Contrasting DNA methylation responses of inbred fish lines to different rearing environments.
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ABSTRACT:
SUBMITTER: Berbel-Filho WM
PROVIDER: S-EPMC6691983 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundInformation on population structure and genetic diversity of germplasm in a breeding programme is useful because it enhances judicious utilisation of genetic resources to achieve breeding objectives. Seventy early maturing provitamin A (PVA) quality protein maize (QPM) inbreds developed by the IITA- maize improvement programme were genotyped using 8171 DArTseq markers. Furthermore, 96 hybrids derived from 24 selected inbreds plus four checks were evaluated under low-N and optimal environments in Nigeria during 2016 and 2017. Genotypic and phenotypic data of inbreds and hybrids respectively, were analysed to (i) assess the level of genetic dissimilarities and population structure of the inbreds, and (ii) investigate the grain yield performance of derived hybrids under low-N, optimal and across environments.ResultsGenetic diversity among the seventy inbreds was high varying from 0.042 to 0.500 with an average of 0.357. Sixty-six inbred lines with probabilities ≥0.70 were assigned to a single group. The population structure analysis, the UPGMA phylogeny, and the principal Coordinate Analysis (PCoA) of the DArTseq markers revealed a clear separation of five groups and each followed pedigree records. Clustered inbreds displayed common characteristics including high PVA levels, and drought and low-N tolerance. The top performing hybrid, TZEIORQ 40 × TZEIORQ 26 out-yielded the best hybrid control, TZEIOR 127 × TZEIOR 57 by 8, 3, and 9% under low-N, optimal, and across environments, respectively. High repeatability estimates were detected for grain yield under each and across environments. Similarly, high breeding efficiency of 71, 70 and 72% were computed under low-N, optimal, and across environments, respectively.ConclusionsThe UPGMA clustering, the structure analysis, and the PCoA consistently revealed five groups which largely followed pedigree information indicating the existence of genetically distinct groups in the inbred lines. High repeatability and breeding efficiency values estimated for grain yield of hybrids under low-N, optimal and across environments demonstrated that high productive hybrids could be developed using inbreds from the opposing clusters identified by the DArTseq markers. The 15 top performing hybrids identified, particularly TZEIORQ 40 × TZEIORQ 26 and TZEIORQ 29 × TZEIORQ 43 should be further evaluated for release and commercialization in SSA.
| S-EPMC7368723 | biostudies-literature
Project description:DNA methylation plays a crucial role in the regulation of gene expression, activity of transposable elements, defense against foreign DNA, and inheritance of specific gene expression patterns. The link between stress exposure and sequence-specific changes in DNA methylation was hypothetical until it was shown that stresses can induce changes in the gene expression through hypomethylation or hypermethylation of DNA. To detect changes in DNA methylation under herbicide stress in two local Zea mays inbred lines exhibiting differential susceptibility to Roundup®, the methylation-sensitive amplified polymorphism (MSAP) technique was used. The overall DNA methylation levels were determined at approximately 60% for both tested lines. The most significant changes were observed for the more sensitive Z. mays line, where 6 h after the herbicide application, a large increase in the level of DNA methylation (attributed to the increase in fully methylated bands (18.65%)) was noted. DNA sequencing revealed that changes in DNA methylation profiles occurred in genes encoding heat shock proteins, membrane proteins, transporters, kinases, lipases, methyltransferases, zinc-finger proteins, cytochromes, and transposons. Herbicide stress-induced changes depended on the Z. mays variety, and the large increase in DNA methylation level in the sensitive line resulted in a lower ability to cope with stress conditions.
| S-EPMC8032638 | biostudies-literature
Project description:Self-incompatible diploid potatoes were altered to self-compatible ones by a function of S-locus inhibitor gene and continued selfing generated highly homozygous inbreds. In this study, this process was investigated for the status of DNA methylation by a simple method using genomic DNA digested by methylation-sensitive restriction enzymes prior to RAPD analysis. We detected 31 methylation-sensitive RAPD bands, of which 11 were newly appeared in the selfed progenies, and 6 of them stably inherited to subsequent generations. Aberrant segregations and paternal- or atavism-like transmission were also found. Segregating methylation-sensitive bands in initial populations became fixed in the advanced selfed progenies by 75.0-93.8%, of which 41.7% were fixed to all present and 58.3% to all absent. Because DNA methylation is generally recognized to suppress gene expression as regulatory factors, homozygosity/heterozygosity of methylated DNA may be involved in inbreeding depression/heterosis.
