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Species & Dataset

Experiment

Foliar Ozone Injury

  • Oryza sativa

  • Common name: Asian rice

  • Family: Poaceae

  • Cultivar: cv. Nipponbare; O. sativa L. japonica-type

  • Tissue: Third and fourth leaves of 2-week old rice plant

  • Ozone concentration: ​ 0.2 ppm

  • Ozone exposure: 24 hours

  • Sampling time: ​ 0, 6, 12 and 24 hrs after ozone treatment

  • Platform: DNA Microarray

  • Year of study: 2013

  • Location: Japan

Injury Rice.jpeg

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.

Gene Identifier
Uniprot ID
Bin Code
Bin name
log2FC (Koshihikari)
log2FC (Takanari)
Functional annotation
LOC_Os07g38380
#N/A
not assigned.unknown
1.27
12007.m08084 protein transmembrane protein 49, putative, expressed
LOC_Os07g39680
35.2
not assigned.unknown
1.39
12007.m079727 protein rhodopsin, putative, expressed
LOC_Os07g40380
#N/A
not assigned.unknown
1.61
12007.m08280 protein hypothetical protein
LOC_Os07g40640
#N/A
not assigned.unknown
1.32
12007.m08304 protein expressed protein
LOC_Os07g40860
#N/A
not assigned.unknown
2.35
12007.m08326 protein vegetative cell wall protein gp1 precursor, putative, expressed
LOC_Os07g40870
35.2
not assigned.unknown
1.55
12007.m08327 protein igA FC receptor precursor, putative, expressed
LOC_Os07g40890
#N/A
not assigned.unknown
3.19
12007.m08329 protein igA FC receptor precursor, putative, expressed
LOC_Os07g41660
35.2
not assigned.unknown
-1.34
12007.m08402 protein expressed protein
LOC_Os07g42390
#N/A
not assigned.unknown
1.26
12007.m08472 protein expressed protein
LOC_Os07g46240
35.2
not assigned.unknown
1.34
12007.m08841 protein expressed protein
LOC_Os07g49350
#N/A
not assigned.unknown
-2.25
12007.m09144 protein expressed protein
LOC_Os08g05660
35.2
not assigned.unknown
1.36
12008.m04709 protein expressed protein
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