scholarly journals Plasticity across levels: relating epigenomic, transcriptomic, and phenotypic responses to osmotic stress in a halotolerant microalga

2021 ◽  
Author(s):  
Christelle Leung ◽  
Daphne Grulois ◽  
Luis-Miguel Chevin
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
Osmotic Stress ◽  
Model Organism ◽  
Methylation Pattern ◽  
Marginal Effect ◽  
Environment Interaction ◽  
Multiple Traits ◽  
Genotype Effect ◽  
Phenotypic Responses

Phenotypic plasticity, the ability of a given genotype to produce alternative phenotypes in response to its environment of development, is an important mechanism for coping with variable environments. While the mechanisms underlying phenotypic plasticity are diverse, their relative contributions need to be investigated quantitatively to better understand the evolvability of plasticity across biological levels. This requires relating plastic responses of the epigenome, transcriptome, and organismal phenotype, and how they vary with the genotype. Here we carried out this approach for responses to osmotic stress in Dunaliella salina, a green microalga that is a model organism for salinity tolerance. We compared two strains that show markedly different demographic responses to osmotic stress, and showed that these phenotypic responses involve strain- and environment-specific variation in gene expression levels, but a relative low - but significant - effect of strain x environment interaction. We also found an important genotype effect on the genome-wide methylation pattern, but little contribution from environmental conditions to the latter. However, we did detect a significant marginal effect of epigenetic variation on gene expression, beyond the influence of genetic differences on epigenetic state, and we showed that hypomethylated regions are correlated with higher gene expression. Our results indicate that epigenetic mechanisms are either not involved in the rapid plastic response to environmental change in this species, or involve only few changes in trans that are sufficient to trigger concerted changes in the expression of many genes, and phenotypic responses by multiple traits.

scholarly journals Genetic basis of phenotypic plasticity and genotype x environment interaction in a multi-parental population

2020 ◽  
Author(s):  
Isidore Diouf ◽  
Laurent Derivot ◽  
Shai Koussevitzky ◽  
Yolande Carretero ◽  
Frédérique Bitton ◽  
...  
Keyword(s):  
Phenotypic Plasticity ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Linear Models ◽  
Global Climate ◽  
Functional Characterization ◽  
Genotype X Environment Interaction ◽  
Environment Interaction ◽  
Multiple Traits ◽  
Genotype X Environment

AbstractDeciphering the genetic basis of phenotypic plasticity and genotype x environment interaction (GxE) is of primary importance for plant breeding in the context of global climate change. Tomato is a widely cultivated crop that can grow in different geographical habitats and which evinces a great capacity of expressing phenotypic plasticity. We used a multi-parental advanced generation intercross (MAGIC) tomato population to explore GxE and plasticity for multiple traits measured in a multi-environment trial (MET) design comprising optimal cultural conditions and water deficit, salinity and heat stress over 12 environments. Substantial GxE was observed for all the traits measured. Different plasticity parameters were estimated through the Finlay-Wilkinson and factorial regression models and used together with the genotypic means for quantitative trait loci (QTL) mapping analyses. Mixed linear models were further used to investigate the presence of interactive QTLs (QEI). The results highlighted a complex genetic architecture of tomato plasticity and GxE. Candidate genes that might be involved in the occurrence of GxE were proposed, paving the way for functional characterization of stress response genes in tomato and breeding for climate-adapted crop.HighlightThe genetic architecture of tomato response to several abiotic stresses is deciphered. QTL for plasticity and QTL x Environment were identified in a highly recombinant MAGIC population.

scholarly journals Response of Regulatory Genetic Variation in Gene Expression to Environmental Change in Drosophila melanogaster

2020 ◽  
Author(s):  
Wen Huang ◽  
Mary Anna Carbone ◽  
Richard F. Lyman ◽  
Robert H. H. Anholt ◽  
Trudy F. C. Mackay
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Genetic Architecture ◽  
Genetic Variance ◽  
Network Connectivity ◽  
Genotype By Environment Interaction ◽  
Stabilizing Selection ◽  
Environment Interaction ◽  
Genotype By Environment ◽  
Phenotypic Responses

