Stigmatic receptivity determines the seed set in Indian mustard, rice and wheat crops.
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ABSTRACT:
SUBMITTER: Gupta R
PROVIDER: S-EPMC4802787 | biostudies-other | 2015 Sep-Oct
REPOSITORIES: biostudies-other
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Project description:In this study, time dependent (4 h to 96 h) transcriptome changes in roots and shoots of Brassica juncea were analyzed under arsenate (AsV) stress by using Agilent platform. A total of 1285 genes showed significant change in expression pattern upon arsenate (AsV) exposure. The genes belonged to various signaling pathways including hormones (jasmonate, abscisic acid (ABA), auxin and ethylene) and kinases. Significant effects were also noticed on genes of sulfur, nitrogen, CHO, and lipid metabolisms along with photosynthesis. These studies indicated interconnections among sulfur metabolism, jasmonate and kinase signaling pathways. Transcriptome results and biochemical analyses highlight that signaling and metabolic pathways work in a dynamic coordination to perceive and respond to the stress.
2015-03-04 | GSE66464 | GEO
Project description:In this study, time dependent (4 h to 96 h) transcriptome changes in roots and shoots of Brassica juncea were analyzed under arsenate (AsV) stress by using Agilent platform. A total of 1285 genes showed significant change in expression pattern upon arsenate (AsV) exposure. The genes belonged to various signaling pathways including hormones (jasmonate, abscisic acid (ABA), auxin and ethylene) and kinases. Significant effects were also noticed on genes of sulfur, nitrogen, CHO, and lipid metabolisms along with photosynthesis. These studies indicated interconnections among sulfur metabolism, jasmonate and kinase signaling pathways. Transcriptome results and biochemical analyses highlight that signaling and metabolic pathways work in a dynamic coordination to perceive and respond to the stress. A set of 53939 sequences, which include EST and nucleotide sequences of Brassica sp., were downloaded from GenBank. These sequences were subjected to clustering and analyzed using CAP3/tgicl program and other in-house tools. A set of 26881 non-redundant sequences was created, which was used for probe design. This set included 1720 Brassica juncea, 15259 Brassica napus and 5075 Brassica rapa sequences; and 6456 from other species. Probes were designed for the non-redundant sequences using Agilent eArray tool. Best probe composition algorithm with the option to design multiple probes for each sequence was the main criteria used for the probe design. AgilentM-bM-^@M-^Ys 4x44 array was selected to print the oligos. A set of positive and negative controls were also added on to the microarray chip. A set of replicate probes were also added for calculating the intra-array reproducibility. The quantity and purity of the RNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively. Each of the total RNA preparations was individually assessed for RNA quality based on the 28S/18S ratio and RIN measured on an Agilent 2100 Bioanalyzer system using the RNA 6000 Nano LabChip Kit .With the use of AgilentM-bM-^@M-^Ys 1-Color Quick Amp Labeling Kit, 500 ng of high quality total RNA was denatured in the presence of a T7 promoter primer and a 1-Color RNA Spike-In Kit. Reverse transcriptase was used to reverse-transcribe the mRNA. cDNA was used as a template for in vitro transcription where a T7 RNA polymerase simultaneously amplified target material and incorporated cyanine 3-labeled CTP. Labeled cRNA was purified using spin columns from the Qiagen RNeasy Mini Kit and the quantity and quality of the cRNA was determined by Nanodrop ND-1000 UV-VIS spectrophotometer. With the use of AgilentM-bM-^@M-^Ys Gene Expression Hybridization Kit, 1.65 M-BM-5g of cyanine 3-labeled linearly amplified cRNA was added to a hybridization cocktail and then fragmented. The hybridization cocktail was then dispensed into the wells of gasket slides on top of which a Brassica 4x44K Gene Expression Microarray was placed. This microarray M-bM-^@M-^\sandwichM-bM-^@M-^] was then sealed in a hybridization chamber. The microarrays were hybridized at 65M-BM-0C rotating at 10 RPMs for 17 hours. Slides were washed in AgilentM-bM-^@M-^Ys Gene Expression Wash Buffers according to manufacturer specifications. The microarrays were scanned on the Agilent Microarray Scanner. Scanner data extraction and analysis was performed using Agilent Technologies Feature Extraction software version 10.7.3.1.Microarray data quality was evaluated by reviewing ten standard QC metrics generated by the Feature Extraction Software [Consult the Agilent Technologies Feature Extraction Software version 10.7.3.1 reference guide for a full explanation of the QC metrics]. To determine if there was a large hybridization, staining, or wash artifacts, a visual examination of each array was performed by loading the array image into Feature Extraction Software. Microarrays were determined to be free of any large artifacts (M-bM-^IM-% 10% of total surface area) that could have affected the quality of the data.