| S-EPMC2793386 | biostudies-other
Project description:Common bean (Phaseolus vulgaris L.) fixes atmospheric nitrogen (N2) through symbiotic nitrogen fixation (SNF) at levels lower than other grain legume crops. An understanding of the genes and molecular mechanisms underlying SNF will enable more effective strategies for the genetic improvement of SNF traits in common bean. In this study, transcriptome profiling was used to identify genes and molecular mechanisms underlying SNF differences between two common bean recombinant inbred lines that differed in their N-fixing abilities. Differential gene expression and functional enrichment analyses were performed on leaves, nodules and roots of the two lines when grown under N-fixing and non-fixing conditions. Receptor kinases, transmembrane transporters, and transcription factors were among the differentially expressed genes identified under N-fixing conditions, but not under non-fixing conditions. Genes up-regulated in the stronger nitrogen fixer, SA36, included those involved in molecular functions such as purine nucleoside binding, oxidoreductase and transmembrane receptor activities in nodules, and transport activity in roots. Transcription factors identified in this study are candidates for future work aimed at understanding the functional role of these genes in SNF. Information generated in this study will support the development of gene-based markers to accelerate genetic improvement of SNF in common bean.
| S-EPMC5305244 | biostudies-literature
Project description:Ocean acidification (OA) is predicted to enhance photosynthesis in many marine taxa. However, photophysiology has multiple components that OA may affect differently, especially under different light environments, with potentially contrasting consequences for photosynthetic performance. Furthermore, because photosynthesis affects energetic budgets and internal acid-base dynamics, changes in it due to OA or light could mediate the sensitivity of other biological processes to OA (e.g. respiration and calcification). To better understand these effects, we conducted experiments on Porolithon onkodes, a common crustose coralline alga in Pacific coral reefs, crossing pCO2 and light treatments. Results indicate OA inhibited some aspects of photophysiology (maximum photochemical efficiency), facilitated others (α, the responsiveness of photosynthesis to sub-saturating light), and had no effect on others (maximum gross photosynthesis), with the first two effects depending on treatment light level. Light also exacerbated the increase in dark-adapted respiration under OA, but did not alter the decline in calcification. Light-adapted respiration did not respond to OA, potentially due to indirect effects of photosynthesis. Combined, results indicate OA will interact with light to alter energetic budgets and potentially resource allocation among photosynthetic processes in P. onkodes, likely shifting its light tolerance, and constraining it to a narrower range of light environments.
| S-EPMC6408467 | biostudies-literature
Project description:The photosynthetic adjustments of macaw palm (Acrocomia aculeata) were evaluated in 30-day-old seedlings exposed to high and low light environments, and sudden transference from low to high light and comparisons were made with the hardening protocol used in nurseries. Furthermore, we evaluated the responses to long-term exposure (265 days) to high and low light environments. Macaw palm seedlings exhibited an efficient mechanism that maximized light capture under scarce conditions, and dissipated excess energy to avoid damaging to the photosystem II under high light. The seedlings showed low saturation irradiance but no photoinhibition when exposed to excess light. When grown under low light intensities, seedlings presented higher photochemical efficiency and minimized the respiratory costs with positive carbon balance at lower irradiance than hardened seedlings did. The hardening procedure did not appear to be an advantageous method during seedling production. Long-term exposure to either low or high light did not cause significant leaf anatomical adjustments. However, the low light seedlings showed higher leaf area and chlorophyll content than those exposed to higher light intensity did, which enabled shaded seedlings to maximize the captured light. Furthermore, the high non-photochemical dissipation allowed rapid acclimation to excessive light exposure. These responses allow macaw palm cultivation and establishment in very different light environments.
| S-EPMC6192989 | biostudies-literature
Project description:AbstractBackgroundThe periconceptional period is a time in which environmentally induced changes to the epigenome could have significant consequences for offspring health. Metastable epialleles (MEs) are genomic loci demonstrating interindividual variation in DNA methylation with intraindividual crosstissue correlation, suggesting that methylation states are established in the very early embryo before gastrulation. In our previous Gambian studies, we have shown that ME methylation states in the offspring are predicted by maternal concentrations of certain nutritional biomarkers around the time of conception.ObjectiveWe aimed to assess whether the profile of maternal biomarker predictors of offspring methylation differs between rainy and dry seasons in a population of rural Gambians, using a larger set of 50 recently identified MEs.MethodsWe measured 1-carbon biomarkers in maternal plasma back-extrapolated to conception, and cytosine-phosphate-guanine (CpG) methylation at 50 ME loci in their infants’ blood at a mean age of 3.3 mo ( = 120 mother-child pairs). We tested for interactions between seasonality and effects of biomarker concentrations on mean ME methylation score. We used backward stepwise linear regression to select the profile of nutritional predictors of methylation in each season and repeated this analysis with biomarker principal components (PCs) to capture biomarker covariation.ResultsWe found preliminary evidence of seasonal differences in biomarker-methylation associations for folate, choline, and homocysteine (interaction values ?0.03). Furthermore, in stratified analyses, biomarker predictors of methylation changed between seasons. In the dry season, vitamin B-2 and methionine were positive predictors. In the rainy season, however, choline and vitamin B-6 were positive predictors, and folate and vitamin B-12 were negative predictors. PC1 captured covariation in the folate metabolism cycle and predicted methylation in dry season conceptions. PC2 represented the betaine remethylation pathway and predicted rainy season methylation.ConclusionsUnderlying nutritional status may modify the association between nutritional biomarkers and methylation, and should be considered in future studies.
