Transcriptome analysis of maize hybrid An’nong 591 and its parental lines under heat stress
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ABSTRACT:
PROVIDER: PRJNA506720 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8239720_1.fastq.gz | Fastqsanger.gz | |||
| SRR8239720_2.fastq.gz | Fastqsanger.gz | |||
| SRR8239730_1.fastq.gz | Fastqsanger.gz | |||
| SRR8239730_2.fastq.gz | Fastqsanger.gz | |||
| SRR8239721_1.fastq.gz | Fastqsanger.gz |
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Project description:Eighteen samples (three replicates) of the maize hybrid An’nong 591 and its parental lines under control and heat treatment were used for RNA sequencing
2018-11-24 | GSE122866 | GEO
Project description:BackgroundHeterosis is the superior performance of F1 hybrids relative to their parental lines for a wide range of traits. In this study, expression profiling and heterosis associated genes were analyzed by RNA sequencing (RNA-Seq) in seedlings of the maize hybrid An'nong 591 and its parental lines under control and heat stress conditions.ResultsThrough performing nine pairwise comparisons, the maximum number of differentially expressed genes (DEGs) was detected between the two parental lines, and the minimum number was identified between the F1 hybrid and the paternal lines under both conditions, which suggested greater genetic contribution of the paternal line to heat stress tolerance. Gene Ontology (GO) enrichment analysis of the 4518 common DEGs indicated that GO terms associated with diverse stress responses and photosynthesis were highly overrepresented in the 76 significant terms of the biological process category. A total of 3970 and 7653 genes exhibited nonadditive expression under control and heat stress, respectively. Among these genes, 2253 (56.8%) genes overlapped, suggesting that nonadditive genes tend to be conserved in expression. In addition, 5400 nonadditive genes were found to be specific for heat stress condition, and further GO analysis indicated that terms associated with stress responses were significantly overrepresented, and 60 genes were assigned to the GO term response to heat. Pathway enrichment analysis indicated that 113 genes were involved in spliceosome metabolic pathways. Nineteen of the 33 overlapping genes assigned to the GO term response to heat showed significantly higher number of alternative splicing (AS) events under heat stress than under control conditions, suggesting that AS of these genes play an important role in response to heat stress.ConclusionsThis study reveals the transcriptomic divergence of the maize F1 hybrid and its parental lines under control and heat stress conditions, and provides insight into the underlying molecular mechanisms of heterosis and the response to heat stress in maize.
| S-EPMC6591960 | biostudies-literature
Project description:Xylose-utilizing yeasts with tolerances to fermentation inhibitors (such as weak organic acids) and high temperature are needed for cost-effective simultaneous saccharification and co-fermentation (SSCF) of lignocellulosic materials. We constructed a novel xylose-assimilating Saccharomyces cerevisiae strain with improved fermentation performance under heat and acid co-stress using the genome shuffling technique. Two xylose-utilizing diploid yeasts with different genetic backgrounds were used as the parental strains for genome shuffling. The hybrid strain Hyb-8 showed significantly higher xylose fermentation ability than both parental strains (Sun049T-Z and Sun224T-K) under co-stress conditions of heat and acids. To screen for genes that might be important for fermentation under heat and acid co-stress, a transcriptomic analysis of hybrid strain Hyb-8 and its parental strains was performed.
2017-07-25 | GSE101786 | GEO
Project description:Closely related lineages can possess phenotypic variation important for adaptation and the evolution of new species; a phenomenon that can be more clearly elucidated by studying hybrid generations. We compare variation in gene expression in response to drought for two taxa and advanced-generation hybrids of the Piriqueta cistoides ssp. caroliniana complex that differ in their levels of tolerance to water limitation. Drought treatments lasted 36 days, through four cycles of drought. Gene expression in drought and control treatments was assessed using heterologous hybridization to a Glycine max microarray. There was a predominance of down-regulated genes in response to sustained drought in all morphotypes. This pattern was more pronounced in the hybrids, which can exhibit greater drought tolerance under field and greenhouse conditions than the parental morphotypes. Expression response profiles were more similar between the hybrid and the drought-tolerant parental morphotype than they were between the hybrid and the parental morphotype that occurs in more mesic habitats. Predominant down-regulation of gene expression contrasts with studies of response to short-term drought and with studies of drought-response in annual and non-drought-tolerant model species, and supports the results of a growing number of studies with other drought-tolerant perennial plants under prolonged drought.