2015-03-04 | E-GEOD-66464 | biostudies-arrayexpress
Project description:Hybrid vigour may help overcome the negative effects of climate change in rice. A popular rice hybrid (IR75217H), a heat-tolerant check (N22), and a mega-variety (IR64) were tested for tolerance of seed-set and grain quality to high-temperature stress at anthesis at ambient and elevated [CO(2)]. Under an ambient air temperature of 29 °C (tissue temperature 28.3 °C), elevated [CO(2)] increased vegetative and reproductive growth, including seed yield in all three genotypes. Seed-set was reduced by high temperature in all three genotypes, with the hybrid and IR64 equally affected and twice as sensitive as the tolerant cultivar N22. No interaction occurred between temperature and [CO(2)] for seed-set. The hybrid had significantly more anthesed spikelets at all temperatures than IR64 and at 29 °C this resulted in a large yield advantage. At 35 °C (tissue temperature 32.9 °C) the hybrid had a higher seed yield than IR64 due to the higher spikelet number, but at 38 °C (tissue temperature 34-35 °C) there was no yield advantage. Grain gel consistency in the hybrid and IR64 was reduced by high temperatures only at elevated [CO(2)], while the percentage of broken grains increased from 10% at 29 °C to 35% at 38 °C in the hybrid. It is concluded that seed-set of hybrids is susceptible to short episodes of high temperature during anthesis, but that at intermediate tissue temperatures of 32.9 °C higher spikelet number (yield potential) of the hybrid can compensate to some extent. If the heat tolerance from N22 or other tolerant donors could be transferred into hybrids, yield could be maintained under the higher temperatures predicted with climate change.
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Project description:Domesticated grain crops evolved from wild plants under human cultivation, losing natural dispersal mechanisms to become dependent upon humans, and showing changes in a suite of other traits, including increasing seed size. There is tendency for seed enlargement during domestication to be viewed as the result of deliberate selection for large seeds by early farmers. However, like some other domestication traits, large seeds may have evolved through natural selection from the activities of people as they gathered plants from the wild, or brought them into cultivation in anthropogenic settings. Alternatively, larger seeds could have arisen via pleiotropic effects or genetic linkage, without foresight from early farmers, and driven by selection that acted on other organs or favored larger plants. We have separated these unconscious selection effects on seed enlargement from those of deliberate selection, by comparing the wild and domesticated forms of vegetable crops. Vegetables are propagated by planting seeds, cuttings, or tubers, but harvested for their edible leaves, stems, or roots, so that seed size is not a direct determinant of yield. We find that landrace varieties of seven vegetable crops have seeds that are 20% to 2.5-times larger than those of their closest wild relatives. These domestication effect sizes fall completely within the equivalent range of 14% to 15.2-times for grain crops, although domestication had a significantly larger overall effect in grain than vegetable crops. Seed enlargement in vegetable crops that are propagated vegetatively must arise from natural selection for larger seeds on the occasions when plants recruit from seed and are integrated into the crop gene pool, or via a genetic link to selection for larger plants or organs. If similar mechanisms operate across all species, then unconscious selection during domestication could have exerted stronger effects on the seed size of our staple crops than previously realized.
