Gene expression studies of barley low tillering mutants
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PROVIDER: PRJNA1072126 | ENA |
REPOSITORIES: ENA
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Project description:Barley (Hordeum vulgare) uniculm2 (cul2) plants produce no tillers, while absent lower laterals (als), uniculm4 (cul4) and low number of tillers (lnt1) plants produce fewer tillers than wild-type barley plants. Gene expression was studied in comparison to wild-type cv. "Bowman" plants in embryo, crown, inflorescence and seedling tissue. Gene expression studies for uniculm2 (Okagaki et al., Funct Integr Genomics (2013) 13:33–41), absent lower laterals (Dabbert et al., Theor Appl Genet (2009) 118:1351–1360) and low number of tillers (Dabbert et al., Theor Appl Genet (2010) 121:705–715) plants have been previously published.
2025-02-01 | GSE254849 | GEO
Project description:The most effective method of micro-propagation for clonal replicates for switchgrass seed production is from the axillary buds of the lower nodes. We hypothesized that buds and nodes from low and high tillering lines from an inbred population will aid in identifying genes important for the different tillering habits of these plants. Since tiller number is directly correlated with biomass yields, identifying genes associated with high tillering trait will provide valuable biomarkers for marker-assisted selection and for QTL mapping of tillering trait in switchgrass. First-generation switchgrass inbred lines derived from selfing a parental genotype M-^QNL94 LYE 16x13M-^R, which was selected from the Oklahoma State University northern lowland breeding population in 2007 was used in this study. The NL94/298 inbred line produced fewer tillers than NL94/145. Stems of the high tillering line had 2-3 phytomers, while the low tillering line had 1-2 phytomers. Eight other inbred lines from this population that showed similar phenotypes as NL94/145 or NL94/298 and similar genotypes based on 380 genomic SSR marker profiles were selected for this study. Individual stems from these nine lines each for high and low tillering habit were harvested from field growing plants in the Agronomy field plots, Stillwater. Vegetative buds from first phytomer and node regions from second phytomer were cut out using a sharp scalpel under a dissection scope and immediately frozen in liquid nitrogen for transcriptomics analysis.
2014-01-14 | E-MTAB-1899 | biostudies-arrayexpress
Project description:Variation in shoot architecture, or tillering, is an important adaptive trait targeted during the domestication of crops. A well-known regulatory factor in shoot architecture is TEOSINTE BRANCHED 1 (TB1). TB1 and its orthologs have a conserved function in integrating environmental signals to regulate axillary branching, or tillering in cereals. The barley ortholog of TB1, VULGARE ROW-TYPE SIX 5 (VRS5) does not only regulate tillering, but is also involved in regulating row-type by inhibiting lateral spikelet development. These discoveries do mainly come from genetic studies, but how VRS5 regulates these processes on a molecular level remains largely unknown. By combining transcriptome analysis between vrs5 and WT at different developmental stages and DAP-sequencing to locate the genome-wide DNA binding sites of VRS5, we identified bona fide targets of VRS5. We found that VRS5 targets in particular abscisic acid related genes to inhibit tillering in a conserved way. Later, during inflorescence development row-type gene VRS1, and some known floral development genes, like MIKCc type MADS-box genes, are targeted. The study presented here offers a solid and crucial starting point for mutant analyses of a selection of bona fide targets to gain a deeper understanding of the VRS5 network and to enlighten its mode of action in shaping barley development.
2025-08-07 | GSE272367 | GEO
Project description:Variation in shoot architecture, or tillering, is an important adaptive trait targeted during the domestication of crops. A well-known regulatory factor in shoot architecture is TEOSINTE BRANCHED 1 (TB1). TB1 and its orthologs have a conserved function in integrating environmental signals to regulate axillary branching, or tillering in cereals. The barley ortholog of TB1, VULGARE ROW-TYPE SIX 5 (VRS5) does not only regulate tillering, but is also involved in regulating row-type by inhibiting lateral spikelet development. These discoveries do mainly come from genetic studies, but how VRS5 regulates these processes on a molecular level remains largely unknown. By combining transcriptome analysis between vrs5 and WT at different developmental stages and DAP-sequencing to locate the genome-wide DNA binding sites of VRS5, we identified bona fide targets of VRS5. We found that VRS5 targets in particular abscisic acid related genes to inhibit tillering in a conserved way. Later, during inflorescence development row-type gene VRS1, and some known floral development genes, like MIKCc type MADS-box genes, are targeted. The study presented here offers a solid and crucial starting point for mutant analyses of a selection of bona fide targets to gain a deeper understanding of the VRS5 network and to enlighten its mode of action in shaping barley development.
