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Transcriptomic analysis of maize developing earshoot from tropical maize hybrid genotypes native to Nigeria

ABSTRACT: Tropical maize genotypes are well known for their traits of late flowering and higher biomass. Carbon/Nitrogen balance in these genotypes is significantly different from temperate genotypes. Microarray analysis of gene expression changes occuring in developing earshoots was done and results were compared with the temperate genotype microarray analysis, previously conducted. A low yielding variety was used as a reference against three high yielding varities. Keywords: Genotype response

ORGANISM(S): Zea mays

PROVIDER: GSE18008 | GEO | 2009/12/11

SECONDARY ACCESSION(S): PRJNA119235

REPOSITORIES: GEO

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Transcriptomic analysis of maize developing earshoot from tropical maize hybrid genotypes native to Nigeria

Project description:Tropical maize genotypes are well known for their traits of late flowering and higher biomass. Carbon/Nitrogen balance in these genotypes is significantly different from temperate genotypes. Microarray analysis of gene expression changes occuring in developing earshoots was done and results were compared with the temperate genotype microarray analysis, previously conducted. A low yielding variety was used as a reference against three high yielding varities. Keywords: Genotype response Technical replicates, dye swaps, technical replicates of dye swaps, no biological replicates

2010-05-18 | E-GEOD-18008 | biostudies-arrayexpress

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Transcriptional Profiling of C. briggsae Temperate and Tropical representative strains after extreme cold

Project description:Different populations of the same species survive different environments through local adaptation. Temperature is one of the most important driving forces that could result in local adaptation. Here, we studied the influence of extreme low temperature on the survival of two genetically and geographically distinct populations of the free-living Caenorhabditis briggsae. We found that Caenorhabditis briggsae strains of temperate origin had a cold resistant phenotype, while those originating from a tropical climate had reduced survival after cold treatment. Using this phenotypic difference between geographically diverse populations as a model for how species adapt to their local environment, we then analyzed the transcriptional profiles of two Caenorhabditis briggsae strains of tropical and temperate origin to find genes that are involved in survival after extreme cold. In summary, the response to the extreme low temperature that clearly distinguishes the temperate and tropical Caenorhabditis briggsae strains could serve as an excellent example for studying local adaption of species that show genetic separation associated with their geographical distribution.

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Temperature-dependent small RNA expression depends on wild genetic backgrounds of Caenorhabditis briggsae

Project description:Geographically distinct populations can adapt to the temperature conditions of their local environment, leading to temperature-dependent fitness differences between populations. Consistent with local adaptation, phylogeographically distinct Caenorhabditis briggsae nematodes show distinct fitness responses to temperature. The genetic mechanisms underlying local adaptation, however, remain unresolved. To investigate the potential role of small noncoding RNAs in genotype-specific responses to temperature, we quantified small RNA expression using high-throughput sequencing of C. briggsae nematodes from tropical and temperate strain genotypes reared under three temperature conditions (14˚, 20˚, 30˚C). Strains representing both tropical and temperate regions showed significantly lower expression of PIWI-interacting RNAs (piRNAs) at high temperatures, primarily mapping to a large ~7 Mb long piRNA cluster on chromosome IV. We also documented decreased expression of 22G-RNAs antisense to protein-coding genes and other genomic features at high rearing temperatures for the thermally-intolerant temperate strain genotype, but not for the tropical strain genotype. Reduced 22G-RNA expression was widespread along chromosomes and among feature types, indicative of a genome-wide response. Targets of the EGO-1/CSR-1 22G-RNA pathway were most strongly impacted compared to other 22G-RNA pathways, implicating the CSR-1 Argonaute and its RNA-dependent RNA polymerase EGO-1 in the genotype-dependent modulation of C. briggsae 22G-RNAs under chronic thermal stress. Our work suggests that gene regulation via small RNAs may be an important contributor to the evolution of local adaptations.

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Gene expression profiling of two Alexandrium genotypes as response to waterborne cues from grazing Polykrikos

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Project description:BACKGROUND: Climate change will lead in the future to an occurrence of heat waves with a higher frequency and duration than observed today, which has the potential to cause severe damage to seedlings of temperate maize genotypes. In this study, we aimed to (I) assess phenotypic variation for heat tolerance of temperate European Flint and Dent maize inbred lines, (II) investigate the transcriptomic response of temperate maize to linearly increasing heat levels and, (III) identify genes associated with heat tolerance in a set of genotypes with contrasting heat tolerance behaviour. RESULTS: Strong phenotypic differences with respect to heat tolerance were observed between the examined maize inbred lines on a multi-trait level. We identified 607 heat responsive genes as well as 39 heat tolerance genes. CONCLUSION: Our findings indicate that individual inbred lines developed different genetic mechanisms in response to heat stress. We applied a novel statistical approach enabling the integration of multiple genotypes and stress levels in the analysis of abiotic stress expression studies.

2016-10-20 | GSE88917 | GEO

Liver proteome of two temperate and one tropical grass lizards

Project description:Patterns in functional diversity of organisms at large spatial scales can provide insight into possible responses to future climate change, but it remains a challenge to link large-scale patterns at the organismal level to their underlying physiological mechanisms. The climate variability hypothesis predicts that temperate ectotherms will be less vulnerable to climate warming than tropical ectotherms, due to their superior acclimatization capacity.We investigate thermal acclimation of three species of Takydromus lizards distributed along a broad latitudinal gradient in China, by studying metabolic modifications at the level of the whole organism,organ, mitochondria, metabolome, and proteome.

2021-12-12 | PXD029083 | Pride

Identification of differentially expressed genes between clinical and bovine-biased Escherichia coli O157:H7 genotypes

Project description:Escherichia coli O157:H7 strains have been classified into different genotypes based on the presence of specific shiga toxin-encoding bacteriophage insertion sites. Genotypes that are predominant in clinical isolates are named clinical genotypes and those that are isolated mostly from bovine sources are bovine-biased genotypes. To determine whether inherent differences in gene expression could possibly explain the variation in infectivity of these genotypes, we compared the expression patterns of O157:H7 strains isolated from cattle, which belonged to either clinical genotype 1 or bovine-biased genotype 5. Important virulence factors of O157, including locus of enterocyte effacement, enterohemolysin, and pO157 plasmid encoded genes, showed increased expression in clinical genotype. Genes essential for acid resistance such as gadA, gadB, and gadC and other stress fitness-associated genes were up-regulated in the bovine-biased genotype 5. Overall, these results suggest that clinical genotype 1 strains more commonly cause human illness because of an enhanced ability to express O157 virulence factors known to be important for disease pathogenesis. By contrast, strains of the bovine-biased genotype 5 appear to be more resistant to adverse environmental conditions, which enable them to survive well in bovines without causing disease.

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