AbstractThe genetics of phenotypic responses to changing environments remains elusive. Using whole genome quantitative gene expression as a model, we studied how the genetic architecture of regulatory variation in gene expression changed in a population of fully sequenced inbred Drosophila melanogaster strains when flies developed at different environments (25 °C and 18 °C). We found a substantial fraction of the transcriptome exhibited genotype by environment interaction, implicating environmentally plastic genetic architecture of gene expression. Genetic variance in expression increased at 18 °C relative to 25 °C for most genes that had a change in genetic variance. Although the majority of expression quantitative trait loci (eQTLs) for the gene expression traits in the two environments were shared and had similar effects, analysis of the environment-specific eQTLs revealed enrichment of binding sites for two transcription factors. Finally, although genotype by environment interaction in gene expression could potentially disrupt genetic networks, the co-expression networks were highly conserved across environments. Genes with higher network connectivity were under stronger stabilizing selection, suggesting that stabilizing selection on expression plays an important role in promoting network robustness.

scholarly journals Genotype by environment interaction for gene expression in Drosophila melanogaster

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Wen Huang ◽  
Mary Anna Carbone ◽  
Richard F. Lyman ◽  
Robert R. H. Anholt ◽  
Trudy F. C. Mackay
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Genetic Architecture ◽  
Genetic Variance ◽  
Network Connectivity ◽  
Genotype By Environment Interaction ◽  
Stabilizing Selection ◽  
Environment Interaction ◽  
Genotype By Environment ◽  
Phenotypic Responses

Abstract The genetics of phenotypic responses to changing environments remains elusive. Using whole-genome quantitative gene expression as a model, here we study how the genetic architecture of regulatory variation in gene expression changed in a population of fully sequenced inbred Drosophila melanogaster strains when flies developed in different environments (25 °C and 18 °C). We find a substantial fraction of the transcriptome exhibited genotype by environment interaction, implicating environmentally plastic genetic architecture of gene expression. Genetic variance in expression increases at 18 °C relative to 25 °C for most genes that have a change in genetic variance. Although the majority of expression quantitative trait loci (eQTLs) for the gene expression traits in the two environments are shared and have similar effects, analysis of the environment-specific eQTLs reveals enrichment of binding sites for two transcription factors. Finally, although genotype by environment interaction in gene expression could potentially disrupt genetic networks, the co-expression networks are highly conserved across environments. Genes with higher network connectivity are under stronger stabilizing selection, suggesting that stabilizing selection on expression plays an important role in promoting network robustness.

The Mechanisms Behind the Biological Activity of Flavonoids

2019 ◽  
Vol 26 (39) ◽  
pp. 6976-6990 ◽  
Author(s):  
Ana María González-Paramás ◽  
Begoña Ayuda-Durán ◽  
Sofía Martínez ◽  
Susana González-Manzano ◽  
Celestino Santos-Buelga
Keyword(s):  
Gene Expression ◽  
Biological Activity ◽  
Phenolic Compounds ◽  
Intracellular Signaling ◽  
Molecular Mechanisms ◽  
Radical Scavenging ◽  
Model Organism ◽  
Stress Theory ◽  
Radical Scavenging Properties

: Flavonoids are phenolic compounds widely distributed in the human diet. Their intake has been associated with a decreased risk of different diseases such as cancer, immune dysfunction or coronary heart disease. However, the knowledge about the mechanisms behind their in vivo activity is limited and still under discussion. For years, their bioactivity was associated with the direct antioxidant and radical scavenging properties of phenolic compounds, but nowadays this assumption is unlikely to explain their putative health effects, or at least to be the only explanation for them. New hypotheses about possible mechanisms have been postulated, including the influence of the interaction of polyphenols and gut microbiota and also the possibility that flavonoids or their metabolites could modify gene expression or act as potential modulators of intracellular signaling cascades. This paper reviews all these topics, from the classical view as antioxidants in the context of the Oxidative Stress theory to the most recent tendencies related with the modulation of redox signaling pathways, modification of gene expression or interactions with the intestinal microbiota. The use of C. elegans as a model organism for the study of the molecular mechanisms involved in biological activity of flavonoids is also discussed.

