Biology subjects

Abdelrahman, M.

Publications and source records attributed to Abdelrahman, M..

4 recordsLinked to original sources

bioRxiv2024

Iron-induced Transcriptional and Microbiome Changes in Host Roots Associated with Drought Tolerance in Sorghum

Drought stress significantly impairs growth, and microbial interactions in sorghum. This study explores the transcriptional and microbial shifts in sorghum under drought, revealing key adaptations to water deficit. LC-MS (Liquid Chromatography-Mass Spectrometry) analyses revealed that drought stress induced abscisic acid while significantly reducing jasmonic acid levels in sorghum roots, likely due to resource conservation strategies during drought. Transcriptional reprogramming highlighted the upregulation of genes in the roots involved in mineral homeostasis (Ferritin 1, Iron dehydrogenase, Nitrate transporter 1), hormone signaling (Ethylene-insensitive protein 3, Gibberellin 2-oxidase), and osmotic regulation (Aquaporin, Dehydrin), underlining key adaptive responses to maintain nutrient uptake, redox status, and cellular turgor. In Fe-supplemented plants, increased Fe in roots correlated with increased Ferritin 1 expression, improved plant health, and reduced Fenton reaction rate and H O levels. This suggests that ferritin helps minimize oxidative stress under drought in sorghum. Drought reduced root-associated bacterial diversity and richness while enriching drought tolerance-associated genera, such as Burkholderia, Caballeronia and Paraburkholderia, known for promoting plant growth through auxin production, phosphate solubilization, and siderophore-mediated iron acquisition. In contrast, fungal diversity and richness remained unchanged, dominated by Talaromyces, which showed a statistically non-significant increase under drought. Random forest models could not identify functional predictors for fungi but revealed a shift in bacterial functional groups under drought, with enrichment in phototrophy, methylotrophy, and nitrate reduction, traits emphasizing microbial roles in nutrient cycling and drought adaptation of sorghum. This study provides insights into the role of ferritin and potential bacterial bioinoculants that could enhance sorghum resilience to drought. Future research should validate these findings to integrate them into breeding programs and biofertilizer formulation for drought-tolerant sorghum and climate-resilient agriculture.

plant biology↗

bioRxiv2024

The effect of constitutive root isoprene emission on root phenotype and physiology under control and salt stress conditions

ABSTRACTIsoprene, a volatile hydrocarbon, is typically emitted from the leaves and other aboveground plant organs; isoprene emission from roots is not well studied. Given its well-known function in plant growth and defense aboveground, isoprene may also be involved in shaping root physiology to resist belowground stress. We used isoprene-emitting transgenic lines (IE) and a non-emitting empty vector and/or wild type lines (NE) of Arabidopsis to elucidate the roles of isoprene in root physiology and salt stress resistance. We assessed root phenotype and metabolic changes, hormone biosynthesis and signaling, and stress-responses under normal and saline conditions of IE and NE lines. We also analyzed the root transcriptome in the presence or absence of salt stress. IE lines emitted isoprene from roots, which was associated with higher primary root growth, root biomass, and root/shoot biomass ratio under both control and salt stress conditions. Transcriptome data indicated that isoprene altered the expression of key genes involved in hormone metabolism and plant responses to stress factors. Our findings reveal that root constitutive isoprene emission sustains root growth also under salinity by regulating and/or priming hormone biosynthesis and signaling mechanisms, amino acids biosynthesis, and expression of key genes relevant to salt stress defense.

plant biology↗

bioRxiv2022

Optimization of capture protocols across species targeting up to 32000 genes and their extension to pooled DNA

PremiseIn-solution based capture is becoming a method of choice for sequencing targeted sequence. Methods and resultsWe assessed and optimized a capture protocol in 20 different species from 6 different plant genus using kits from 20,000 to 200,000 baits targeting from 300 to 32,000 genes. We evaluated both the effectiveness of the capture protocol and the fold enrichment in targeted sequences. We proposed a protocol with multiplexing up to 96 samples in a single hybridization and showed it was an efficient and cost-effective strategy. We also extended the use of capture to pools of 100 samples and proved the efficiency of the method to assess allele frequency. Using a set of various organisms with different genome sizes, we demonstrated a correlation between the percentage of on-target reads vs. the relative size of the targeted sequences. ConclusionAltogether, we proposed methods, strategies, cost-efficient protocols and statistics to better evaluate and more effectively use hybridization capture.

evolutionary biology↗

bioRxiv2021

Chromosome-scale haplotype-phased genome assemblies of the male and female lines of wild asparagus (Asparagus kiusianus), a dioecious plant species

Asparagus kiusianus is a disease-resistant dioecious plant species and a wild relative of garden asparagus (A. officinalis). To enhance A. kiusianus genomic resources, advance plant science, and facilitate asparagus breeding, we determined the genome sequences of the male and female lines of A. kiusianus. Genome sequence reads obtained with a linked-read technology were assembled into four haplotype-phased contig sequences (~1.6 Gb each) for the male and female lines. The contig sequences were aligned onto the chromosome sequences of garden asparagus to construct pseudomolecule sequences. Approximately 55,000 potential protein-encoding genes were predicted in each genome assembly, and ~70% of the genome sequence was annotated as repetitive. Comparative analysis of the genomes of the two species revealed structural and sequence variants between the two species as well as between the male and female lines of each species. Genes with high sequence similarity with the male-specific sex determinant gene in A. officinalis, MSE1/AoMYB35/AspTDF1, were presented in the genomes of the male line but absent from the female genome assemblies. Overall, the genome sequence assemblies, gene sequences, and structural and sequence variants determined in this study will reveal the genetic mechanisms underlying sexual differentiation in plants, and will accelerate disease-resistance breeding in garden asparagus.

genomics↗