Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1133950 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29761140.fastq.gz | Fastqsanger.gz | |||
| SRR29761140_1.fastq.gz | Fastqsanger.gz | |||
| SRR29761140_2.fastq.gz | Fastqsanger.gz | |||
| SRR29761141.fastq.gz | Fastqsanger.gz | |||
| SRR29761141_1.fastq.gz | Fastqsanger.gz |
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Project description:Expression profiling analyses for 5 maize inbreds and 4 hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. This is a companion dataset to an Affymetrix profiling experiment (GEO Series GSE10236). Keywords: Genotype comparison series Expression profiling was used to study gene expression in aerial tissue from 11-day seedlings of maize. Three biological replicates were performed for nine different genotypes; B37, B73, B84, Mo17, Oh43, B37xB73, B84xB73, Oh43xB73 and Oh43xMo17.
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2013-12-10 | E-MTAB-4239 | biostudies-arrayexpress
Project description:Expression profiling analyses for 5 maize inbreds and 4 hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. This is a companion dataset to an Affymetrix profiling experiment (GEO Series GSE10236). Keywords: Genotype comparison series
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Project description:Sustainability of maize cultivation would benefit tremendously from early sowing but is hampered by low temperatures during early development in temperate climate. We show that allelic variation of subunit M of NADH-dehydrogenase-like (NDH) complex (ndhm1), discovered in a European maize landrace affects several quantitative traits relevant during early development in cold climates through NDH mediating cyclic electron transport (CET) around photosystem I, a process crucial for photosynthesis. Starting from a GWAS for maximum potential quantum yield of photosystem II in dark-adapted leaves (Fv/Fm) we capitalized on large phenotypic effects of a hAT transposon insertion in ndhm1 on quantitative traits early plant height (EPH), Fv/Fm, chlorophyll content and cold tolerance caused by reduced protein levels of NDHM and associated NDH components. Analysis of the native allelic series of ndhm1 revealed a rare allele of ndhm1 which is associated with smaller but significant effects on maximum potential quantum yield of photosystem II in dark- and light adapted leaves (Fv/Fm, ΦPSII) and early plant height compared to common alleles. Our work showcases the extraction of novel, favorable alleles from locally adapted landraces, offering an efficient strategy for broadening the genetic variation of elite germplasm by breeding or genome editing.
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Project description:DNA methylation is a ubiquitous chromatin feature — in maize, more than 25% of cytosines in the genome are methylated. Recently, major progress has been made in describing the molecular mechanisms driving methylation, yet variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here we leveraged whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to investigate the adaptive and phenotypic consequences of methylation variations in maize. By using a novel estimation approach, we inferred the methylome site frequency spectrum (mSFS) to estimate forward and backward methylation mutation rates and selection coefficients. We only found weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) were identified in population-wide that are correlated with recent selection. Further investigation revealed that DMRs are enriched in 5’ untranslated regions, and that maize hypomethylated DMRs likely helped rewire distal gene regulation. For two trait-associated DMRs, vgt1-DMR and tb1DMR, our HiChIP data indicated that the interactive loops between DMRs and respective downstream genes were present in B73, a modern maize line, but absent in teosinte. Functional analyses suggested that these DMRs likely served as cis-acting elements that modulated gene regulation after domestication. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.
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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.
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Project description:Purpose: Maize somatic embryogenesis is usually required to achieve genetic transformation and represents an important alternative in plant development. Although many embryogenesis-related genes have been studied in this model, the molecular mechanisms underlying cell dedifferentiation and further plant regeneration are not completely understood. Methods: Immature embryos smRNA profiles of 15-day-after-pollination (IE) and Embryogenic Callus from one (C1), four (C4), and ten months (C10) were generated by deep sequencing, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed with two methods: Bowtie 1.1.2 and ShortStack 3.4. qRT–PCR validation for selected miRNAs was performed using SYBR Green assays. Results: We used high throughput sequencing to explore the sRNA populations during maize embryogenic callus induction and established subcultures from the Mexican cultivar VS-535, Tuxpeño landrace. We detected readjustments in 24 nt and 21-22 nt sRNA populations during the embryogenic callus establishment and maintenance. miRNAs related to stress response substantially increased upon callus proliferation establishment, correlating with a reduction in some of their target levels. On the other hand, while 24 nt-long hc-siRNAs derived from transposable retroelements transiently decreased in abundance during the embryogenic callus establishment, a population of 22 nt- hc-siRNAs increased. This was accompanied by reduction in transposon expression in the established callus subcultures. Conclusions: Stress- and development-related miRNAs are highly expressed upon maize EC callus induction and during maintenance subcultures, while miRNAs involved in hormone response only transiently increase during induction. The establishment of proliferative maize embryogenic callus is accompanied by important readjustments in the length of hc-siRNAs mapping to LTR retrotransposons, and their expression regulation.
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