Seeds use environmental cues to sense the seasons and their surroundings to initiate the life cycle of the plant. The dormancy cycling underlying this process is extensively described, but the molecular mechanism is largely unknown. To address this we selected a range of representative genes from published array experiments in the laboratory, and investigated their expression patterns in seeds of Arabidopsis ecotypes with contrasting life cycles over an annual dormancy cycle in the field. We show how mechanisms identified in the laboratory are coordinated in response to the soil environment to determine the dormancy cycles that result in winter and summer annual phenotypes. Our results are consistent with a seed-specific response to seasonal temperature patterns (temporal sensing) involving the gene DELAY OF GERMINATION 1 (DOG1) that indicates the correct season, and concurrent temporally driven co-opted mechanisms that sense spatial signals, i.e. nitrate, via CBL-INTERACTING PROTEIN KINASE 23 (CIPK23) phosphorylation of the NITRATE TRANSPORTER 1 (NRT1.1), and light, via PHYTOCHROME A (PHYA). In both ecotypes studied, when all three genes have low expression there is enhanced GIBBERELLIN 3 BETA-HYDROXYLASE 1 (GA3ox1) expression, exhumed seeds have the potential to germinate in the laboratory, and the initiation of seedling emergence occurs following soil disturbance (exposure to light) in the field. Unlike DOG1, the expression of MOTHER of FLOWERING TIME (MFT) has an opposite thermal response in seeds of the two ecotypes, indicating a role in determining their different dormancy cycling phenotypes.
SUMMARYLegume research and cultivar development are important for sustainable food production, especially of high-protein seed. Thanks to the development of deep-sequencing technologies, crop species have been taken to the front line, even without completion of their genome sequences. Black-eyed pea (Vigna unguiculata) is a legume species widely grown in semi-arid regions, which has high potential to provide stable seed protein production in a broad range of environments, including drought conditions. The black-eyed pea reference genotype has been used to generate a gene expression atlas of the major plant tissues (i.e. leaf, root, stem, flower, pod and seed), with a developmental time series for pods and seeds. From these various organs, 27 cDNA libraries were generated and sequenced, resulting in more than one billion reads. Following filtering, these reads were de novo assembled into 36 529 transcript sequences that were annotated and quantified across the different tissues. A set of 24 866 unique transcript sequences, called Unigenes, was identified. All the information related to transcript identification, annotation and quantification were stored into a gene expression atlas webserver (http://vugea.noble.org), providing a user-friendly interface and necessary tools to analyse transcript expression in black-eyed pea organs and to compare data with other legume species. Using this gene expression atlas, we inferred details of molecular processes that are active during seed development, and identified key putative regulators of seed maturation. Additionally, we found evidence for conservation of regulatory mechanisms involving miRNA in plant tissues subjected to drought and seeds undergoing desiccation.
Background and AimsSeed yield and dormancy status are key components of species fitness that are influenced by the maternal environment, in particular temperature. Responses to environmental conditions can differ between ecotypes of the same species. Therefore, to investigate the effect of maternal environment on seed production, this study compared two contrasting Arabidopsis thaliana ecotypes, Cape Verdi Isle (Cvi) and Burren (Bur). Cvi is adapted to a hot dry climate and Bur to a cool damp climate, and they exhibit winter and summer annual phenotypes, respectively.MethodsBur and Cvi plants were grown in reciprocal controlled environments that simulated their native environments. Reproductive development, seed production and subsequent germination behaviour were investigated. Measurements included: pollen viability, the development of floral structure, and germination at 10 and 25 °C in the light to determine dormancy status. Floral development was further investigated by applying gibberellins (GAs) to alter the pistil:stamen ratio.Key ResultsTemperature during seed development determined seed dormancy status. In addition, seed yield was greatly reduced by higher temperature, especially in Bur (>90 %) compared with Cvi (approx. 50 %). The reproductive organs (i.e. stamens) of Bur plants were very sensitive to high temperature during early flowering. Viability of pollen was unaffected, but limited filament extension relative to that of the pistils resulted in failure to pollinate. Thus GA applied to flowers to enhance filament extension largely overcame the effect of high temperature on yield.ConclusionsHigh temperature in the maternal environment reduced dormancy and negatively affected the final seed yield of both ecotypes; however, the extent of these responses differed, demonstrating natural variation. Reduced seed yield in Bur resulted from altered floral development not reduced pollen viability. Future higher temperatures will impact on seed performance, but the consequences may differ significantly between ecotypes of the same species.
BackgroundTransposable elements constitute an important part of the genome and are essential in adaptive mechanisms. Transposition events associated with phenotypic changes occur naturally or are induced in insertional mutant populations. Transposon mutagenesis results in multiple random insertions and recovery of most/all the insertions is critical for forward genetics study. Using genome next-generation sequencing data and appropriate bioinformatics tool, it is plausible to accurately identify transposon insertion sites, which could provide candidate causal mutations for desired phenotypes for further functional validation.ResultsWe developed a novel bioinformatics tool, ITIS (Identification of Transposon Insertion Sites), for localizing transposon insertion sites within a genome. It takes next-generation genome re-sequencing data (NGS data), transposon sequence, and reference genome sequence as input, and generates a list of highly reliable candidate insertion sites as well as zygosity information of each insertion. Using a simulated dataset and a case study based on an insertional mutant line from Medicago truncatula, we showed that ITIS performed better in terms of sensitivity and specificity than other similar algorithms such as RelocaTE, RetroSeq, TEMP and TIF. With the case study data, we demonstrated the efficiency of ITIS by validating the presence and zygosity of predicted insertion sites of the Tnt1 transposon within a complex plant system, M. truncatula.ConclusionThis study showed that ITIS is a robust and powerful tool for forward genetic studies in identifying transposable element insertions causing phenotypes. ITIS is suitable in various systems such as cell culture, bacteria, yeast, insect, mammal and plant.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0507-2) contains supplementary material, which is available to authorized users.
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