BACKGROUND: The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize. RESULTS: The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes. CONCLUSIONS: The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website ( https://soykb.org/SoybeanAlleleCatalogTool/ ), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website ( https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana ). Researchers can use this tool to connect variant alleles of genes with meta-information of species.
- MeSH
- alely * MeSH
- Arabidopsis * genetika MeSH
- data mining * metody MeSH
- datové soubory jako téma * MeSH
- frekvence genu MeSH
- genotyp MeSH
- Glycine max * genetika MeSH
- internet * MeSH
- kukuřice setá * genetika MeSH
- metadata MeSH
- mutace MeSH
- pigmentace genetika MeSH
- rostlinné geny genetika MeSH
- software * MeSH
- substituce aminokyselin MeSH
- vegetační klid genetika MeSH
- vizualizace dat MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: A water-impermeable testa acts as a barrier to a seed's imbibition, thereby imposing dormancy. The physical and functional properties of the macrosclereids are thought to be critical determinants of dormancy; however, the mechanisms underlying the maintenance of and release from dormancy in pea are not well understood. METHODS: Seeds of six pea accessions of contrasting dormancy type were tested for their ability to imbibe and the permeability of their testa was evaluated. Release from dormancy was monitored following temperature oscillation, lipid removal and drying. Histochemical and microscopic approaches were used to characterize the structure of the testa. KEY RESULTS: The strophiole was identified as representing the major site for the entry of water into non-dormant seeds, while water entry into dormant seeds was distributed rather than localized. The major barrier for water uptake in dormant seeds was the upper section of the macrosclereids, referred to as the 'light line'. Dormancy could be released by thermocycling, dehydration or chloroform treatment. Assays based on either periodic acid or ruthenium red were used to visualize penetration through the testa. Lipids were detected within a subcuticular waxy layer in both dormant and non-dormant seeds. The waxy layer and the light line both formed at the same time as the establishment of secondary cell walls at the tip of the macrosclereids. CONCLUSIONS: The light line was identified as the major barrier to water penetration in dormant seeds. Its outer border abuts a waxy subcuticular layer, which is consistent with the suggestion that the light line represents the interface between two distinct environments - the waxy subcuticular layer and the cellulose-rich secondary cell wall. The mechanistic basis of dormancy break includes changes in the testa's lipid layer, along with the mechanical disruption induced by oscillation in temperature and by a decreased moisture content of the embryo.
- MeSH
- hrách setý * MeSH
- klíčení * MeSH
- semena rostlinná MeSH
- teplota MeSH
- vegetační klid MeSH
- voda MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Seed coats of six pea genotypes contrasting in dormancy were studied by laser desorption/ionization mass spectrometry (LDI-MS). Multivariate statistical analysis discriminated dormant and non-dormant seeds in mature dry state. Separation between dormant and non-dormant types was observed despite important markers of particular dormant genotypes differ from each other. Normalized signals of long-chain hydroxylated fatty acids (HLFA) in dormant JI64 genotype seed coats were significantly higher than in other genotypes. These compounds seem to be important markers likely influencing JI64 seed imbibition and germination. HLFA importance was supported by study of recombinant inbred lines (JI64xJI92) contrasting in dormancy but similar in other seed properties. Furthemore HLFA distribution in seed coat was studied by mass spectrometry imaging. HLFA contents in strophiole and hilum are significantly lower compared to other parts indicating their role in water uptake. Results from LDI-MS experiments are useful in understanding (physical) dormancy (first phases of germination) mechanism and properties related to food processing technologies (e.g., seed treatment by cooking).
Seed germination traits in alpine grasslands are poorly understood, despite the sensitivity of these communities to climate change. We hypothesise that germination traits predict species occurrence along the alpine-subalpine elevation gradient. Phylogenetic comparative analyses were performed using fresh seeds of 22 species from alpine and subalpine grasslands (1600-2400 m) of the Cantabrian Mountains, Spain (43° N, 5° W). Laboratory experiments were conducted to characterise germinability, optimum germination temperature and effect of cold and warm stratification on dormancy breaking. Variability in these traits was reduced by phylogenetic principal component analysis (phyl.PCA). Phylogenetic generalised least squares regression (PGLS) was used to fit a model in which species average elevation was predicted from their position on the PCA axes. Most subalpine species germinated in snow-like conditions, whereas most alpine species needed accumulation of warm temperatures. Phylogenetic signal was low. PCA1 ordered species according to overall germinability, whilst PCA2 ordered them according to preference for warm or cold germination. PCA2 significantly predicted species occurrence in the alpine-subalpine gradient, as higher elevation species tended to have warmer germination preferences. Our results show that germination traits in high-mountain grasslands are closely linked to the alpine-subalpine gradient. Alpine species, especially those from stripped and wind-edge communities, prefer warmer germination niches, suggesting that summer emergence prevents frost damage during seedling establishment. In contrast, alpine snowfield and subalpine grassland plants have cold germination niches, indicating that winter emergence may occur under snow to avoid drought stress.
