Project description: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.
Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs 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 an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari. Comparison between O. sativa L. indica cv. Takanari and japonica cv. Koshihikari grown under ozone for their lifetime was performed. Controls were plants grown under filtered air. Three biological replicates (4 plants in each biological replicate in each small open top chamber - seed; pooled) were used, and dye-swaped.
Project description:Rice grain yield is predicted to decrease in the future because of an increase in tropospheric ozone concentration. However, the underlying mechanisms are unclear. Here, we investigated the responses to ozone of two rice (Oryza Sativa L.) cultivars, Sasanishiki and Habataki. Sasanishiki showed ozone-induced leaf injury, but no grain yield loss. By contrast, Habataki showed grain yield loss with minimal leaf injury. A QTL associated with grain yield loss caused by ozone was identified in Sasanishiki/Habataki chromosome segment substitution lines and included the ABERRANT PANICLE ORGANIZATION 1 (APO1) gene. The Habataki allele of the APO1 locus in a near-isogenic line also resulted in grain yield loss upon ozone exposure, suggesting APO1 involvement in ozone-induced yield loss. Only a few differences in the APO1 amino acid sequences were detected between the cultivars, but the APO1 transcript level was oppositely regulated by ozone exposure: i.e., it increased in Sasanishiki and decreased in Habataki. Interestingly, the levels of some phytohormones (jasmonic acid, jasmonoyl-L-isoleucine, and abscisic acid) known to be involved in attenuation of ozone-induced leaf injury tended to decrease in Sasanishiki but to increase in Habataki upon ozone exposure. These data indicate that ozone-induced grain yield loss in Habataki is caused by a reduction in the APO1 transcript level through an increase in the levels of phytohormones that reduce leaf damage. Ozone induced gene expression in rice inflorescence meristem was measured at 6 month after exposure to dose of 43.7 nL L-1 (ambient air) and 85.7 nL L-1 (2-fold concentration compared to ambient air) (12 hours mean). The two culticars, Sasanishiki and Habataki, were used for each experiment.
Project description:Rice grain yield is predicted to decrease in the future because of an increase in tropospheric ozone concentration. However, the underlying mechanisms are unclear. Here, we investigated the responses to ozone of two rice (Oryza Sativa L.) cultivars, Sasanishiki and Habataki. Sasanishiki showed ozone-induced leaf injury, but no grain yield loss. By contrast, Habataki showed grain yield loss with minimal leaf injury. A QTL associated with grain yield loss caused by ozone was identified in Sasanishiki/Habataki chromosome segment substitution lines and included the ABERRANT PANICLE ORGANIZATION 1 (APO1) gene. The Habataki allele of the APO1 locus in a near-isogenic line also resulted in grain yield loss upon ozone exposure, suggesting APO1 involvement in ozone-induced yield loss. Only a few differences in the APO1 amino acid sequences were detected between the cultivars, but the APO1 transcript level was oppositely regulated by ozone exposure: i.e., it increased in Sasanishiki and decreased in Habataki. Interestingly, the levels of some phytohormones (jasmonic acid, jasmonoyl-L-isoleucine, and abscisic acid) known to be involved in attenuation of ozone-induced leaf injury tended to decrease in Sasanishiki but to increase in Habataki upon ozone exposure. These data indicate that ozone-induced grain yield loss in Habataki is caused by a reduction in the APO1 transcript level through an increase in the levels of phytohormones that reduce leaf damage.
Project description:The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant aus cultivar N22, 56 differentially expressed genes in developing seeds were identified at combined heat and drought in the field. The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding not present in the reference transcriptomes/genomes. In addition, our approach provides a cost-effective alternative to genome sequencing for identification of candidate genes in highly stress tolerant genotypes.
Project description:Rice flag leaves are major source organs providing more than half of the nutrition needed for rice seed development. The dynamic metabolic changes in rice flag leaves and the detailed metabolic relationship between source and sink organs in rice, however, remain largely unknown. In this study, the metabolic changes of flag leaves in two japonica and two indica rice cultivars were investigated using non-targeted metabolomics approach. Principal component analysis (PCA) revealed that flag leaf metabolomes varied significantly depending on both species and developmental stage. Only a few of the metabolites in flag leaves displayed the same change pattern across the four tested cultivars along the process of seed development. Further association analysis found that levels of 45 metabolites in seeds that are associated with human nutrition and health correlated significantly with their levels in flag leaves. Comparison of metabolomics of flag leaves and seeds revealed that some flavonoids were specific or much higher in flag leaves while some lipid metabolites such as phospholipids were much higher in seeds. This reflected not only the function of the tissue specific metabolism but also the different physiological properties and metabolic adaptive features of these two tissues.
Project description:Drought and salinity are the major environmental factors that affect rice productivity. Comparative transcriptome analysis between tolerant and sensitive rice cultivars can provide insights into the regulatory mechanisms involved in these stress responses. In this study, the comparison of transcriptomes of a drought-tolerant [Nagina 22 (N22)] and a salinity-tolerant (Pokkali) rice cultivar with IR64 (susceptible cultivar) revealed variable transcriptional responses under control and stress conditions. A total of 801 and 507 transcripts were exclusively differentially expressed in N22 and Pokkali rice cultivars, respectively, under stress conditions. Gene ontology analysis suggested the enrichment of transcripts involved in response to abiotic stress and regulation of gene expression in stress-tolerant rice cultivars. A larger number of transcripts encoding for members of NAC and DBP transcription factor (TF) families in N22 and members of bHLH and C2H2 TF families in Pokkali exhibited differential regulation under desiccation and salinity stresses, respectively. Transcripts encoding for thioredoxin and involved in phenylpropanoid metabolism were up-regulated in N22, whereas transcripts involved in wax and terpenoid metabolism were up-regulated in Pokkali. Overall, common and cultivar-specific stress-responsive transcripts identified in this study can serve as a helpful resource to explore novel candidate genes for abiotic stress tolerance in rice.
