Plastic and adaptive gene expression patterns associated with temperature stress in Arabidopsis thaliana

Swindell, William R.; Huebner, Marianne; Weber, Andreas P.M.

doi:10.1038/sj.hdy.6800975

Cited by 64 publications

(63 citation statements)

References 41 publications

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“…Moreover, comparisons “Home versus Away” were made to identify genes which exhibited a plastic pattern of gene expression between test and control groups of the same population and thus are the most involved in the acclimation processes (see, e.g., Swindell et al., 2007). In the “Home versus Away” comparisons (Table S3a, c), shallow plants (i.e., SS vs. SD) during the low‐light acclimation exhibited plastic regulation in five target genes (i.e., LHCHA‐4, PSBS, psbA, PHYC, and ZTL; Table S3a).…”

Section: Resultsmentioning

confidence: 99%

“…When changes in environmental conditions occur, species can shift their distributional range (i.e., Parmesan & Yohe, 2003; Perry, Low, Ellis, & Reynolds, 2005) in order to migrate in more suitable habitats. Alternatively, organisms can compensate environmental fluctuations with phenotypic plasticity (Franks, Sim, & Weis, 2007; Franks, Weber, & Aitken, 2014; Ghalambor, McKay, Carroll, & Reznick, 2007; Gienapp, Teplitsky, Alho, Mills, & Merilä, 2008; Merilä & Hendry, 2014), which can be highlighted at different hierarchy levels of the biological organization, through adjustments of gene expression (i.e., Granados‐Cifuentes, Bellantuono, Ridgway, Hoegh‐Guldberg, & Rodriguez‐Lanetty, 2013; Jeukens, Bittner, Knudsen, & Bernatchez, 2009; Larsen, Nielsen, Williams, & Loeschcke, 2008; Larsen et al., 2007; Pavey, Collin, Nosil, & Rogers, 2010; Swindell, Huebner, & Weber, 2007), developmental features (i.e., Sultan, 2000; West‐Eberhard, 2005), and life‐history traits (Dowdall et al., 2012). Moreover, species can also evolve genetic differentiation among populations (i.e., local adaptation; Kawecki & Ebert, 2004) due to ecological selection (Keller & Seehausen, 2012; Schluter, 2009) and intraspecific competition (García‐Ramos & Huang, 2013).…”

Section: Introductionmentioning

confidence: 99%

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Long‐term acclimation to reciprocal light conditions suggests depth‐related selection in the marine foundation speciesPosidonia oceanica

Dattolo

Marín-Guirao

Ruiz

et al. 2017

Ecology and Evolution

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Phenotypic differences among populations of the same species reflect selective responses to ecological gradients produced by variations in abiotic and biotic factors. Moreover, they can also originate from genetic differences among populations, due to a reduced gene flow. In this study, we examined the extent of differences in photo‐acclimative traits of Posidonia oceanica (L.) Delile clones collected above and below the summer thermocline (i.e., −5 and −25 m) in a continuous population extending along the water depth gradient. During a reciprocal light exposure and subsequent recovery in mesocosms, we assessed degree of phenotypic plasticity and local adaptation of plants collected at different depths, by measuring changes in several traits, such as gene expression of target genes, photo‐physiological features, and other fitness‐related traits (i.e., plant morphology, growth, and mortality rates). Samples were also genotyped, using microsatellite markers, in order to evaluate the genetic divergence among plants of the two depths. Measures collected during the study have shown a various degree of phenotypic changes among traits and experimental groups, the amount of phenotypic changes observed was also dependent on the type of light environments considered. Overall plants collected at different depths seem to be able to acclimate to reciprocal light conditions in the experimental time frame, through morphological changes and phenotypic buffering, supported by the plastic regulation of a reduced number of genes. Multivariate analyses indicated that plants cluster better on the base of their depth origin rather than the experimental light conditions applied. The two groups were genetically distinct, but the patterns of phenotypic divergence observed during the experiment support the hypothesis that ecological selection can play a role in the adaptive divergence of P. oceanica clones along the depth gradient.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Long‐term acclimation to reciprocal light conditions suggests depth‐related selection in the marine foundation speciesPosidonia oceanica

