References
Ainsworth E.A. (2008) Rice production in a changing climate: A meta-analysis of responses to elevated carbon dioxide and elevated ozone concentration. Global Change Biology 14 , 1642–1650.
Ainsworth E.A. (2017) Understanding and improving global crop response to ozone pollution. Plant Journal 90 , 886–897.
Ainsworth E.A., Yendrek C.R., Sitch S., Collins W.J. & Emberson L.D. (2012) The effects of tropospheric ozone on net primary productivity and implications for climate change. Annual Review of Plant Biology63 , 637–661.
Baker N.R. (2008) Chlorophyll fluorescence: A probe of photosynthesis in vivo. Annual Review of Plant Biology 59 , 89–113.
Betzelberger A.M., Gillespie K.M., Mcgrath J.M., Koester R.P., Nelson R.L. & Ainsworth E.A. (2010) Effects of chronic elevated ozone concentration on antioxidant capacity, photosynthesis and seed yield of 10 soybean cultivars. Plant, Cell and Environment 33 , 1569–1581.
Brosché M., Merilo E., Mayer F., Pechter P., Puzõrjova I., Brader G., … Kollist H. (2010) Natural variation in ozone sensitivity among Arabidopsis thaliana accessions and its relation to stomatal conductance. Plant, Cell and Environment 33 , 914–925.
Ceulemans R., Van Praet L. & Jiang X.N. (1995) Effects of CO2 enrichment, leaf position and clone on stomatal index and epidermal cell density in poplar (Populus ). New Phytologist 131 , 99–107.
Cho K., Shibato J., Agrawal G.K., Jung Y.H., Kubo A., Jwa N.S., … Rakwal R. (2008) Integrated transcriptomics, proteomics, and metabolomics analyses to survey ozone responses in the leaves of rice seedling. Journal of Proteome Research 7 , 2980–2998.
Cho K., Shibato J., Kubo A., Kohno Y., Satoh K., Kikuchi S., … Rakwal R. (2013a) Genome-wide mapping of the ozone-responsive transcriptomes in rice panicle and seed tissues reveals novel insight into their regulatory events. Biotechnology Letters 35 , 647–656.
Cho K., Shibato J., Kubo A., Kohno Y., Satoh K., Kikuchi S., … Rakwal R. (2013b) Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars. Plant Signaling and Behavior 8 .
Choquette N.E., Ogut F., Wertin T.M., Montes C.M., Sorgini C.A., Morse A.M., … Ainsworth E.A. (2019) Uncovering hidden genetic variation in photosynthesis of field-grown maize under ozone pollution.Global Change Biology 25 , 4327–4338.
Conway J.R., Lex A. & Gehlenborg N. (2017) UpSetR: An R package for the visualization of intersecting sets and their properties.Bioinformatics 33 , 2938–2940.
Cooley D.R. & William J.M. (1987) The impact of ozone on assimilate partitioning in plants: A review. Environmental Pollution47 95–113.
Farquhar G.D. & Sharkey T.D. (1982) Stomatal Conductance and Photosynthesis. Annual Review of Plant Physiology 33 , 317–345.
Farquhar G.D., von Caemmerer S. & Berry J.A. (1980) A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. Planta 149 , 78–90.
Feng Z., Xu Y., Kobayashi K., Dai L., Zhang T., Agathokleous E., … Yue X. (2022) Ozone pollution threatens the production of major staple crops in East Asia. Nature Food 3 , 47–56.
Fiscus E.L., Booker F.L. & Burkey K.O. (2005) Crop responses to ozone : uptake , modes of action , carbon assimilation and partitioning. 997–1011.
Franks P.J. & Beerling D.J. (2009) Maximum leaf conductance driven by CO2 effects on stomatal size and density over geologic time. Proceedings of the National Academy of Sciences of the United States of America 106 , 10343–10347.
Frei M. (2015) Breeding of ozone resistant rice: Relevance, approaches and challenges. Environmental Pollution 197 , 144–155.
Frei M., Tanaka J.P., Chen C.P. & Wissuwa M. (2010) Mechanisms of ozone tolerance in rice: Characterization of two QTLs affecting leaf bronzing by gene expression profiling and biochemical analyses. Journal of Experimental Botany 61 , 1405–1417.
Fuhrer J. & Booker F. (2003) Ecological issues related to ozone: agricultural issues. Environmental international 29 , 141–154.
Hashida Y., Tezuka A., Nomura Y., Kamitani M., Kashima M., Kurita Y. & Nagano A.J. (2022) Fillable and unfillable gaps in plant transcriptome under field and controlled environments. Plant Cell and Environment , 2410–2427.
Hoigné J. & Bader H. (1976) The role of hydroxyl radical reactions in ozonation processes in aqueous solutions. Water Research10 , 377–386.
