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Preformed aerenchyma determines the differential tolerance response under partial submergence imposed by fresh and saline water flooding in rice

ABSTRACT: In this project we are investigating the differential mechanism of tolerance in rice under combined stresses of salinity and partial submergence as encountered during saline water flooding by looking into expression profile of DEGs and uniquely expressed genes.

ORGANISM(S): Oryza sativa

PROVIDER: GSE124618 | GEO | 2021/06/30

REPOSITORIES: GEO

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Preformed aerenchyma determines the differential tolerance response under partial submergence imposed by fresh and saline water flooding in rice

Project description:Preformed aerenchyma determines the differential tolerance response under partial submergence imposed by fresh and saline water flooding in rice

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Transcription profiling of 4-week old Arabidopsis plants grown in soil flooded to the soil surface (root flooding) or completely submerged under 6 cm of water (submergence)

Project description:4-week old Arabidopsis plants grown in soil were flooded to the soil surface (root flooding) or completely submerged under 6 cm of water (submergence). Samples are collected at the time specified.

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Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize

Project description:Maize is highly sensitive to short term flooding and submergence. We aimed to discover genetic variation for submergence tolerance in maize and elucidate the genetic basis of submergence tolerance through transcriptional profiling of contrasting genotypes. A diverse set of maize nested association mapping (NAM) founder lines were screened, and two highly tolerant (Mo18W and M162W) and sensitive (B97 and B73) genotypes were identified. Transcriptome analysis was performed on these inbreds to provide genome level insights into the molecular responses to submergence.

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The molecular response of two Brassica napus cultivars to submergence

Project description:Heavy rainfall causes flooding of natural ecosystems as well as farmland, negatively affecting crop performance and yield. While the response of the wild model organism Arabidopsis thaliana to such stress conditions is well understood, we hardly know anything about the response of its relative, the important oil crop plant Brassica napus. Here, we analyzed the molecular response of leaves of rapeseed seedlings to full submergence under illumination. RNAseq experiments revealed a strong carbon starvation response under submergence, but no indication for a low-oxygen response. We used two cultivars in this study, one Asian flooding-tolerant cultivar and one European hybrid cultivar, but those genotypes did not show strong differences in their responses to submergence.

2020-10-28 | GSE140828 | GEO

Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize

2015-01-01 | E-GEOD-63429 | biostudies-arrayexpress

Study of comparative proteomics reveals the molecular mechanisms underlying the flooding tolerance of Syzygium cumini against long-term partial submergence.

Project description:Proteome profiling contributes a better understanding of physiological and biochemical readjustment of Syzygium cumini seedlings after prolonged partial submergence. After 100 days flooding treatment, S. cumini has formed a new level of physiological balance in the present of well-developed adventitious roots. Comparative proteome analysis can illuminate the biological process involved in this maintenance mechanisms of new balance.

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Comparative Transcriptional Profiling of Two Rice Genotypes, FR13A and Goda Heenati, Under Submergence Stress

Project description:Most rice (Oryza sativa L.) cultivars die within several days of complete submergence, but some indica cultivars, such as FR13A, can survive up to 2 weeks of complete submergence. In FR13A, a major quantitative trait locus (QTL), named Sub1, provides mature plants with submergence tolerance. However, the Sub1 locus can not confer flooding tolerance during germination to FR13A. Another indica cultivar, Goda Heenati, shows both tolerance to flooding during germination and submergence in mature plants. It was once reported that submergence tolerance in FR13A and Goda Heenati cultivars was controlled by their respective genetic locus. These evidences indicate that tolerance to submergence in these two cultivars may involve differential mechanisms. To gain insight into their putatively differential responses to submergence stress, the Agilent rice genome 4×44 K oligonucleotide microarray was used to explore the transcriptome of FR13A and Goda Heenati under control and submergence-stressed conditions. Two-way ANOVA analysis with Benjamini-Hochberg false discovery rate demonstrated that at an overall P＜0.01 level, 2810, 8207, and 4 probes were significantly regulated for genotype, treatment, and genotype×treatment interaction, respectively. To identify statistically significant differentially expressed genes, a combined criterion of 2-fold or more change and unpaired t-test P value < 0.01 was uesd for both FR13A and Goda Heenati. A total of 504 probes were up-regulated and 592 probes were down-regulated in FR13A under submergence stress. In Goda Heenati, 998 probes were induced and 1186 probes were suppressed by submergence treatment.