Dattolo

Marín-Guirao

Ruiz

et al. 2017

Ecology and Evolution

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“…Auxin is an important plant hormone, modulating many aspects of plant growth, development and responses to biotic and abiotic stress (Wolters and Jürgens, 2009;Peleg and Blumwald, 2011). Variation at loci underlying auxin expression may thus have profound fitness consequences, as has been demonstrated in the context of temperature stress (for example, Swindell et al, 2007;Lee et al, 2014), plant-pathogen interactions (Kazan and Manners, 2009) and symbiotic interactions (for example, Reddy et al, 2006). We correspondingly observed a significant association between SNP a2 and temperature at the regional scale (Table 2).…”

Section: Discussionmentioning

confidence: 61%

The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales

Kort¹,

Vandepitte²,

Mergeay³

et al. 2015

Heredity

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The evaluation of the molecular signatures of selection in species lacking an available closely related reference genome remains challenging, yet it may provide valuable fundamental insights into the capacity of populations to respond to environmental cues. We screened 25 native populations of the tree species Frangula alnus subsp. alnus (Rhamnaceae), covering three different geographical scales, for 183 annotated single-nucleotide polymorphisms (SNPs). Standard population genomic outlier screens were combined with individual-based and multivariate landscape genomic approaches to examine the strength of selection relative to neutral processes in shaping genomic variation, and to identify the main environmental agents driving selection. Our results demonstrate a more distinct signature of selection with increasing geographical distance, as indicated by the proportion of SNPs (i) showing exceptional patterns of genetic diversity and differentiation (outliers) and (ii) associated with climate. Both temperature and precipitation have an important role as selective agents in shaping adaptive genomic differentiation in F. alnus subsp. alnus, although their relative importance differed among spatial scales. At the 'intermediate' and 'regional' scales, where limited genetic clustering and high population diversity were observed, some indications of natural selection may suggest a major role for gene flow in safeguarding adaptability. High genetic diversity at loci under selection in particular, indicated considerable adaptive potential, which may nevertheless be compromised by the combined effects of climate change and habitat fragmentation.

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“…Comparative genomics studies have offered insight into mechanisms of divergence in salt tolerance between Arabidopsis and a close relative (Taji et al, 2004), and in metal accumulation among Arabidopsis species (Weber et al, 2006). Moreover, microarray analysis has shown that genome expression is highly responsive to temperature stress, and for some of these temperature-responsive genes expression variation among ecotypes correlates with the latitude from which they originate (Swindell et al, 2007): a pattern suggestive of adaptive divergence. Extensive genome resources for Arabidopsis are enabling genome re-sequencing of populations (e.g.…”

Section: Future Researchmentioning

confidence: 99%

Comparative genomics in ecological physiology: toward a more nuanced understanding of acclimation and adaptation

Whitehead

2012

Journal of Experimental Biology

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SummaryOrganisms that live in variable environments must adjust their physiology to compensate for environmental change. Modern functional genomics technologies offer global top-down discovery-based tools for identifying and exploring the mechanistic basis by which organisms respond physiologically to a detected change in the environment. Given that populations and species from different niches may exhibit different acclimation abilities, comparative genomic approaches may offer more nuanced understanding of acclimation responses, and provide insight into the mechanistic and genomic basis of variable acclimation. The physiological genomics literature is large and growing, as is the comparative evolutionary genomics literature. Yet, expansion of physiological genomics experiments to exploit taxonomic variation remains relatively undeveloped. Here, recent advances in the emerging field of comparative physiological genomics are considered, including examples of plants, bees and fish, and opportunities for further development are outlined particularly in the context of climate change research. Elements of robust experimental design are discussed with emphasis on the phylogenetic comparative approach. Understanding how acclimation ability is partitioned among populations and species in nature, and knowledge of the relevant genes and mechanisms, will be important for characterizing and predicting the ecological and evolutionary consequences of human-accelerated environmental change.

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Plastic and adaptive gene expression patterns associated with temperature stress in Arabidopsis thaliana

Cited by 64 publications

References 41 publications

Long‐term acclimation to reciprocal light conditions suggests depth‐related selection in the marine foundation speciesPosidonia oceanica

Long‐term acclimation to reciprocal light conditions suggests depth‐related selection in the marine foundation speciesPosidonia oceanica

The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales

Comparative genomics in ecological physiology: toward a more nuanced understanding of acclimation and adaptation

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