Iseki K., Homma K., Endo T. & Shiraiwa T. (2013) Genotypic diversity of cross-tolerance to oxidative and drought stresses in rice seedlings evaluated by the maximum quantum yield of photosystem ii and membrane stability. Plant Production Science 16 , 295–304.
Kanna M., Tamaoki M., Kubo A., Nakajima N., Rakwal R., Agrawal G.K., … Aono M. (2003) Isolation of an ozone-sensitive and jasmonate-semi-insensitive Arabidopsis mutant (oji1). Plant and Cell Physiology 44 , 1301–1310.
Kanno K., Suzuki Y. & Makino A. (2017) A small decrease in rubisco content by individual suppression of RBCS genes leads to improvement of photosynthesis and greater biomass production in rice under conditions of elevated CO2. Plant and Cell Physiology58 , 635–642.
Kimura H., Hashimoto-Sugimoto M., Iba K., Terashima I. & Yamori W. (2020) Improved stomatal opening enhances photosynthetic rate and biomass production in fluctuating light. Journal of Experimental Botany 71 , 2339–2350.
Kitao M., Komatsu M., Yazaki K., Kitaoka S. & Tobita H. (2015) Growth overcompensation against O3 exposure in two japanese oak species, Quercus mongolica var. crispula and Quercus serrata , grown under elevated CO2. Environmental Pollution 206 , 133–141.
Kobayashi K., Okada M. & Nouchi I. (1995) Effects ofozone on dry matter partitioning and yield ofJapanese cultivars ofrice (Oryza sativaL.). Agriculture, Ecosystems & Environment 53 ,109–122.
Kollist T., Moldau H., Rasulov B., Oja V., Rämma H., Hüve K., … Kollist H. (2007) A novel device detects a rapid ozone-induced transient stomatal closure in intact Arabidopsis and its absence in abi2 mutant.Physiologia Plantarum 129 , 796–803.
Langfelder P. & Horvath S. (2008) WGCNA: An R package for weighted correlation network analysis. BMC Bioinformatics 9 .
Li P., Mane S.P., Sioson A.A., Robinet C.V., Heath L.S., Bohnert H.J. & Grene R. (2006) Effects of chronic ozone exposure on gene expression in Arabidopsis thaliana ecotypes and in Thellungiella halophila.Plant, Cell and Environment 29 , 854–868.
Ludwikow A. & Sadowski J. (2008) Gene networks in plant ozone stress response and tolerance. Journal of Integrative Plant Biology50 , 1256–1267.
Matange N., Podobnik M. & Visweswariah S.S. (2015) Metallophosphoesterases: structural fidelity with functional promiscuity. Biochemical Journal 467 , 201–216.
Miyazaki S., Fredricksen M., Hollis K.C., Poroyko V., Shepley D., Galbraith D.W., … Bohnert H.J. (2004) Transcript expression profiles of Arabidopsis thaliana grown under controlled conditions and open-air elevated concentrations of CO2 and of O3. Field Crops Research 90 , 47–59.
Monks P.S., Archibald A.T., Colette A., Cooper O., Coyle M., Derwent R., … Williams M.L. (2015) Tropospheric ozone and its precursors from the urban to the global scale from air quality to short-lived climate forcer. Atmospheric Chemistry and Physics 15 , 8889–8973.
Morita K., Hatanaka T., Misoo S. & Fukayama H. (2014) Unusual small subunit that is not expressed in photosynthetic cells alters the catalytic properties of Rubisco in rice. Plant Physiology164 , 69–79.
Nagatoshi Y., Mitsuda N., Hayashi M., Inoue S., Okuma E., Kubo A., … Ohme-Takagi M. (2016) GOLDEN 2-LIKE transcription factors for chloroplast development affect ozone tolerance through the regulation of stomatal movement. Proceedings of the National Academy of Sciences 113 , 4218–4223.
Omasa K., Saji H., Youssefian S. & Kondo N. (2002) Air pollution and plant biotechnology -Prospects for phytomonitoring and phytoremediation, Springer-Verlag, Tokyo.
Qu Y., Sakoda K., Fukayama H., Kondo E., Suzuki Y., Makino A., … Yamori W. (2021) Overexpression of both Rubisco and Rubisco activase rescues rice photosynthesis and biomass under heat stress. Plant, Cell & Environment , 1–13.
Raudvere U., Kolberg L., Kuzmin I., Arak T., Adler P., Peterson H. & Vilo J. (2019) G:Profiler: A web server for functional enrichment analysis and conversions of gene lists. Nucleic Acids Research47 , 191–198.
Saji S., Bathula S., Kubo A., Tamaoki M., Aono M., Sano T., … Saji H. (2017) Ozone-sensitive arabidopsis mutants with deficiencies in photorespiratory enzymes. Plant and Cell Physiology 58 , 914–924.
