AIMC Topic: Gene Expression Regulation, Plant

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De novo assembly of Agave sisalana transcriptome in response to drought stress provides insight into the tolerance mechanisms.

Scientific reports
Agave, monocotyledonous succulent plants, is endemic to arid regions of North America, exhibiting exceptional tolerance to their xeric environments. They employ various strategies to overcome environmental constraints, such as crassulacean acid metab...

Comparative Analysis of the Cytology and Transcriptomes of the Cytoplasmic Male Sterility Line H276A and Its Maintainer Line H276B of Cotton (Gossypium barbadense L.).

International journal of molecular sciences
In this study, the tetrad stage of microspore development in a new cotton ( L.) cytoplasmic male sterility (CMS) line, H276A, was identified using paraffin sections at the abortion stage. To explore the molecular mechanism underlying CMS in cotton, a...

Coincidence of the threshold temperature of seasonal switching for diel transcriptomic oscillations and growth.

Plant & cell physiology
Predicting plant responses to global warming is essential for ecosystem management and crop yields. As many genes are controlled by the circadian clock, understanding the effects of temperature on transcriptomic rhythmicity under natural conditions i...

Gene expression and regulatory networks provide new insights into the similarity between nitrogen fixing and arbuscular mycorrhizal symbioses.

Plant & cell physiology
Although the evolutionarily younger nitrogen-fixing symbioses (NFS) occurring between plants and rhizobia are predominantly confined to legume species, they exhibit a series of highly conserved characteristics in common with the more ancestral arbusc...

Interspecies predictions of growth traits from quantitative transcriptome data acquired during fruit development.

Journal of experimental botany
Linking genotype and phenotype is a fundamental challenge in biology. In this respect, machine learning is playing a pivotal role in systems biology. As central phenotypic traits, fruit development and relative growth rate (RGR) result from interacti...

Machine learning based prediction by PlantCdMiner and experimental validation of cadmium-responsive genes in plants.

Journal of hazardous materials
Plants have evolved diverse adaptive mechanisms to sense and respond to environmental stimuli such as cadmium stress. The regulation of gene expression plays a critical role in plant responses to abiotic stress. However, homologous genes from differe...

Structure and function of Vitis vinifera Arabidopsis Response Regulator 1 (VvARR1) protein provide insights into the regulatory mechanism of grape fruit shape through gibberellin-cytokinin crosstalk.

International journal of biological macromolecules
Grape fruit shape is a crucial agricultural trait that significantly impacts the commercial value of grapes. In this study, we developed a machine learning system to classify grape fruit shapes, offering an objective phenotypic assessment method. Mul...

Machine-learning meta-analysis reveals ethylene as a central component of the molecular core in abiotic stress responses in Arabidopsis.

Nature communications
Understanding how plants adapt their physiology to overcome severe and often multifactorial stress conditions in nature is vital in light of the climate crisis. This remains a challenge given the complex nature of the underlying molecular mechanisms....

Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency.

The Plant cell
Systems biology aims to uncover gene regulatory networks (GRNs) for agricultural traits, but validating them in crops is challenging. We addressed this challenge by learning and validating model-to-crop transcription factor (TF) regulons governing ni...

Predicting Fitness-Related Traits Using Gene Expression and Machine Learning.

Genome biology and evolution
Evolution by natural selection occurs at its most basic through the change in frequencies of alleles; connecting those genomic targets to phenotypic selection is an important goal for evolutionary biology in the genomics era. The relative abundance o...