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Project description:Genetic diversity among 23 rice genotypes including wild species and cultivars of indica, japonica, aus and aromatic type was investigated using 165 genomewide core set microsatellite (SSR) markers. This genotypic characterization was undertaken to know the genetic similarity among the parental lines to be used in developing a set of chromosome segment substitution lines. In all, 253 alleles were identified using 77 polymorphic SSRs, and polymorphism information content ranged from 0.31 to 0.97 with a mean of 0.79. Cluster analysis grouped the genotypes into three clusters at a genetic similarity of 0.26-0.75. Wild accessions grouped together in cluster-I, indica cultivars formed cluster-II, and aromatic, japonica and aus types came under cluster-III. Principal component analysis also showed similar results. The genotypic data was analyzed using STRUCTURE, and genotypes were grouped into four populations. RM1018 on chromosome 4, RM8009 on chromosome 7, and RM273 on chromosome 12 amplified alleles specific to wild accessions. The information obtained from core set markers would help in selecting diverse parents including wild accessions and for tracking alleles in mapping or breeding populations.
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Project description:affy_seed_kinetic_wheat - affy_seed_kinetic_wheat - Study gene expression during the grain developmental -The aim of the study is to identify the genes that are differentially expressed during the grain development in wheat.-Study gene expression during the grain developmental Sample at 100 degree days, year 2004 and 2006 Sample at 200 degree days, year 2004 and 2006 Sample at 250 degree days, year 2004 and 2006 Sample at 300 degree days, year 2004 and 2006 Sample at 400 degree days, year 2004 and 2006 Keywords: time course
2010-05-01 | GSE16457 | GEO
Project description:BackgroundSeed germination is a complex physiological process during which mobilization of nutrient reserves happens. In different crops, this event might be mediated by different regulatory and metabolic pathways. Proteome profiling has been proved to be an efficient way that can help us to construct these pathways. However, no such studies have been performed in soybean germinating seeds up to date.ResultsProteome profiling was conducted through one-dimensional gel electrophoresis followed by liquid chromatography and tandem mass spectrometry strategy in the germinating seeds of soybean (glycine max). Comprehensive comparisons were also carried out between rice and soybean germinating seeds. 764 proteins belonging to 14 functional groups were identified and metabolism related proteins were the largest group. Deep analyses of the proteins and pathways showed that lipids were degraded through lipoxygenase dependent pathway and proteins were degraded through both protease and 26S proteosome system, and the lipoxygenase could also help to remove the reactive oxygen species during the rapid mobilization of reserves of soybean germinating seeds. The differences between rice and soybean germinating seeds proteome profiles indicate that each crop species has distinct mechanism for reserves mobilization during germination. Different reserves could be converted into starches before they are totally utilized during the germination in different crops seeds.ConclusionsThis study is the first comprehensive analysis of proteome profile in germinating soybean seeds to date. The data presented in this paper will improve our understanding of the physiological and biochemical status in the imbibed soybean seeds just prior to germination. Comparison of the protein profile with that of germinating rice seeds gives us new insights on mobilization of nutrient reserves during the germination of crops seeds.
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Project description:The long-term autonomous existence of man in extraterrestrial conditions is associated with the need to cultivate plants-the only affordable and effective means for both providing oxygen and CO2 utilization, and providing one of the most habitual and energetically valuable products: plant food. In this study, we analyzed the results of the space odyssey of wheat and compared the morphological features of parental grains harvested from soil grown wheat plants, the grains obtained from plants grown in a specialized device for plant cultivation-the "Lada" space greenhouses during space flight in the ISS, and the grains obtained from plants in the same device on Earth. The seeds obtained under various conditions were studied using scanning electron microscopy. We studied the mutual location of the surface layers of the kernel cover tissues, the structural features of the tube and cross cells of the fruit coat (pericarp), and the birsh hairs of the kernels. It was found that the grains obtained under wheat plants cultivation on board of the ISS in near space had some specific differences from the parental, original grains, and the grains obtained from plants grown in the "Lada" greenhouse in ground conditions. These changes were manifested in a shortening of the birsh hairs, and a change in the size and relative arrangement of the cells of the kernel coat. We suggest that such changes are a manifestation of the sensitivity of the cytoskeleton reorganization systems and water exchange to the influence of particular physical conditions of space flight (microgravity, increased doses of radiation, etc.). Thus, the revealed changes did not hinder the wheat grains production "from seed to seed", which allows the cultivation of this crop in stable life support systems in near earth orbit.
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