title: Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars.
abstract: High ozone (O3) concentrations not only damage plant life but also cause considerable losses in plant productivity. To screen for molecular factors usable as potential biomarkers to identify for O3-sensitive and -tolerant lines and design O3 tolerant crops, our project examines the effects of O3 on rice, using high-throughput omics approaches. In this study, we examined growth and yield parameters of 4 rice cultivars fumigated for a life-time with ambient air (mean O3: 31.4-32.7 ppb) or filtered air (mean O3: 6.6-8.3 ppb) in small open-top chambers (sOTCs) to select O3-sensitive (indica cv Takanari) and O3-tolerant (japonica cv Koshihikari) cultivars for analysis of seed transcriptomes using Agilent 4 × 44K rice oligo DNA chip. Total RNA from dry mature dehusked seeds of Takanari and Koshihikari cultivars was extracted using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment, followed by DNA microarray analysis using the established dye-swap method. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in sOTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in sensitive cv Takanari and tolerant cv Koshihikari. MapMan analysis further mapped the molecular factors activated by O3, confirming Takanari is rightly classified as an O3 sensitive genotype.
authors.affiliation: Environmental Biology Division; National Institute for Environmental Studies (NIES); Tsukuba, Ibaraki Japan; Seoul Center; Korea Basic Science Institute (KBSI); Seoul, South Korea.
authors.forename: Kyoungwon
authors.initials: K
authors.lastname: Cho
authors.affiliation: Environmental Biology Division; National Institute for Environmental Studies (NIES); Tsukuba, Ibaraki Japan; Department of Anatomy; Showa University School of Medicine; Shinagawa, Tokyo Japan; Laboratory of Exercise Biochemistry & Neuroendocrinology; Institute for Health and Sports Science; University of Tsukuba; Tsukuba, Japan.
authors.forename: Junko
authors.initials: J
authors.lastname: Shibato
authors.affiliation: Environmental Biology Division; National Institute for Environmental Studies (NIES); Tsukuba, Ibaraki Japan.
authors.forename: Akihiro
authors.initials: A
authors.lastname: Kubo
authors.affiliation: Environmental Science Research Laboratory; Central Research Institute of Electric Power Industry (CRIEPI); Chiba, Japan.
authors.forename: Yoshihisa
authors.initials: Y
authors.lastname: Kohno
authors.affiliation: Plant Genome Research Unit; Division of Genome and Biodiversity Research; National Institute of Agrobiological Sciences (NIAS); Tsukuba, Ibaraki Japan.
authors.forename: Kouji
authors.initials: K
authors.lastname: Satoh
authors.affiliation: Plant Genome Research Unit; Division of Genome and Biodiversity Research; National Institute of Agrobiological Sciences (NIAS); Tsukuba, Ibaraki Japan.
authors.forename: Shoshi
authors.initials: S
authors.lastname: Kikuchi
authors.affiliation: Research Laboratory for Biotechnology and Biochemistry (RLABB); Kathmandu, Nepal.
authors.forename: Abhijit
authors.initials: A
authors.lastname: Sarkar
authors.affiliation: Research Laboratory for Biotechnology and Biochemistry (RLABB); Kathmandu, Nepal.
authors.forename: Ganesh Kumar
authors.initials: GK
authors.lastname: Agrawal
authors.affiliation: Department of Anatomy; Showa University School of Medicine; Shinagawa, Tokyo Japan; Research Laboratory for Biotechnology and Biochemistry (RLABB); Kathmandu, Nepal; Organization for Educational Initiatives; University of Tsukuba, Tsukuba, Ibaraki Japan.
