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

High ozone (O-3) 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 O-3-sensitive and -tolerant lines and design O3 tolerant crops, our project examines the effects of O-3 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 O-3: 31.4-32.7 ppb) or filtered air (mean O-3: 6.6-8.3 ppb) in small open-top chambers (sOTCs) to select O-3-sensitive (indica cv Takanari) and O-3-tolerant (japonica cv Koshihikari) cultivars for analysis of seed transcriptomes using Agilent 4 x 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 O-3 transcriptomes in seeds of rice plants fumigated with ambient O-3 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 O-3, confirming Takanari is rightly classified as an O-3 sensitive genotype.