2011)  Differential responses in two varieties of winter wheat to elevated ozone concentration under fully open-air conditions.  Global Change Biology 17:  580-591

Long SP and Ort DR (2010)  More than taking the heat:  crops and global change.  Current Opinion in Plant Biology 13: 241-248

Ainsworth EA and Ort DR (2010)  How do we improve crop production in a warming world?  Plant Physiology 154: 526-530

Bilgin DD, Zavala JA, Zhu J, Clough SJ, Ort DR and DeLucia EH (2010)  Biotic stress globally down regulates photosynthesis genes.  Plant Cell and Environment 33:  1597-1613

Zhu X-G, Long SP, and Ort DR (2010)  Improving photosynthetic efficiency for greater yield.  Annual Reviews of Plant Biology  61:  235-261