scholarly journals Transcriptome analysis reveals plasticity in gene regulation due to environmental cues in Primula sikkimensis, a high altitude plant species

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Priya Darshini Gurung ◽  
Atul Kumar Upadhyay ◽  
Pardeep Kumar Bhardwaj ◽  
Ramanathan Sowdhamini ◽  
Uma Ramakrishnan
Keyword(s):  
Climate Change ◽  
Gene Expression ◽  
Plant Species ◽  
Ambient Condition ◽  
Differentially Expressed ◽  
Transplant Experiment ◽  
Range Limit ◽  
Ambient Conditions ◽  
Adaptation To Climate Change ◽  
Altitudinal Range

Abstract Background Studying plasticity in gene expression in natural systems is crucial, for predicting and managing the effects of climate change on plant species. To understand the contribution of gene expression level variations to abiotic stress compensation in a Himalaya plant (Primula sikkimensis), we carried out a transplant experiment within (Ambient), and beyond (Below Ambient and Above Ambient) the altitudinal range limit of species. We sequenced nine transcriptomes (three each from each altitudinal range condition) using Illumina sequencing technology. We compared the fitness variation of transplants among three transplant conditions. Results A large number of significantly differentially expressed genes (DEGs) between below ambient versus ambient (109) and above ambient versus ambient (85) were identified. Transcripts involved in plant growth and development were mostly up-regulated in below ambient conditions. Transcripts involved in signalling, defence, and membrane transport were mostly up-regulated in above ambient condition. Pathway analysis revealed that most of the genes involved in metabolic processes, secondary metabolism, and flavonoid biosynthesis were differentially expressed in below ambient conditions, whereas most of the genes involved in photosynthesis and plant hormone signalling were differentially expressed in above ambient conditions. In addition, we observed higher reproductive fitness in transplant individuals at below ambient condition compared to above ambient conditions; contrary to what we expect from the cold adaptive P. sikkimensis plants. Conclusions We reveal P. sikkimensis’s capacity for rapid adaptation to climate change through transcriptome variation, which may facilitate the phenotypic plasticity observed in morphological and life history traits. The genes and pathways identified provide a genetic resource for understanding the temperature stress (both the hot and cold stress) tolerance mechanism of P. sikkimensis in their natural environment.

scholarly journals Phenotypic variation and differentiated gene expression of Australian plants in response to declining rainfall

2016 ◽  
Vol 3 (11) ◽  
pp. 160637 ◽  
Author(s):  
Haylee D'Agui ◽  
William Fowler ◽  
Sim Lin Lim ◽  
Neal Enright ◽  
Tianhua He
Keyword(s):  
Climate Change ◽  
Gene Expression ◽  
Plant Species ◽  
Phenotypic Variation ◽  
Regulation Of Gene Expression ◽  
Annual Rainfall ◽  
Severe Drought ◽  
Rapid Adaptation ◽  
Adaptation To Climate Change ◽  
Winter Rainfall

Declining rainfall is projected to have negative impacts on the demographic performance of plant species. Little is known about the adaptive capacity of species to respond to drying climates, and whether adaptation can keep pace with climate change. In fire-prone ecosystems, episodic recruitment of perennial plant species in the first year post-fire imposes a specific selection environment, offering a unique opportunity to quantify the scope for adaptive response to climate change. We examined the growth of seedlings of four fire-killed species under control and drought conditions for seeds from populations established in years following fire receiving average-to-above-average winter rainfall, or well-below-average winter rainfall. We show that offspring of plants that had established under drought had more efficient water uptake, and/or stored more water per unit biomass, or developed denser leaves, and all maintained higher survival in simulated drought than did offspring of plants established in average annual rainfall years. Adaptive phenotypic responses were not consistent across all traits and species, while plants that had established under severe drought or established in years with average-to-above-average rainfall had an overall different physiological response when growing either with or without water constraints. Seedlings descended from plants established under severe drought also had elevated gene expression in key pathways relating to stress response. Our results demonstrate the capacity for rapid adaptation to climate change through phenotypic variation and regulation of gene expression. However, effective and rapid adaptation to climate change may vary among species depending on their capacity to maintain robust populations under multiple stresses.

scholarly journals Selenium Regulates Gene Expression for Glucosinolate and Carotenoid Biosynthesis in Arabidopsis

