Biology subjects

Mahboub, S.

Publications and source records attributed to Mahboub, S..

3 recordsLinked to original sources

bioRxiv2023

Rhythmic lipid and gene expression responses to chilling in panicoid grasses

Chilling stress threatens plant growth and development, particularly affecting membrane fluidity and cellular integrity. Understanding plant membrane responses to chilling stress is important for unraveling the molecular mechanisms of stress tolerance. Whereas core transcriptional responses to chilling stress and stress tolerance are conserved across species, the associated changes in membrane lipids appear to be less conserved, as which lipids are affected by chilling stress varies by species. Here, we investigated changes in gene expression and membrane lipids in response to chilling stress during one diurnal cycle in sorghum (Sorghum bicolor), Urochloa (browntop signal grass, Urochloa fusca) (lipids only), and foxtail millet (Setaria italica), leveraging their evolutionary relatedness and differing levels of chilling-stress tolerance. We show that most chilling-induced lipid changes are conserved across the three species, while we observed distinct, time-specific responses in chilling-tolerant foxtail millet, indicating the presence of a finely orchestrated adaptive mechanism. We detected diurnal rhythmicity in lipid responses to chilling stress in the three grasses, which were also present in Arabidopsis (Arabidopsis thaliana), suggesting the conservation of rhythmic patterns across species and highlighting the importance of accounting for diurnal effects. When integrating lipid datasets with gene expression profiles, we identified potential candidate genes that showed corresponding transcriptional changes in response to chilling stress, providing insights into the differences in regulatory mechanisms between chilling-sensitive sorghum and chilling-tolerant foxtail millet. Significance StatementPlants respond to low-temperature stress in myriad ways. While core transcriptional changes are conserved across species, specific adaptive strategies do exist. However, membrane lipid responses during chilling do not appear to be conserved. Here, we collected samples from control and chilling stress-treated seedlings [PSC4] to assess gene expression and membrane lipids in three panicoid grasses to show that lipid metabolic changes follow a daily rhythm. Lipid changes in chilling-tolerant foxtail millet occurred at specific time points, partly explaining the difficulty in finding conserved chilling-induced lipid changes in previous reports. We identified specific orthologs in sorghum and foxtail millet that showed a correlation between gene expression and lipid metabolic changes; these orthologs may be used as potential target genes for developing chilling-tolerant sorghum varieties.

plant biology↗

bioRxiv2020

Predicting transcriptional responses to cold stress across plant species

Although genome sequence assemblies are available for a growing number of plant species, gene expression responses to stimuli have been catalogued for only a subset of these species. Many genes show altered transcription patterns in response to abiotic stresses. However, orthologous genes in related species often exhibit different responses to a given stress. Accordingly, data on the regulation of gene expression in one species are not reliable predictors of orthologous gene responses in a related species. Here, we trained a supervised classification algorithm to identify genes that transcriptionally respond to cold stress. A model trained with only features calculated directly from genome assemblies exhibited only modest decreases in performance relative to models trained using genomic, chromatin, and evolution/diversity features. Models trained with data from one species successfully predicted which genes would respond to cold stress in other related species. Cross-species predictions remained accurate when training was performed in cold-sensitive species and predictions were performed in cold-tolerant species and vice versa. Models trained with data on gene expression in multiple species outperformed models trained with data from any single species. These results suggest that classifiers trained on stress data from well-studied species may suffice for predicting gene expression patterns in related, less-studied species with sequenced genomes.

plant biology↗

bioRxiv2017

Parallels between artificial selection in temperate maize and natural selection in the cold-adapted crop-wild relative Tripsacum

Artificial selection has produced varieties of domesticated maize which thrive in temperate climates around the world. However, the direct progenitor of maize, teosinte, is indigenous only to a relatively small range of tropical and sub-tropical latitudes and grows poorly or not at all outside of this region. Tripsacum, a sister genus to maize and teosinte, is naturally endemic to the majority of areas in the western hemisphere where maize is cultivated. A full-length reference transcriptome for Tripsacum dactyloides generated using long-read isoseq data was used to characterize independent adaptation to temperate climates in this clade. Genes related to phospholipid biosynthesis, a critical component of cold acclimation on other cold adapted plant lineages, were enriched among those genes experiencing more rapid rates of protein sequence evolution in T. dactyloides. In contrast with previous studies of parallel selection, we find that there is a significant overlap between the genes which were targets of artificial selection during the adaptation of maize to temperate climates and those which were targets of natural selection in temperate adapted T. dactyloides. This overlap between the targets of natural and artificial selection suggests genetic changes in crop-wild relatives associated with adaptation to new environments may be useful guides for identifying genetic targets for breeding efforts aimed at adapting crops to a changing climate.

plant biology↗