| S-EPMC6351729 | biostudies-literature
Project description:Phosphorus (P) is an essential plant nutrient, and deficiency of P is one of the most important factors restricting maize yield. Therefore, it is necessary to develop a more efficient program of P fertilization and breeding crop varieties with enhanced Pi uptake and use efficiency, which required understanding how plants respond to Pi starvation. To understand how maize plants adapt to P-deficiency stress, we screened 116 inbred lines in the field and identified two lines, DSY2 and DSY79 that were extreme low-P resistant and sensitive, respectively. We further conducted physiological, transcriptomic, and proteomic studies using the roots of DSY2 and DSY79 under normal or low-P conditions. The results showed that the low-P resistant line, DSY2 had larger root length, surface area and volume, higher root vitality, as well as acid phosphatase activity as compared with the low-P sensitive line, DSY79 under the low-P condition. The transcriptomic and proteomic results suggest that dramatic more genes were induced in DSY2, including the plant hormone signaling, acid phosphatase, and metabolite genes, as compared with DSY79 after being challenged by low-P stress. The new insights generated in this study will be useful toward the improvement of P-utilize efficiency in maize.
| S-EPMC5343578 | biostudies-literature
Project description:Genetic and epigenetic variations are commonly known to underlie phenotypic plastic responses to environmental cues. However, the role of epigenetic variation in plastic responses harboring ecological significance in nature remains to be assessed. The shade avoidance response (SAR) of plants is one of the most prevalent examples of phenotypic plasticity. It is a phenotypic syndrome including stem elongation and multiple other traits. Its ecological significance is widely acknowledged, and it can be adaptive in the presence of competition for light. Underlying genes and pathways were identified, but evidence for its epigenetic basis remains scarce. We used a proven and accessible approach at the population level and compared global DNA methylation between plants exposed to regular light and three different magnitudes of shade in seven highly inbred lines of snapdragon plants (Antirrhinum majus) grown in a greenhouse. Our results brought evidence of a strong SAR syndrome for which magnitude did not vary between lines. They also brought evidence that its magnitude was not associated with the global DNA methylation percentage for five of the six traits under study. The magnitude of stem elongation was significantly associated with global DNA demethylation. We discuss the limits of this approach and why caution must be taken with such results. In-depth approaches at the DNA sequence level will be necessary to better understand the molecular basis of the SAR syndrome.
| S-EPMC6523709 | biostudies-literature
Project description:Salinity is a major abiotic stress that limits maize yield and quality throughout the world. We investigated phosphoproteomics differences between a salt-tolerant inbred line (Zheng58) and a salt-sensitive inbred line (Chang7-2) in response to short-term salt stress using label-free quantitation. A total of 9448 unique phosphorylation sites from 4116 phosphoproteins in roots and shoots of Zheng58 and Chang7-2 were identified. A total of 209 and 243 differentially regulated phosphoproteins (DRPPs) in response to NaCl treatment were detected in roots and shoots, respectively. Functional analysis of these DRPPs showed that they were involved in carbon metabolism, glutathione metabolism, transport, and signal transduction. Among these phosphoproteins, the expression of 6-phosphogluconate dehydrogenase 2, pyruvate dehydrogenase, phosphoenolpyruvate carboxykinase, glutamate decarboxylase, glutamate synthase, l-gulonolactone oxidase-like, potassium channel AKT1, high-affinity potassium transporter, sodium/hydrogen exchanger, and calcium/proton exchanger CAX1-like protein were significantly regulated in roots, while phosphoenolpyruvate carboxylase 1, phosphoenolpyruvate carboxykinase, sodium/hydrogen exchanger, plasma membrane intrinsic protein 2, glutathione transferases, and abscisic acid-insensitive 5-like protein were significantly regulated in shoots. Zheng58 may activate carbon metabolism, glutathione and ascorbic acid metabolism, potassium and sodium transportation, and the accumulation of glutamate to enhance its salt tolerance. Our results help to elucidate the mechanisms of salt response in maize seedlings. They also provide a basis for further study of the mechanism underlying salt response and tolerance in maize and other crops.
| S-EPMC6515243 | biostudies-literature