2011 ◽  
Vol 136 (1) ◽  
pp. 23-34 ◽  
Author(s):  
Carl E. Sams ◽  
Dilip R. Panthee ◽  
Craig S. Charron ◽  
Dean A. Kopsell ◽  
Joshua S. Yuan
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Plant Species ◽  
Chlorophyll Biosynthesis ◽  
Plant Secondary Metabolites ◽  
Carotenoid Biosynthesis ◽  
Differentially Expressed ◽  
Biosynthesis Pathway ◽  
Tissue Samples ◽  
Expression Of Genes

Glucosinolates (GSs) and carotenoids are important plant secondary metabolites present in several plant species, including arabidopsis (Arabidopsis thaliana). Although genotypic and environmental regulation of GSs and carotenoid compounds has been reported, few studies present data on their regulation at the molecular level. Therefore, the objective of this study was to explore differential expression of genes associated with GSs and carotenoids in arabidopsis in response to selenium fertilization, shown previously to impact accumulations of both classes of metabolites in Brassica species. Arabidopsis was grown under 0.0 or 10.0 μM Na2SeO4 in hydroponic culture. Shoot and root tissue samples were collected before anthesis to measure GSs and carotenoid compounds and conduct gene expression analysis. Gene expression was determined using arabidopsis oligonucleotide chips containing more than 31,000 genes. There were 1274 differentially expressed genes in response to selenium (Se), of which 516 genes were upregulated. Ontology analysis partitioned differentially expressed genes into 20 classes. Biosynthesis pathway analysis using AraCyc revealed that four GSs, one carotenoid, and one chlorophyll biosynthesis pathways were invoked by the differentially expressed genes. Involvement of the same gene in more than one biosynthesis pathway indicated that the same enzyme may be involved in multiple GS biosynthesis pathways. The decrease in carotenoid biosynthesis under Se treatment occurred through the downregulation of phytoene synthase at the beginning of the carotenoid biosynthesis pathway. These findings may be useful to modify the GS and carotenoid levels in arabidopsis and may lead to modification in agriculturally important plant species.

scholarly journals Molecular Tools for Adapting Viticulture to Climate Change

2021 ◽  
Vol 12 ◽  
Author(s):  
Éric Gomès ◽  
Pascale Maillot ◽  
Éric Duchêne
Keyword(s):  
Climate Change ◽  
Gene Expression ◽  
Management Practices ◽  
New Technologies ◽  
Developmental Stages ◽  
Current Knowledge ◽  
Sugar Content ◽  
Regulation Of Gene Expression ◽  
Molecular Tools ◽  
Adaptation To Climate Change

Adaptation of viticulture to climate change includes exploration of new geographical areas, new training systems, new management practices, or new varieties, both for rootstocks and scions. Molecular tools can be defined as molecular approaches used to study DNAs, RNAs, and proteins in all living organisms. We present here the current knowledge about molecular tools and their potential usefulness in three aspects of grapevine adaptation to the ongoing climate change. (i) Molecular tools for understanding grapevine response to environmental stresses. A fine description of the regulation of gene expression is a powerful tool to understand the physiological mechanisms set up by the grapevine to respond to abiotic stress such as high temperatures or drought. The current knowledge on gene expression is continuously evolving with increasing evidence of the role of alternative splicing, small RNAs, long non-coding RNAs, DNA methylation, or chromatin activity. (ii) Genetics and genomics of grapevine stress tolerance. The description of the grapevine genome is more and more precise. The genetic variations among genotypes are now revealed with new technologies with the sequencing of very long DNA molecules. High throughput technologies for DNA sequencing also allow now the genetic characterization at the same time of hundreds of genotypes for thousands of points in the genome, which provides unprecedented datasets for genotype-phenotype associations studies. We review the current knowledge on the genetic determinism of traits for the adaptation to climate change. We focus on quantitative trait loci and molecular markers available for developmental stages, tolerance to water stress/water use efficiency, sugar content, acidity, and secondary metabolism of the berries. (iii) Controlling the genome and its expression to allow breeding of better-adapted genotypes. High-density DNA genotyping can be used to select genotypes with specific interesting alleles but genomic selection is also a powerful method able to take into account the genetic information along the whole genome to predict a phenotype. Modern technologies are also able to generate mutations that are possibly interesting for generating new phenotypes but the most promising one is the direct editing of the genome at a precise location.

scholarly journals Gene Regulatory Divergence Between Locally Adapted Ecotypes in Their Native Habitats

2017 ◽  
Author(s):  
Billie A. Gould ◽  
Yani Chen ◽  
David B. Lowry
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Specific Gene ◽  
Transplant Experiment ◽  
Ecological Specialization ◽  
Reciprocal Transplant Experiment ◽  
Chromosome Inversion ◽  
Gene Regulatory