Project description:Tropospheric ozone causes severe oxidative stress in plants. To investigate the transcriptional responsiveness of adult trees to ozone, fully-expanded sun and shade leaves of mature beech trees were harvested at four time points over the entire vegetation period in 2005 and 2006. Microarray analyses were conducted on leaves from trees grown in the field under ambient and twice-ambient ozone concentrations at Kranzberger Forst (Bavarian). Beech trees changed their transcript levels in response to ozone. In the years 2005 and 2006 different transcription patterns were observed; this may have been a result of different weather conditions and ozone uptake. Furthermore, we obtained differences in mRNA expression patterns between shade and sun leaves. In the ozone-treated sun leaves of 2005, slightly up- and down-regulated transcript levels were detected, particularly in the spring and autumn, whereas shade leaves clearly exhibited reduced mRNA-levels, particularly at the end of the vegetation period. In 2006, this pattern could not be confirmed, and in the autumn, four other transcripts were slightly up-regulated in ozone-treated shade leaves. In addition, two additional transcripts were found to be influenced in sun leaves in the spring/summer. While we detected changes in the levels of only a few transcripts, the observed effects were not identical in both years. In conclusion, elevated ozone exhibited very small influence on the transcription levels of genes of mature beech trees. Overall design: The study was carried out at the Kranzberger Forst research site (near Freising, Germany: 48°25’08’’N, 11°39’41’””E, 485m (Pretzsch et al., 1998) in a mixed 60-year old stand (closed canopy) with about 30m high European beech (Fagus sylvatica) and Norway spruce (Picea abies) trees. Free-air ozone fumigation started in May 2000 at double the ambient ozone concentrations with a cut-off at 150 nl l-1 (Werner and Fabian, 2002), thereby avoiding acute damage to the leaves. The ozone concentrations were measured at four heights within the fumigated space and were additionally monitored with 200 passive samplers (Werner and Fabian, 2002). In 2005 the AOT40 value under twice ambient ozone was 64.3 μmol mol-1 h and in 2006 69.0 μmol mol-1 h. Detailed ozone concentration data over the growing seasons have been reported elsewhere (Gielen et al., 2007; Kitao et al., 2009). Sun and shade leaves from 60-year-old European beech trees were harvested in a total of 8 sampling campaigns in 2005 and 2006. Using scaffolding, five leaves of sun crown (height of about 25 m) and five shade (height of about 19 m) leaves were taken from each of five control and ozone-treated trees. The sampling was carried out in May, June, August, and September of 2005 and in June, August, September and October of 2006. To avoid diurnal effects, the samples were always taken around 11 a.m. For each tree, the four leaves (sun or shade) were combined, frozen in liquid nitrogen and stored at -80 °C until RNA isolation. For one time point we had five microarrays and two dye-swaps for shade leaves, and three microarrays and two dye-swaps for sun leaves. The probes of the trees under ambient ozone were labelled with Cy3 and probes of the trees under 2x ambient were labelled with Cy5. For every pair of trees a dye control were carried out, where the control trees were labelled with Cy5 and the ozone-treated one with Cy3. For statistical analysis a coefficient of variation about all microarrays of one time point was calculated using Acuity 4.0 microarray informatics software [Axon Instruments]. We used only those spots that had a coefficient of variation < 50 and were present on at least half of identical slides. The ozone-changed transcript level of genes were expressed in the median values as log2 ratios.
Project description:BACKGROUND:It is becoming clear that ozone affects not only grain yield but also grain quality in rice. However, the biochemical mechanisms responsible for ozone-induced changes in appearance quality or components are poorly understood. We analyzed appearance quality and starch composition in the rice cultivars "Koshihikari" (japonica) and "Kasalath" (indica) grown under elevated ozone conditions. RESULTS:Elevated ozone significantly increased the proportion of immature (mainly chalky) kernels in "Koshihikari" but not in "Kasalath". Scanning electron microscopy of transverse sections of kernels showed that endosperm starch granules of "Koshihikari" ripened under elevated ozone were loosely packed with large spaces and contained irregular rounded granules. Amylose content was increased in "Koshihikari" kernels with ozone exposure, but was unchanged in "Kasalath" kernels. Distribution analysis of amylopectin chain length showed that ozone induces a decrease of long-side chains and alterations of short side-chains in "Koshihikari" kernels. Furthermore, Starch Synthase (SS) IIIa transcript levels in "Koshihikari" caryopses were decreased by elevated ozone. CONCLUSIONS:The japonica cultivar "Koshihikari" showed significant deterioration in appearance quality of kernels caused by abnormal starch accumulation due to exposure to ozone. The alteration patterns of amylose and amylopectin in ozone-exposed rice kernels are similar to those in rice kernels harvested from SSIIIa-deficient mutants. These findings suggest that the increase of chalky kernels in ozone-treated "Koshihikari" is partly attributable to the repressed expression of SSIIIa involved in amylopectin side-chain elongation with ozone exposure. Elevated ozone reduced appearance quality in "Koshihikari" although it did not impair starch properties contributing to the eating quality of cooked rice.