- MeSH
- fylogeneze MeSH
- klíčení * MeSH
- klimatické změny MeSH
- nízká teplota MeSH
- období sucha MeSH
- pastviny MeSH
- roční období MeSH
- semena rostlinná genetika fyziologie MeSH
- semenáček genetika fyziologie MeSH
- teplota MeSH
- tundra MeSH
- vegetační klid MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
- Geografické názvy
- Španělsko MeSH
The precocious germination of cereal grains before harvest, also known as pre-harvest sprouting, is an important source of yield and quality loss in cereal production. Pre-harvest sprouting is a complex grain defect and is becoming an increasing challenge due to changing climate patterns. Resistance to sprouting is multi-genic, although a significant proportion of the sprouting variation in modern wheat cultivars is controlled by a few major quantitative trait loci, including Phs-A1 in chromosome arm 4AL. Despite its importance, little is known about the physiological basis and the gene(s) underlying this important locus. In this study, we characterized Phs-A1 and show that it confers resistance to sprouting damage by affecting the rate of dormancy loss during dry seed after-ripening. We show Phs-A1 to be effective even when seeds develop at low temperature (13 °C). Comparative analysis of syntenic Phs-A1 intervals in wheat and Brachypodium uncovered ten orthologous genes, including the Plasma Membrane 19 genes (PM19-A1 and PM19-A2) previously proposed as the main candidates for this locus. However, high-resolution fine-mapping in two bi-parental UK mapping populations delimited Phs-A1 to an interval 0.3 cM distal to the PM19 genes. This study suggests the possibility that more than one causal gene underlies this major pre-harvest sprouting locus. The information and resources reported in this study will help test this hypothesis across a wider set of germplasm and will be of importance for breeding more sprouting resilient wheat varieties.
- MeSH
- chromozomy rostlin genetika fyziologie MeSH
- genotypizační techniky MeSH
- jednonukleotidový polymorfismus genetika MeSH
- klíčení genetika fyziologie MeSH
- lokus kvantitativního znaku genetika fyziologie MeSH
- mapování chromozomů MeSH
- pšenice genetika růst a vývoj MeSH
- rostlinné geny genetika fyziologie MeSH
- vegetační klid genetika fyziologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Seed germination is an important life-cycle transition because it determines subsequent plant survival and reproductive success. To detect optimal spatiotemporal conditions for germination, seeds act as sophisticated environmental sensors integrating information such as ambient temperature. Here we show that the delay of germination 1 (DOG1) gene, known for providing dormancy adaptation to distinct environments, determines the optimal temperature for seed germination. By reciprocal gene-swapping experiments between Brassicaceae species we show that the DOG1-mediated dormancy mechanism is conserved. Biomechanical analyses show that this mechanism regulates the material properties of the endosperm, a seed tissue layer acting as germination barrier to control coat dormancy. We found that DOG1 inhibits the expression of gibberellin (GA)-regulated genes encoding cell-wall remodeling proteins in a temperature-dependent manner. Furthermore we demonstrate that DOG1 causes temperature-dependent alterations in the seed GA metabolism. These alterations in hormone metabolism are brought about by the temperature-dependent differential expression of genes encoding key enzymes of the GA biosynthetic pathway. These effects of DOG1 lead to a temperature-dependent control of endosperm weakening and determine the optimal temperature for germination. The conserved DOG1-mediated coat-dormancy mechanism provides a highly adaptable temperature-sensing mechanism to control the timing of germination.
- MeSH
- Arabidopsis genetika růst a vývoj fyziologie MeSH
- biomechanika MeSH
- diploidie MeSH
- geneticky modifikované rostliny MeSH
- gibereliny metabolismus MeSH
- klíčení genetika fyziologie MeSH
- konzervovaná sekvence MeSH
- Lepidium sativum genetika růst a vývoj fyziologie MeSH
- molekulární sekvence - údaje MeSH
- mutace MeSH
- proteiny huseníčku genetika MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné geny MeSH
- semena rostlinná růst a vývoj MeSH
- teplota MeSH
- vegetační klid genetika fyziologie MeSH
- vývojová regulace genové exprese MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
