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Comparative transcriptomics and co-expression networks reveal tissue- and genotype-specific responses to reproductive-stage drought stress in rice (Oryza sativa L.)

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Oryza sativa

PROVIDER: GSE145870 | GEO | 2020/02/25

REPOSITORIES: GEO

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Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of qDTYs to Reproductive-Stage Drought Stress in Rice (Oryza sativa L.).

Project description:Rice (Oryza sativa L.) is more sensitive to drought stress than other cereals. To dissect molecular mechanisms underlying drought-tolerant yield in rice, we applied differential expression and co-expression network approaches to transcriptomes from flag-leaf and emerging panicle tissues of a drought-tolerant yield introgression line, DTY-IL, and the recurrent parent Swarna, under moderate reproductive-stage drought stress. Protein turnover and efficient reactive oxygen species scavenging were found to be the driving factors in both tissues. In the flag-leaf, the responses further included maintenance of photosynthesis and cell wall reorganization, while in the panicle biosynthesis of secondary metabolites was found to play additional roles. Hub genes of importance in differential drought responses included an expansin in the flag-leaf and two peroxidases in the panicle. Overlaying differential expression data with allelic variation in DTY-IL quantitative trait loci allowed for the prioritization of candidate genes. They included a differentially regulated auxin-responsive protein, with DTY-IL-specific amino acid changes in conserved domains, as well as a protein kinase with a DTY-IL-specific frameshift in the C-terminal region. The approach highlights how the integration of differential expression and allelic variation can aid in the discovery of mechanism and putative causal contribution underlying quantitative trait loci for drought-tolerant yield.

| S-EPMC7650634 | biostudies-literature

Comparative transcriptomics and co-expression networks reveal tissue- and genotype-specific responses to reproductive-stage drought stress in rice (Oryza sativa L.) [panicle]

Project description:Purpose: The goal of the study is to compare the transcriptomic differences of the panicle tissue at the reproductive-stage of the Introgression Line (IR 96321-1447-165-B-3-1-2), which is drought-tolerant, to Swarna (recipient parent), which is drought-sensitive.

2020-02-25 | GSE145869 | GEO

Comparative transcriptomics and co-expression networks reveal tissue- and genotype-specific responses to reproductive-stage drought stress in rice (Oryza sativa L.) [flag-leaf]

Project description:Purpose: The goal of the study is to compare the transcriptomic differences of the flag-leaf tissue at the reproductive-stage of the Introgression Line (IR 96321-1447-165-B-3-1-2), which is drought-tolerant, to Swarna (recipient parent), which is drought-sensitive.

2020-02-25 | GSE145868 | GEO

Incorporating Drought and Submergence Tolerance QTL in Rice (Oryza sativa L.)-The Effects under Reproductive Stage Drought and Vegetative Stage Submergence Stresses.

Project description:Drought and submergence have been the major constraint in rice production. The present study was conducted to develop high-yielding rice lines with tolerance to drought and submergence by introgressing Sub1 into a rice line with drought yield QTL (qDTY; QTL = quantitative trait loci) viz. qDTY3.1 and qDTY12.1 using marker-assisted breeding. We report here the effect of different combinations of Sub1 and qDTY on morpho-physiological, agronomical traits and yield under reproductive stage drought stress (RS) and non-stress (NS) conditions. Lines with outstanding performance in RS and NS trials were also evaluated in vegetative stage submergence stress (VS) trial to assess the tolerance level. The QTL class analysis revealed Sub1 + qDTY3.1 as the best QTL combination affecting the measured traits in RS trial followed by Sub1 + qDTY12.1. The effects of single Sub1, qDTY3.1 and qDTY12.1 were not as superior as when the QTLs are combined, suggesting the positive interaction of Sub1 and qDTY. Best performing lines selected from the RS and NS trials recorded yield advantage up to 4453.69 kg ha-1 and 6954 kg ha-1 over the parents, respectively. The lines were also found having great tolerance to submergence ranging from 80% to 100%, contributed by a lower percentage of shoot elongation and reduction of chlorophyll content after 14 days of VS. These lines could provide yield sustainability to farmers in regions impacted with drought and submergence while serving as important genetic materials for future breeding programs.

| S-EPMC7912027 | biostudies-literature

Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.).

Project description:BACKGROUND:The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS:The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5-20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance. CONCLUSION:The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.

| S-EPMC5436998 | biostudies-literature

Epigenetic responses to drought stress in rice (Oryza sativa L.).