Phenotypic plasticity

2018 ◽  
Author(s):  
Karen D. Williams ◽  
Marla B. Sokolowski
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
Environmental Change ◽  
Behavioral Plasticity ◽  
Behavioral Flexibility ◽  
Insect Behavior ◽  
Behavioral Variability ◽  
Gene By Environment Interactions ◽  
Affect Gene Expression

Why is there so much variation in insect behavior? This chapter will address the sources of behavioral variability, with a particular focus on phenotypic plasticity. Variation in social, nutritional, and seasonal environmental contexts during development and adulthood can give rise to phenotypic plasticity. To delve into mechanism underlying behavioral flexibility in insects, examples of polyphenisms, a type of phenotypic plasticity, will be discussed. Selected examples reveal that environmental change can affect gene expression, which in turn can affect behavioral plasticity. These changes in gene expression together with gene-by-environment interactions are discussed to illuminate our understanding of insect behavioral plasticity.

scholarly journals A comparison of the nutrient composition and statistical profile in red pepper fruits (Capsicums annuum L.) based on genetic and environmental factors

2019 ◽  
Vol 62 (1) ◽  
Author(s):  
Eun-Ha Kim ◽  
So-Young Lee ◽  
Da-Young Baek ◽  
Soo-Yun Park ◽  
Sang-Gu Lee ◽  
...  
Keyword(s):  
Amino Acids ◽  
Dietary Fiber ◽  
Compositional Data ◽  
Environment Interaction ◽  
Free Sugars ◽  
Insoluble Dietary Fiber ◽  
Genotype Effect ◽  
Year Effect ◽  
Genotype Environment Interaction ◽  
Red Peppers

Abstract Red peppers are a remarkable source of nutrients in the human diet. However, comprehensive studies have not reported on the effects of genotype, cultivation region, and year on pepper fruit characteristics. To address this, 12 commercial pepper varieties were grown at two locations in South Korea, during 2016 and 2017, representing four environments, and concentrations of proximate, minerals, amino acids, fatty acids, capsaicinoids, and free sugars in pepper pericarps were determined. Variation in most nutrients was observed among the 12 varieties grown within each location in each year, indicating a significant genotype effect. Statistical analysis of combined data showed significant differences among varieties, locations, and years for the measured components. The % variability analysis demonstrated that environment (location and year) and genotype-environment interaction contributed more to the nutritional contents than genotype alone. Particularly, variation in many amino acids, capsaicinoids, free sugars, and myristic acid was attributed to location. Year effect was significant for palmitoleic acid, ash, tryptophan, copper, linolenic acid, crude fiber, and tyrosine. Insoluble dietary fiber, soluble dietary fiber, sodium, sulfate, linoleic acid, and alanine were primarily varied by genotype–environment interaction. Palmitic acid was the trait the most highly affected by genotype. Cultivation and the genotype–environment interaction have a major role in determining the composition of 12 pepper varieties across four environments. The data from this study could explain the natural variation in the compositional data of peppers by genotypes and environments.

scholarly journals Genotype X Environment Interaction of Food Barley

2015 ◽  
Vol 21 ◽  
pp. 41-48
Author(s):  
Gebremedhin Welu
Keyword(s):  
Grain Yield ◽  
Block Design ◽  
Genotype X Environment Interaction ◽  
Environment Interaction ◽  
Genotype X Environment ◽  
Genotype Effect ◽  
Environment Effects ◽  
Randomized Complete Block Design ◽  
Barley Genotypes

The objective of this experiment was to estimate the magnitude of genotype X environment interaction on grain yield and yield related traits. Twelve varieties of food barley were included in the study planted in randomized complete block design with three replications. The ANOVA of combined and individual location revealed significant differences among the food barley genotypes for grain yield and other traits. The results of ANOVA for grain yield showed highly significant (p≤0.01) differences among genotypes evaluated for grain yield at Maychew and significant (p≤0.05) differences in Korem, Alage and Mugulat. The ANOVA over locations showed a highly significant (p≤0.01) variation for the genotype effect, environment effects, genotype X environment interaction (GEI) effect and significant (p≤0.05) variation for GEI effect of yield and for most of the yield related traits of food barley genotypes. Haftysene, Yidogit, Estayish and Basso were the genotypes with relatively high mean grain yield across all locations and they are highly performing genotypes to the area. Among locations, the highest mean grain yield was recorded at Korem and it was a suited environment to all the genotypes whereas Mugulat is unfavoured one. ECOPRINT 21: 41-48, 2014DOI: http://dx.doi.org/10.3126/eco.v21i0.11903