Saji S., Bathula S., Kubo A., Tamaoki M., Kanna M., Aono M., … Saji H. (2008) Disruption of a gene encoding C4-dicarboxylate transporter-like protein increases ozone sensitivity through deregulation of the stomatal response in Arabidopsis thaliana. Plant and Cell Physiology 49 , 2–10.
Sakoda K., Tanaka Y., Long S.P. & Shiraiwa T. (2016) Genetic and physiological diversity in the leaf photosynthetic capacity of soybean.Crop Science 56 , 2731–2741.
Sakoda K., Watanabe T., Sukemura S., Kobayashi S., Nagasaki Y., Tanaka Y. & Shiraiwa T. (2019) Genetic diversity in stomatal density among soybeans elucidated using high-throughput technique based on an algorithm for object detection. Scientific Reports 9 , 1–9.
Sawada H. & Kohno Y. (2009) Differential ozone sensitivity of rice cultivars as indicated by visible injury and grain yield. Plant Biology 11 , 70–75.
Sawada H., Komatsu S., Nanjo Y., Khan N.A. & Kohno Y. (2012) Proteomic analysis of rice response involved in reduction of grain yield under elevated ozone stress. Environmental and Experimental Botany77 , 108–116.
Sawada H., Tsukahara K., Kohno Y., Suzuki K., Nagasawa N. & Tamaoki M. (2016) Elevated ozone deteriorates grain quality of japonica rice cv. Koshihikari, even if it does not cause yield reduction. Rice9 , 1–10.
Schneider C.A., Rasband W.S. & Eliceiri K.W. (2012) NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9 , 671–675.
Shannon P., Markiel A., Ozier O., Baliga N.S., T. J., Wang, … Ideker T. (2003) Cytoscape: A software environment for integrated models. Genome Research 13 , 2504.
Su W., Sun J., Shimizu K. & Kadota K. (2019) TCC-GUI: A Shiny-based application for differential expression analysis of RNA-Seq count data.BMC Research Notes 12 , 1–6.
Suzuki Y., Miyamoto T., Yoshizawa R., Mae T. & Makino A. (2009) Rubisco content and photosynthesis of leaves at different positions in transgenic rice with an overexpression of RBCS. Plant, Cell and Environment 32 , 417–427.
Tamaoki M., Nakajima N., Kubo A., Aono M., Matsuyama T. & Saji H. (2003) Transcriptome analysis of O3-exposed Arabidopsis reveals that multiple signal pathways act mutually antagonistically to induce gene expression. Plant Molecular Biology 53 , 443–456.
Tatsumi K., Abiko T., Kinose Y., Inagaki S. & Izuta T. (2019) Effects of ozone on the growth and yield of rice (Oryza sativa L.) under different nitrogen fertilization regimes. Environmental Science and Pollution Research 26 , 32103–32113.
Tsukahara K., Sawada H., Kohno Y., Matsuura T., Mori I.C., Terao T., … Tamaoki M. (2015) Ozone-induced rice grain yield loss is triggered via a change in panicle morphology that is controlled byABERRANT PANICLE ORGANIZATION 1 gene. PLoS ONE10 , 1–14.
Tsukahara K., Sawada H., Matsumura H., Kohno Y. & Tamaoki M. (2013) Quantitative trait locus analyses of ozone-induced grain yield reduction in rice. Environmental and Experimental Botany 88 , 100–106.
Ueda Y., Frimpong F., Qi Y., Matthus E., Wu L., Höller S., … Frei M. (2015) Genetic dissection of ozone tolerance in rice (Oryza sativa L.) by a genome-wide association study. Journal of Experimental Botany 66 , 293–306.
Vahisalu T., Puzõrjova I., Brosché M., Valk E., Lepiku M., Moldau H., … Kollist H. (2010) Ozone-triggered rapid stomatal response involves the production of reactive oxygen species, and is controlled by SLAC1 and OST1. Plant Journal 62 , 442–453.
Wang Y., Yang L., Höller M., Zaisheng S., Pariasca-Tanaka J., Wissuwa M. & Frei M. (2014) Pyramiding of ozone tolerance QTLs OzT8 andOzT9 confers improved tolerance to season-long ozone exposure in rice. Environmental and Experimental Botany 104 , 26–33.
Wilkinson S., Mills G., Illidge R. & Davies W.J. (2012) How is ozone pollution reducing our food supply? Journal of Experimental Botany 63 , 527–536.
Yendrek C.R., Koester R.P. & Ainsworth E.A. (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 66 , 7101–7112.
Zhang W., Gruszewski H.A., Chevone B.I. & Nessler C.L. (2008) An arabidopsis purple acid phosphatase with phytase activity increases foliar ascorbate. Plant Physiology 146 , 431–440.
Zhu X., Feng Z., Sun T., Liu X., Tang H., Zhu J., … Kobayashi K. (2011) Effects of elevated ozone concentration on yield of four Chinese cultivars of winter wheat under fully open-air field conditions.Global Change Biology 17 , 2697–2706.