2025-08-07 | GSE272368 | GEO
Project description:In this study we used the Affymetrix Barley 1 GeneChip to investigate transcriptome responses of barley cv. Morex to low temperature, including triplicated measurements of cold, freeze/thaw cycles and de-acclimation over 33 days. Keywords: stress response
2008-02-02 | GSE6993 | GEO
Project description:The barley brittle stem mutants, fs2, designated X054 and M245, have reduced levels of cellulose compared with their isogenic parents Ohichi and Shiroseto. A custom-designed microarray, based on Agilent technology and including genes involved in cell wall metabolism, was used to compare transcript levels in the mutant and parental lines. For both mutants, the microarray revealed a marked decrease in mRNA for the HvCesA4 cellulose synthase gene in specific zones of stem internodes, and this was confirmed by quantitative PCR.
2010-07-23 | GSE17873 | GEO
Project description:Affymetrix Barley1 GeneChip microarray was used to study the transcriptome of two fast neutron barley mutants FN362 and FN363 allelic to characterized necrotic leaf spot 3 (nec3) mutants. PCR screening of the 21 genes at least two-fold down-regulated in mutants did not show any deletions in the genome of mutants and, thus, failed to identify a gene responsible for the nec3 mutant phenotype suggesting that either probe set for the NEC3 gene is not on the Barley1 GeneChip, or that the expression of wt NEC3 is confined to specific developmental stage or tissue type.
2010-08-25 | GSE23775 | GEO
Project description:Soil potassium deficiency has become a global problem in agricultural production, seriously restricting crops productions and agricultural sustainable development. Identification of the microRNAs and understanding their functions in response to low K stress will be helpful for developing crop varieties with low K tolerance. Our previous study identified a low K tolerant accession XZ153 from Tibetan wild barley. In this study, small RNA and degradome analysis were performed on two barley genotypes differing in low K tolerance (XZ153, tolerant; ZD9, sensitive) to identify the miRNAs and their targets responding to low K stress. A total of 1108 miRNAs were detected in shoots of XZ153, and ZD9 at 2 d and 7 d after low K stress, and their targets were identified through bioinformatics prediction and degradome analysis. We identified 65 differentially expressed miRNAs responding to low K stress. The results also showed that miR164c, miR169h and miR395a modules could mediate TCA cycle, glycolysis pathway and pentose phosphate pathway responding to low K stress. The osa-miR166g-3p and ghr-miR482b may act as the regulators in Ca2+ signaling pathway in response to low K stress. The methionine salvage cycle involved in ethylene biosynthesis process mediated by miR396c-3p and osa-miR171e-5p might be also involved in responding to low K stress. Some miRNAs, including miR160a, miR396c and miR169h modules, which participated in photosynthesis regulation under low K stress, differed between the two barley genotypes. In conclusion, these exclusively expressed miRNAs and their targets play the crucial roles in low K tolerance.
2020-12-06 | GSE162540 | GEO
Project description:Affymetrix Barley1 GeneChip microarray was used to study the transcriptome of two fast neutron barley mutants FN362 and FN363 allelic to characterized necrotic leaf spot 3 (nec3) mutants. PCR screening of the 21 genes at least two-fold down-regulated in mutants did not show any deletions in the genome of mutants and, thus, failed to identify a gene responsible for the nec3 mutant phenotype suggesting that either probe set for the NEC3 gene is not on the Barley1 GeneChip, or that the expression of wt NEC3 is confined to specific developmental stage or tissue type. Transcriptome of the two barley fast neutron mutants was compared to the transcriptome of parental variety Steptoe
2010-08-25 | E-GEOD-23775 | biostudies-arrayexpress