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90 results for “maize genomics”
Data from: Insights into the maize pan-genome and pan-transcriptome
Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.
Data from: Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize
Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2,500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7,128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.
Data from: Genetic dissection of a genomic region with pleiotropic effects on domestication traits in maize reveals multiple linked QTL
The domesticated crop maize and its wild progenitor, teosinte, have been used in numerous experiments to investigate the nature of divergent morphologies. This study examines a poorly understood region on the fifth chromosome of maize associated with a number of traits under selection during domestication using a QTL mapping population specific to the fifth chromosome. In contrast with other major domestication loci in maize where large effect, highly pleiotropic, single genes are responsible for phenotypic effects, our study found the region on chromosome five fractionates into multiple QTL regions, none with singularly large effects. The smallest 1.5 LOD support interval for a QTL contained 54 genes, one of which was a MADS MIKCC transcription factor, a family of proteins implicated in many developmental programs. We also used simulated trait datasets to investigate the power of our mapping population to identify QTL for which there is a single underlying causal gene. This analysis showed that while QTL for traits controlled by single genes can be accurately mapped, our population design can detect no more than ~4.5 QTL per trait even when there are 100 causal genes. Thus when a trait is controlled by 5 or more genes in the simulated data, the number of detected QTL can represent a simplification of the underlying causative factors. Our results show how a QTL region with effects on several domestication traits may be due to multiple linked QTL of small effect as opposed to a single gene with large and pleiotropic effects.
Discovery of Genomic Regions Associated with Grain Yield and Agronomic Traits in Bi-parental Populations of Maize (Zea mays. L) under Optimum and Low Nitrogen Conditions
<p>Supplementary material_ BLUEs across location for grain yield and other agronomic traits for four F3 populations evaluated under optimum and low N management conditions. </p><p>Genotypic data - SNP Marker data for four F3 populations used in the manuscript "Discovery of Genomic Regions Associated with Grain Yield and Agronomic Traits in Bi-parental Populations of Maize (Zea mays. L) under Optimum and Low Nitrogen Conditions" from Front in Genet</p>
Data from: Shared genomic regions between derivatives of a large segregating population of maize identified using bulked segregant analysis sequencing and traditional linkage analysis
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Data from: Genome-wide discovery and characterization of maize long non-coding RNAs
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Data from: Genetic dissection of a genomic region with pleiotropic effects on domestication traits in maize reveals multiple linked QTL
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Data from: Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize
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Data from: Genome-wide association analysis of stalk biomass and anatomical traits in maize
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Data from: The genomic basis for short-term evolution of environmental adaptation in maize
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Data from: Insights into the maize pan-genome and pan-transcriptome
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Data from: Archaeological Central American maize genomes suggest ancient gene flow from South America
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Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize
GEO Series GSE189317. Zea mays. 322 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize
GEO Series GSE47886. Zea mays. 4 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Three groups of transposable elements with contrasting copy number dynamics and host responses in the maize (Zea mays ssp. mays) genome
GEO Series GSE55730. Zea mays. 3 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Genome-wide mapping of Zea maize TSSs
GEO Series GSE70251. Zea mays subsp. mays. 8 samples. Type: Expression profiling by high throughput sequencing.
The maize genome encodes novel members of the purple acid phosphatase (PAP) subgroup Ia
GEO Series GSE63779. Zea mays. 8 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide analysis of leafbladeless1-regulated and phased small RNAs provides new insights into the tas3 pathway in maize-
GEO Series GSE50557. Zea mays. 10 samples. Type: Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Genome-wide characterization of cis-acting DNA targets of Opaque2 in maize
GEO Series GSE63991. Zea mays. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genome-wide transcriptome analysis of maize (Zea mays c.v. Nathan) plants infected by Colletotrichum graminicola strains.
GEO Series GSE48208. Zea mays. 3 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.