authors.forename: Randeep
authors.initials: R
authors.lastname: Rakwal
mesh_terms: D000222:Adaptation, Physiological / Q000187:drug effects / Q000235:genetics; D060146:Ecotype; D005651:Fumigation; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant; D053858:Metabolic Networks and Pathways / Q000187:drug effects / Q000235:genetics; D012275:Oryza / Q000187:drug effects* / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D010126:Ozone / Q000494:pharmacology*; D012639:Seeds / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D059467:Transcriptome / Q000187:drug effects / Q000235:genetics*
chemical_list: D010126:Ozone
keywords: MapMan analysis; ozone; rice; whole genome DNA microarray; yield loss
references.citation: PLoS Genet. 2005 Aug;1(2):e26
references.pmid: 16121258
references.citation: New Phytol. 2005 Jul;167(1):129-41
references.pmid: 15948836
references.citation: Plant Cell Environ. 2009 Sep;32(9):1211-29
references.pmid: 19389052
references.citation: Curr Biol. 2001 Dec 11;11(24):1914-22
references.pmid: 11747817
references.citation: Plant Physiol. 2008 Feb;146(2):333-50
references.pmid: 18065552
references.citation: Plant J. 1998 Mar;13(5):629-40
references.pmid: 9681005
references.citation: Environ Health Perspect. 2004 Mar;112(4):480-7
references.pmid: 15033598
references.citation: Rev Environ Contam Toxicol. 2011;212:61-111
references.pmid: 21432055
references.citation: Appl Bioinformatics. 2005;4(1):33-44
references.pmid: 16000011
references.citation: Plant Physiol. 2009 Apr;149(4):1751-60
references.pmid: 19211695
references.citation: Plant Physiol. 2009 Sep;151(1):253-61
references.pmid: 19605548
references.citation: Mol Cells. 2006 Apr 30;21(2):197-205
references.pmid: 16682813
references.citation: Congenit Anom (Kyoto). 2011 Sep;51(3):110-25
references.pmid: 21848995
references.citation: Genes Dev. 2003 Apr 15;17(8):1043-54
references.pmid: 12672693
references.citation: Plant Physiol. 2008 Feb;146(2):623-35
references.pmid: 18162593
references.citation: Eur J Biochem. 1992 Jun 1;206(2):331-6
references.pmid: 1597177
references.citation: J Biol Chem. 2001 Apr 27;276(17):14139-52
references.pmid: 11133985
references.citation: Plant J. 2004 Mar;37(6):914-39
references.pmid: 14996223
references.citation: J Biol Chem. 1999 Apr 2;274(14):9175-82
references.pmid: 10092589
references.citation: Plant Cell. 2003 Jan;15(1):165-78
references.pmid: 12509529
references.citation: Plant Mol Biol. 2007 Dec;65(6):719-32
references.pmid: 17874224
references.citation: Dis Model Mech. 2012 Mar;5(2):270-83
references.pmid: 22015461
references.citation: Plant Cell. 2008 Oct;20(10):2763-82
references.pmid: 18952777
references.citation: J Proteome Res. 2008 Jun;7(6):2471-89
references.pmid: 18457438
references.citation: Bioinformatics. 2005 May 1;21(9):1995-2000
references.pmid: 15691855
references.citation: Biotechnol Lett. 2013 Apr;35(4):647-56
references.pmid: 23264265
references.citation: Plant Mol Biol. 2003 Nov;53(4):443-56
references.pmid: 15010611
references.citation: Proteomics. 2002 Aug;2(8):947-59
references.pmid: 12203890
references.citation: New Phytol. 2006;170(2):333-43
references.pmid: 16608458
references.citation: Proteomics. 2007 May;7(10):1584-99
references.pmid: 17486556
references.citation: DNA Res. 2003 Dec 31;10(6):239-47
references.pmid: 15029955
references.citation: New Phytol. 2011 Sep;191(4):958-969
references.pmid: 21569035
references.citation: Electrophoresis. 2007 Dec;28(23):4369-81
references.pmid: 17987633
references.citation: J Proteome Res. 2008 Jul;7(7):2980-98
references.pmid: 18517257
references.citation: FEBS Lett. 2010 Nov 19;584(22):4575-80
references.pmid: 20937273
references.citation: Plant Cell Environ. 2006 Jul;29(7):1357-71
references.pmid: 17080957
references.citation: Environ Sci Technol. 2006 Jun 1;40(11):3586-94
references.pmid: 16786698