ABSTRACTLocal adaptation is a key driver of ecological specialization and the formation of new species. Despite its importance, the evolution of gene regulatory divergence among locally-adapted populations is poorly understood, especially how that divergence manifests in nature. Here, we evaluate gene expression divergence and allele-specific gene expression responses for locally-adapted coastal perennial and inland annual accessions of the yellow monkeyflower, Mimulus guttatus, in a field reciprocal transplant experiment. Overall, 6765 (73%) of surveyed genes were differentially expressed between coastal and inland habitats, while 7213 (77%) were differentially expressed between the coastal perennial and inland annual accessions. Further, 18% of transcripts had significant genotype x site (GxE) effects. Habitat-specific differential expression was found for 62% of the GxE transcripts (differential expression in one habitat, but not the other), while only 94 (∼5%) GxE transcripts had crossing reaction norms. Cis-regulatory variation was pervasive, affecting 79% (5532) of differentially expressed genes. We detected trans effects for 52% (3611) of differentially expressed genes. Consistent with the supergene hypothesis of chromosome inversion evolution, a locally adaptive inversion was enriched for cis-regulatory divergence. These results provide multiple new insights into the evolution of transcriptome-wide gene regulatory divergence and plasticity among locally adapted populations.

scholarly journals Evolutionary trade-offs between baseline and plastic gene expression in two congeneric oyster species

2019 ◽  
Vol 15 (6) ◽  
pp. 20190202 ◽  
Author(s):  
Ao Li ◽  
Li Li ◽  
Wei Wang ◽  
Guofan Zhang
Keyword(s):  
Climate Change ◽  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Thermal Adaptation ◽  
Common Garden ◽  
Evolutionary Strategy ◽  
Genetic Adaptation ◽  
Ambient Conditions ◽  
Oyster Species ◽  
Trade Offs

Organismal responses to environmental stresses are a determinant of the effect of climate change. These can occur through the regulation of gene expression, involving genetic adaptation and plastic changes as evolutionary strategy. Heat shock protein ( hsp ) family genes are extensively expanded and play important roles in thermal adaptation in oysters. We investigated expression of all heat-responsive hsp s in two allopatric congeneric oyster species, Crassostrea gigas and C. angulata , which are respectively distributed along the northern and southern coasts of China, using common garden and reciprocal transplant experiments. Our results showed that hsp s in C. gigas have evolved higher basal levels of expression under ambient conditions at each field site, with lower expression plasticity in response to heat stress in comparison to C. angulata , which exhibited lower baseline expression but higher expression plasticity. This pattern was fixed regardless of environmental disturbance, potentially implying genetic assimilation. Our findings indicate divergent adaptive strategies with underlying evolutionary trade-offs between genetic adaptation and plasticity at the molecular level in two oyster congeners in the face of rapid climate change.

scholarly journals Climate change and anthropogenic food manipulation interact in shifting the distribution of a large herbivore at its altitudinal range limit

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Julius G. Bright Ross ◽  
Wibke Peters ◽  
Federico Ossi ◽  
Paul R. Moorcroft ◽  
Emanuele Cordano ◽  
...  
Keyword(s):  
Climate Change ◽  
Snow Cover ◽  
Roe Deer ◽  
Space Use ◽  
Resource Provisioning ◽  
Range Limits ◽  
Range Limit ◽  
Large Herbivore ◽  
Altitudinal Range ◽  
Snow Conditions

AbstractUngulates in alpine ecosystems are constrained by winter harshness through resource limitation and direct mortality from weather extremes. However, little empirical evidence has definitively established how current climate change and other anthropogenic modifications of resource availability affect ungulate winter distribution, especially at their range limits. Here, we used a combination of historical (1997–2002) and contemporary (2012–2015) Eurasian roe deer (Capreolus capreolus) relocation datasets that span changes in snowpack characteristics and two levels of supplemental feeding to compare and forecast probability of space use at the species’ altitudinal range limit. Scarcer snow cover in the contemporary period interacted with the augmented feeding site distribution to increase the elevation of winter range limits, and we predict this trend will continue under climate change. Moreover, roe deer have shifted from historically using feeding sites primarily under deep snow conditions to contemporarily using them under a wider range of snow conditions as their availability has increased. Combined with scarcer snow cover during December, January, and April, this trend has reduced inter-annual variability in space use patterns in these months. These spatial responses to climate- and artificial resource-provisioning shifts evidence the importance of these changing factors in shaping large herbivore spatial distribution and, consequently, ecosystem dynamics.

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