Project description:Cytosine methylation polymorphism plays a key role in gene regulation, mainly in expression of genes in crop plants. The differential expression of cytosine methylation over drought stress response was analyzed in rice using drought susceptible but agronomically superior lines IR 20 and CO 43, and drought tolerant genotypes PL and PMK 3 and their F1 hybrids. The parents and hybrids were subjected to two moisture regimes viz., one under drought condition and another under control condition. The cytosine methylation polymorphism in genomic DNA was quantified under both the conditions at the reproductive stage of the plant using the Methylation Sensitive Amplified Polymorphism (MSAP) technique devised by Xiong et al. (261:439-446, 1999). The results depicted that under drought condition, hyper-methylation was predominant in the drought susceptible genotypes while drought tolerant genotypes presented hypo-methylation behavior. While imposing drought, spikelet sterility per cent was positively correlated to percentage of methylation whereas, panicle length, number of seed per panicle, panicle weight, 100 seed weight, and yield/plant were negatively correlated indicating the role of epigenetic regulation in yield attributing traits in response to drought. Thus, methylation can be considered as an important epigenetic regulatory mechanism in rice plants to adapt drought situation. From this study, we speculate that the hyper- methylation may be an indicator of drought susceptibility and the hypo-methylation for drought tolerance and this methylation polymorphism can be effectively used in drought screening program.

| S-EPMC3715639 | biostudies-literature

Root attributes affecting water uptake of rice (Oryza sativa) under drought.

Project description:Lowland rice roots have a unique physiological response to drought because of their adaptation to flooded soil. Rice root attributes that facilitate growth under flooded conditions may affect rice response to drought, but the relative roles of root structural and functional characteristics for water uptake under drought in rice are not known. Morphological, anatomical, biochemical, and molecular attributes of soil-grown rice roots were measured to investigate the genotypic variability and genotype×environment interactions of water uptake under variable soil water regimes. Drought-resistant genotypes had the lowest night-time bleeding rates of sap from the root system in the field. Diurnal fluctuation predominated as the strongest source of variation for bleeding rates in the field and root hydraulic conductivity (Lpr) in the greenhouse, and was related to expression trends of various PIP and TIP aquaporins. Root anatomy was generally more responsive to drought treatments in drought-resistant genotypes. Suberization and compaction of sclerenchyma layer cells decreased under drought, whereas suberization of the endodermis increased, suggesting differential roles of these two cell layers for the retention of oxygen under flooded conditions (sclerenchyma layer) and retention of water under drought (endodermis). The results of this study point to the genetic variability in responsiveness to drought of rice roots in terms of morphology, anatomy, and function.

| S-EPMC3427995 | biostudies-literature

Comparative transcriptomics and co-expression networks reveal tissue- and genotype-specific responses to reproductive-stage drought stress in rice (Oryza sativa L.)

Project description:Comparative transcriptomics and co-expression networks reveal tissue- and genotype-specific responses to reproductive-stage drought stress in rice (Oryza sativa L.)

| PRJNA608548 | ENA

Comparative transcriptomics and co-expression networks reveal tissue- and genotype-specific responses to reproductive-stage drought stress in rice (Oryza sativa L.) [panicle]

Project description:Comparative transcriptomics and co-expression networks reveal tissue- and genotype-specific responses to reproductive-stage drought stress in rice (Oryza sativa L.) [panicle]

| PRJNA608552 | ENA

Effects of Salinity Stress at Reproductive Growth Stage on Rice (Oryza sativa L.) Composition, Starch Structure, and Physicochemical Properties

Project description:This study aimed to investigate the changes in polished rice composition, starch structure, and physicochemical properties from three rice cultivars treated with medium and high salinity stress at the reproductive growth stage. The results showed that salt stress led to poor milling and appearance quality, higher total starch content, protein content, higher proportion of the medium, and long chains of amylopectin, as well as gelatinization temperature (GT) but lower amylose content and lower proportion of the short chain of amylopectin. Compared with salt-sensitive cultivars, the salt-tolerant cultivars exhibited lower GT and gelatinization enthalpy, better pasting properties, and more stable crystal structure; therefore, their eating and cooking quality (ECQ) was less affected. The above results imply that salt stress at the reproductive growth stage can degrade ECQ and can slightly increase the pasting property of starch from salt-tolerant rice cultivar.

| S-EPMC9277441 | biostudies-literature

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