Undefined
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB64293 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12115500_1.fastq.gz | Fastqsanger.gz | |||
| ERR12115500_2.fastq.gz | Fastqsanger.gz | |||
| ERR12115600_1.fastq.gz | Fastqsanger.gz | |||
| ERR12115600_2.fastq.gz | Fastqsanger.gz | |||
| ERR12115501_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 378 |
Similar Datasets
Project description:Gene transcription is an essential step of gene function and transcriptome variation is of agronomical, ecological and evolutionary importance. To explore global expression patterns and dissect the underlying genetic mechanisms are important scientific inquires which are still largely unknown, especially between a segregating population and the parents. In our study, we used RNA-Seq to profile the shoot apex transcriptome variation (including protein coding genes and non-coding genes) in maize IBM RIL population, to map eQTLs underlying the transcriptome variations and to utilize eQTLs to clone genes involved in maize shoot apices development. We revealed that: Much of the variation (the population mean, the coefficient of variation) of gene expression levels in RILs is reflective of differences present among the parents; These transcriptome variations could be explained by 30,774 eQTLs with 96 trans-eQTL hotspots; In many cases, the genes commonly regulated by a trans-eQTL hotspot are enriched for a specific function or act in the same genetic pathway; Structural variation within and near genes contributs to cis-regulatory variation. All of these results indicate Mendelian factors play as major contributors to the transcriptome variation. Meanwhile, non-Mendelian regulations were also observed as paramutation-like expression pattern for 145 genes, of which 88% genes were predicted to be potential targets of miRNAs or ta-siRNAs, and as unexpected presence/absence expression patterns for 210 genes. These genes with unexpected presence/absence expression patterns in the RILs likely include examples of functional genes as well as transposed gene fragments that may contribute to regulatory variation of their ancestral syntenic genes.
2013-01-30 | E-MTAB-4227 | biostudies-arrayexpress
Project description:To assess plasticity in genetic regulation of gene expression in Arabidopsis thaliana, genome wide gene expression variation was analyzed in a Ler/Cvi recombinant inbred line (RIL) population treated with low-light. The variation in expression could be explained for many genes by expression quantitative trait loci (eQTLs), which were compared to a previous genetical genomics study in the same untreated population. Please note Characteristics[StrainOrLine] is the population of 162 recombinant inbred lines between the accessions Ler x Cvi. Ler and Cvi are the names of the parental accessions.
2013-03-01 | E-MTAB-1357 | biostudies-arrayexpress
Project description:Gene expression and complex phenotypes are determined by the activity of cis-regulatory elements. However, an understanding of how extant genetic variants affect cis-regulatory activity remains limited. Here, we investigated the consequences of cis-regulatory diversity using single-cell genomics of >0.7 million nuclei across 172 maize inbreds. Our analyses pinpointed cis-regulatory elements distinct to domesticated maize and how transposons rewired the regulatory landscape. We found widespread chromatin accessibility variation associated with >4.6 million genetic variants with largely cell-type-specific effects. Variants in TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR binding sites were the most prevalent determinants of chromatin accessibility. Finally, integration of genetic variants associated with chromatin accessibility, organismal trait variation, and population differentiation revealed how local adaptation has rewired regulatory networks in unique cellular context to alter maize flowering phenotypes.
2024-11-19 | GSE273478 | GEO
Project description:Crop resilience and yield stability are complex traits essential for food security. Sorghum bicolor is an important grain crop that shows promise for its natural resilience to drought and potential for marginal land production. We have developed sorghum lines in the Tx430 genetic background suppressed for MSH1 expression as a means of inducing de novo epigenetic variation and have used these materials to evaluate changes in plant growth vigor. Plant crossing and selection in two distinct environments revealed features of phenotypic plasticity derived from MSH1 manipulation. Introduction of epigenetic variation to an isogenic sorghum population, in the absence of selection, resulted in 10% yield increase under ideal field conditions and 20% increase under extreme low nitrogen conditions. However, incorporation of early-stage selection amplified these outcomes to 36% yield increase under ideal conditions and 64% increase under marginal field conditions. Interestingly, the best outcomes were derived by selecting mid-range performance early-generation lines rather than highest performing. Data also suggested that phenotypic plasticity derived from epigenetic variation was non-uniform in its response to environmental variability but served to reduce genotype x environment interaction. The MSH1-derived growth vigor appeared to be associated with enhanced seedling root growth and altered expression of auxin response pathways, and plants showed evidence of cold tolerance, features consistent with observations made previously in Arabidopsis. These data imply that the MSH1 system is conserved across plant species, pointing to the value of parallel model plant studies to help devise effective plant selection strategies for epigenetic breeding in multiple crops.
2021-12-31 | GSE189686 | GEO
Project description:Origin Matters: Using a Local Reference Genome Improves Measures in Population Genomics
| PRJEB54679 | ENA
Project description:DNA methylation is a chromatin modification that is frequently associated with epigenetic regulation in plants and mammals. However, other genetic changes such as transposon insertions also can lead to changes in DNA methylation levels. Genome-wide profiles of DNA methylation levels for 20 maize inbreds were used to discover differentially methylated regions (DMRs). The methylation level for each of these DMRs was also assayed in 31 additional maize genotypes resulting in the discovery of 1,966 common DMRs and 1,754 rare DMRs. Analysis of recombinant inbred lines provides evidence that the majority of DMRs are heritable. A local association scan found that nearly half of the DMRs with common variation are significantly associated with SNPs found within or near the DMR. Many of the DMRs that are significantly associated with local genetic variation are found near transposable elements that may contribute to the DNA methylation variation. The analysis of gene expression in the same samples used for DNA methylation profiling identifies over 300 genes with expression patterns that are significantly associated with the DNA methylation variation among genotypes. Collectively, our results suggest that DNA methylation variation is influenced by genetic and epigenetic variation is often stably inherited and can influence expression level of genes in the population.
2013-08-12 | GSE46949 | GEO
Project description:Genetic population structure of Xiongnu Empire at imperial and local scales
| PRJEB55185 | ENA