Title: Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars

Summary: 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.

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Data Repository: NCBI’s Gene Expression Omnibus (GEO), accessible through GEO Series (Accession number GSE49963) (http:// www.ncbi.nlm.nih.gov/geo/info/linking.html)

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Reference: Cho, K., Shibato, J., Kubo, A., Kohno, Y., Satoh, K., Kikuchi, S., Sarkar, A., Agrawal, G.K. and Rakwal, R., 2013. Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars. Plant signaling & behavior, 8(11), p.e26300.