Phenotypic plasticity in gene expression contributes to divergence of locally adapted populations ofFundulus heteroclitus

2015 ◽  
Vol 24 (13) ◽  
pp. 3345-3359 ◽  
Author(s):  
David I. Dayan ◽  
Douglas L. Crawford ◽  
Marjorie F. Oleksiak
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity

scholarly journals Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

2017 ◽  
Author(s):  
Marina Pais ◽  
Kentaro Yoshida ◽  
Artemis Giannakopoulou ◽  
Mathieu A. Pel ◽  
Liliana M. Cano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phenotypic Plasticity ◽  
South American ◽  
Nucleotide Polymorphisms ◽  
Natural Ecosystems ◽  
Asexual Lineage ◽  
Irish Famine ◽  
Eukaryotic Microbes ◽  
And Migration ◽  
Potato Famine

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are an expanding threat to crops, wild animals and natural ecosystems (Fisher et al. 2012,Kupferschmidt 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl and Thomma 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Cooke et al. 2012, Yoshida et al. 2013,Yoshida et al. 2014). Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by compared sibling strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Forbes et al. 1997, Oyarzun et al. 1998, Delgado et al. 2013, Yoshida et al. 2013, Yoshida et al. 2014). We detected numerous examples of structural variation, nucleotide polymorphisms and gene conversion within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. These results highlight the exceptional genetic and phenotypic plasticity that underpins host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen.

scholarly journals Assessment of Tuber Yield Stability and Adaptability of Some Elite Yam Genotypes in the Guinea Savannah Ecology of Northern Ghana

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Joseph Adjebeng-Danquah ◽  
Kwabena Acheremu ◽  
Emmanuel Boachie Chamba ◽  
Freda Ansaah Agyapong ◽  
Alhassan Sayibu
Keyword(s):  
Yield Components ◽  
Tuber Yield ◽  
Block Design ◽  
Genotypic Variation ◽  
Sum Of Squares ◽  
Yield Stability ◽  
Northern Ghana ◽  
Environment Interaction ◽  
Genotype Effect ◽  
Gxe Interaction

Studies were conducted to determine tuber yield stability and adaptability of some elite yam (Dioscorea sp.) genotypes in northern Ghana. Ten elite exotic yam genotypes alongside one locally cultivated farmer-preferred variety, Laribako, were grown in five environments between 2010 and 2012. These 11 genotypes were arranged in a randomised complete block design with three replications and assessed for tuber yield and yield components. Analysis of variance indicated significant p < 0.05 genotypic variation for tuber yield and the yield components studied. Genotype × environment interaction effect was significant p < 0.05 for tuber yield and mean tuber weight but not significant p > 0.05 for number of tubers per mound. Apart from genotype 95/18922, all the exotic genotypes had significantly p < 0.05 higher tuber yields than the local check, Laribako. The highest tuber yield (16.03 t ha−1) across environments was obtained from 96/19158 followed by 95/00594 (14.9 t ha−1). According to the additive main effect multiplicative interaction (AMMI) analysis, genotype (G), environment (E), and GxE interaction, respectively, explained 39.71%, 36.03%, and 24.26% of the total sum of squares for tuber yield. For number of tubers per plant, GxE effect explained the greatest percentage (60.46%) of the total sum of squares compared to genotype effect (22.00%) and environment effect (17.54%). The local variety, Laribako, was more stable across all environments though low yielding compared to the exotic genotypes. Three genotypes, 95/19158, 95/19177, and 96/02025, were more stable across environments than the other exotic genotypes. Genotype 95/18544 was the most sensitive and for that matter responded positively in the favorable environments. The study identified genotypes with specific and general adaptation potential across different environments for tuber yield that can be further tested in on-farm trials for possible release.

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