2010-05-27 | GSE19410 | GEO
Project description:Closely related lineages can possess phenotypic variation important for adaptation and the evolution of new species; a phenomenon that can be more clearly elucidated by studying hybrid generations. We compare variation in gene expression in response to drought for two taxa and advanced-generation hybrids of the Piriqueta cistoides ssp. caroliniana complex that differ in their levels of tolerance to water limitation. Drought treatments lasted 36 days, through four cycles of drought. Gene expression in drought and control treatments was assessed using heterologous hybridization to a Glycine max microarray. There was a predominance of down-regulated genes in response to sustained drought in all morphotypes. This pattern was more pronounced in the hybrids, which can exhibit greater drought tolerance under field and greenhouse conditions than the parental morphotypes. Expression response profiles were more similar between the hybrid and the drought-tolerant parental morphotype than they were between the hybrid and the parental morphotype that occurs in more mesic habitats. Predominant down-regulation of gene expression contrasts with studies of response to short-term drought and with studies of drought-response in annual and non-drought-tolerant model species, and supports the results of a growing number of studies with other drought-tolerant perennial plants under prolonged drought. A total of 18 array hyridizations. Two conditions (drought and control), three morphotypes (caroliniana, viridis, and hybrid), for a total of 6 morphotype/treatment combinations. Three samples of each morphotypes/treatment combination were hybridized twice in dye swap in a loop design.
2010-04-22 | E-GEOD-19410 | 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. The majority of differentially expressed genes in each of the different hybrids exhibited additive expression patterns, and ~25% exhibited statistically significant non-additive expression profiles. Among the non-additive profiles, ~80% exhibited hybrid expression levels between the parental levels, ~20% exhibited hybrid expression levels at the parental levels and ~1% exhibited hybrid levels outside the parental range. These findings indicate that the frequencies of additive and non-additive expression patterns are very similar across a range of hybrid lines. Experiment Overall Design: Affymetrix 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.
2008-06-11 | E-GEOD-10236 | biostudies-arrayexpress
Project description:Using a whole-genome oligonucleotide microarray designed based on known and predicted indica rice genes, we investigated transcriptome profiles in developing leaves and panicles of super hybrid rice LYP9 and its parental cultivar 93-11 and PA64s. We detected 22,266 expressed genes out of 36,926 total gene set collectively from seven tissues, including leaves at seedling and tillering stages, flag leaves at booting, heading, flowering, and filling stages, and panicle at filling stage. Clustering result showed that expression profiles between F1 and its parental lines were always more similar than that between the two parental lines. Out of the total gene set, 7,078 were shared by all sampled tissues and 3,926 (10.6%) were differentially-expressed genes (DG). As we divided DG into those between the parents (DGPP) and between the hybrid and its parents (DGHP), the comparative results showed that genes in the two categories, Energy metabolism and transport, were enriched in DGHP rather than in DGPP. The majority of genes were identified as additive expression, and non-additive expression only took a minority (0.53%-1.35%) of the total genes. In addition, we correlated the concurrence of DG and yield-related QTL, providing a potential group of genes as heterosis-related. We investigated transcriptome profiles in developing leaves and panicles of super hybrid rice LYP9 and its parental cultivar 93-11 and PA64s for seven tissues, and there are at least three independent replicates for each sample pair.
2009-04-22 | E-GEOD-14729 | biostudies-arrayexpress
Project description:Using a whole-genome oligonucleotide microarray designed based on known and predicted indica rice genes, we investigated transcriptome profiles in developing leaves and panicles of super hybrid rice LYP9 and its parental cultivar 93-11 and PA64s. We detected 22,266 expressed genes out of 36,926 total gene set collectively from seven tissues, including leaves at seedling and tillering stages, flag leaves at booting, heading, flowering, and filling stages, and panicle at filling stage. Clustering result showed that expression profiles between F1 and its parental lines were always more similar than that between the two parental lines. Out of the total gene set, 7,078 were shared by all sampled tissues and 3,926 (10.6%) were differentially-expressed genes (DG). As we divided DG into those between the parents (DGPP) and between the hybrid and its parents (DGHP), the comparative results showed that genes in the two categories, Energy metabolism and transport, were enriched in DGHP rather than in DGPP. The majority of genes were identified as additive expression, and non-additive expression only took a minority (0.53%-1.35%) of the total genes. In addition, we correlated the concurrence of DG and yield-related QTL, providing a potential group of genes as heterosis-related.
2009-04-22 | GSE14729 | GEO
Project description:Non-additive gene regulation has been recently suggested as an important factor promoting phenotypic variation and plasticity. In order to obtain a description of gene expression status at an early stage of ear development in a maize (Zea mays L.) F1 hybrid as relative to its parental inbreds, we compared gene expression profiles in immature ears of elite inbred lines B73 and H99 to one of their F1 hybrids (B73xH99) using cDNA microarray technology. Results show several genes expressed at a significantly different level between both inbred lines and their hybrid. In addition, gene expression non-additivity in the hybrid was detected on a broad scale, consisting of both dominance and over-dominance components, indicating that complex non-additive interactions at the molecular level exist in the developing ear of the studied maize hybrid. Non-additively regulated genes belong to a wide range of molecular functions, indicating that several regulatory and metabolic patterns are possibly affected during ear development in the investigated hybrid. We discuss the possibility that observed gene expression non-additivity in immature ear might be an early molecular manifestation of hybrid vigor, the most exploited factor for maize agronomic improvement.
2007-10-01 | GSE2771 | GEO
Project description:This study aimed to investigate the heat tolerance and inheritance patterns of leukocyte transcriptomics in F1 hybrid cattle (AN♂ × DR♀) and their parents Red Angus (AN) and Droughtmaster (DR) under heat stress.
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