Biology subjects

Calic, I.

Publications and source records attributed to Calic, I..

4 recordsLinked to original sources

bioRxiv2025

The complex molecular basis of enhanced stress resilience in extreme drought-tolerant Arabis grassland species

Background and AimsPlant species in competitive meadows must tolerate extreme stress, yet the mechanisms underlying resilience remain poorly understood. Arabis nemorensis, an endangered selfing species of Euro- pean floodplain grasslands, experiences both flooding and drought and hybridizes with its close relative, A. sagittata. We investigated how these species differ in drought survival and the molec- ular basis of their responses. MethodsSympatric lineages of A. nemorensis and A. sagittata were compared in a controlled dry-down experiment, complemented by transcriptome and small RNA profiling, and machine-learning anal- ysis of cis-regulatory motifs. Key ResultsBoth species wilted at 5% soil moisture, but A. sagittata recovered more effectively (90% vs. 50%). This difference was not explained by a major QTL, suggesting a polygenic basis. Transcrip- tome profiling revealed stronger induction in A. sagittata (6,359 vs. 5,571 differentially expressed genes). Small RNA analysis identified species-specific regulation of miR408, a conserved drought regulator. Machine-learning identified 307 sequence motifs predictive of stress-responsive expres- sion, with motif distributions indicating distinct regulatory networks. ConclusionsThis study reveals the polygenic and regulatory complexity underlying divergent drought resili- ence strategies in the closely related species thriving in grassland environments. Arabis nemorensis and its close relative A. sagittata co-occur in a floodplain meadow exposed to flooding and drought. In dry-down experiments, A. sagittata recovered more effectively than A. nemorensis. Transcriptome and small RNA analyses revealed stronger stress responses in A. sagittata, including regulation of miR408. These differences result from different regulatory networks and have a polygenic basis.

plant biology↗

bioRxiv2025

Environment-dependent selection impacts heritable developmental stability and trait canalization in rice

Canalization, or the maintenance of trait values regardless of environmental or genetic variability, is fundamentally important for maintaining developmental stability. While this concept was described decades ago, we still know relatively little about how canalization is influenced by environmental stress, how it is shaped by natural selection, and the genetic underpinnings of canalization. In this study, we examined natural selection on microenvironmental canalization in rice (Oryza sativa) in wet and dry field conditions. We measured developmental stability in genetically identical replicates obtained from geographically widespread Indica and Japonica rice accessions, providing precise estimates of canalization in thousands of plants. We found that drought stress decreased canalization, showing that stress can increase instability. We also found evidence that canalization can evolve, given that canalization of several traits was heritable and under selection. We further uncovered specific genes underlying canalization, with genetic mapping and functional genetic experiments showing that the bZIP transcription factor-encoding gene OsTGA5/rTGA2.3, which is part of a module that balances stress response and plant growth, regulates canalization of several traits in an environment-dependent manner. At a genome-wide scale, canalization was associated with lower gene expression stochasticity at an earlier life stage, indicating that expression variation can reduce canalization and increase instability. Trait canalization was also positively correlated to temperature at accessions source environments, suggesting that selection on canalization can vary among environments. Overall, our study provides novel insights into the molecular genetic basis of environmental differences in developmental stability and how it might be shaped by selection. SignificanceMechanisms stabilizing organismal development in response to genetic mutations or environmental stressors (canalization) have been reported for numerous animals and plants, but their underlying genetic basis and whether they may be shaped by selection remain unclear. Here, we report patterns of drought-induced trait decanalization in populations of rice (Oryza sativa) grown in field environments. We determined that trait canalization is heritable and can evolve separately from trait means. We identified the gene OsTGA5, part of a regulatory module shaping trade-offs between growth and stress responses, as impacting trait canalization. Plants with less noisy gene expression and evolving in warmer environments display greater developmental stability, contributing to the notion that canalization in rice may be adaptive.

evolutionary biology↗

bioRxiv2024

System genomics of salinity stress response in rice

Populations can adapt to stressful environments through changes in gene expression. However, the fitness effect of gene expression in mediating stress response and adaptation remains largely unexplored. Here, we use an integrative field dataset obtained from 780 plants of Oryza sativa ssp. indica (rice) grown in a field experiment under normal or moderate salt stress conditions to examine selection and evolution of gene expression variation under salinity stress conditions. We find that salinity stress induces increased selective pressure on gene expression. Further, we show that trans-eQTLs rather than cis-eQTLs are primarily associated with rices gene expression under salinity stress, potentially via a few master-regulators. Importantly, and contrary to the expectations, we find that cis-trans reinforcement is more common than cis-trans compensation which may be reflective of rice diversification subsequent to domestication. We further identify genetic fixation as the likely mechanism underlying this compensation/reinforcement. Additionally, we show that cis- and trans-eQTLs are under balancing and purifying selection, respectively, giving us insights into the evolutionary dynamics of gene expression variation. By examining genomic, transcriptomic, and phenotypic variation across a rice population, we gain insights into the molecular and genetic landscape underlying adaptive salinity stress responses, which is relevant for other crops and other stresses.

systems biology↗

bioRxiv2021

Fitness costs and benefits of gene expression plasticity in rice under drought

Genome-wide gene expression changes in response to environmental variability have been widely documented, but we lack detailed and comprehensive understanding of the interplay between this form of phenotypic plasticity and natural selection. Selection on expression plasticity may be limited by environment-specific costs, and plasticity may in turn affect selection on baseline expression levels. Here, we address this fundamental issue by measuring selection on drought-induced plasticity of leaf transcripts in field-grown rice populations. Selection disfavored switching off housekeeping genes under drought. This stress-induced dysregulation did not constrain selection on baseline transcript levels, suggesting compensatory evolution may be possible. Selection rarely acted strongly on individual transcripts but worked polygenically on gradual (continuous) plasticity of co-expressed gene modules regulating photosynthesis via known drought-responsive transcription factors. Finally, selection was tied to inefficient gene architectural features and metabolic costs of expression. Our study provides a genome-wide view of costs and benefits of gene expression plasticity.

evolutionary biology↗