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Transcriptome profiling of contrasting rice genotypes in response to submergence during seed germination

Project description:This transcriptome experiment identified a core set of genes differentially regulated under submergence between tolerant and sensitive rice genotypes. This differential modulation of gene expressions could contribute to the level of flooding tolerance in diverse rice genotypes. Rare allele-specific gene regulations and genotype-specific adaptive mechanisms could further promote the submergence tolerance in those genotypes with extremely adaptive phenotype.

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Root transcript profiles of two Rorippa (Brassicaceae) species and their F1 hybrid after complete submergence

Project description:Complete submergence represses photosynthesis and aerobic respiration causing rapid mortality in most terrestrial plants, but some species have evolved traits allowing them to survive prolonged flooding. Here, we studied the response to submergence of two species and their F1 hybrid in the genus Rorippa, which is related to the model Arabidopsis. We showed that these species have high tolerance to complete, deep submergence, but R. sylvestris survived longer than R. amphibia and the F1 hybrid. While the former restricted growth upon submergence, the latter two genotypes showed induced stem and petiole elongation and had higher aerenchyma contents, indicative of a low oxygen escape strategy. Arabidopsis GeneChip microarrays were used for whole-genome transcript profiling of roots of young plants exposed to air or a 24-h submergence treatment, using a probe mask based on hybridisation of genomic DNA of both species to the arrays. The induction by the submergence treatment of genes involved in glycolysis and fermentation and repression of many energy consuming pathways was similar to the response to low oxygen of Arabidopsis and rice. Notably, sucrose synthases, glycolysis and fermentation genes were more strongly induced in the less tolerant R. amphibia than in R. sylvestris, which might indicate faster carbohydrate consumption of the former, while some genes involved in hydrogen peroxide scavenging were strongly and specifically induced in the latter. F1 hybrids showed a generally weaker response to submergence and an additive mode of gene action, which did not change by the submergence treatment. Keywords: stress response and a comparison of genotypes

2009-12-01 | GSE13641 | GEO

The flooding resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in rice seedlings established underwater

Project description:Little is known of the consequences of genetic pyramiding of abiotic stress tolerance loci in crops. In rice (Oryza sativa L.), ANAEROBIC GERMINATION1 (AG1) encodes TREHALOSE 6-PHOSPHATE PHOSPHATASE 7 (OsTPP7) that enhances mobilization of endosperm reserves to the embryo, promoting formation of a highly elongated hollow coleoptile in seeds sown directly into shallow paddies. This trait reduces labor costs and herbicide use. SUBMERGENCE1 (SUB1) includes the ethylene-responsive transcription factor SUB1A that confers tolerance to complete submergence by dampening shoot elongation of vegetative-phase plants and enhancing regrowth upon desubmergence. As OsTPP7 and SUB1A-1 mRNAs simultaneously accumulate in shoots, we evaluated the independent contribution and interactions between these loci in rice seeded under complete submergence until the four-leaf stage (14 d). Evaluating growth, carbohydrates, and the transcriptome of shoot tissue of four near-isogenic genotypes uncovered independent and interacting effects including: (a) early enhanced coleoptile elongation by IR64(AG1); (b) precocious transition to phototrophy followed by limited elongation by IR64(SUB1); and (c) delayed phototrophy by IR64(AG1, SUB1). mRNA-sequencing highlighted time-dependent and genotype-specific regulation of mRNAs associated with energy sensing, carbohydrate catabolism, photomorphogenesis, elongation, and defense responses. Although SUB1A did not antagonize AG1 in direct seeding, seedling establishment could be negatively impacted if submergence escape does not occur before the transition to photoautotrophy, due to antithetical regulation of carbohydrate catabolism by AG1 and SUB1.

2020-07-05 | GSE136885 | GEO

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