Project description:Illumina HiSeq technology was used to generate mRNA profiles from mycorrhizal Quercus robur roots. Tuber melanosporum, T. aestivum and T.magnatum mycorrhizal root tips were harvested and used for RNA extraction. Paired-end reads of 100 bp were generated and aligned to Quercus robur CDS using CLC Genomics Workbench 9.
Project description:Identification of genes involved in the regulation of taproot and lateral root growth in Quercus robur seedlings under drought stress and well-watered conditions. Genes involved in the regulation of taproot and lateral root growth in Quercus robur seedlings were identified using RNA-seq, miRNA-seq, and degradome-seq. The analysis focused on the gene expression, miRNA regulation, and mRNA degradation profiles of taproots and lateral roots under both drought stress and well-watered conditions. Key genes and their regulatory miRNAs were identified, along with the role of mRNA degradation pathways in response to stress, providing insights into the molecular mechanisms controlling root growth and development in oak seedlings under varying water availability. This research was funded by National Science Center, Poland [grant number 2021/41/N/NZ9/00433].
Project description:Identification of genes involved in the regulation of taproot and lateral root growth in Quercus robur seedlings under drought stress and well-watered conditions. Genes involved in the regulation of taproot and lateral root growth in Quercus robur seedlings were identified using RNA-seq, miRNA-seq, and degradome-seq. The analysis focused on the gene expression, miRNA regulation, and mRNA degradation profiles of taproots and lateral roots under both drought stress and well-watered conditions. Key genes and their regulatory miRNAs were identified, along with the role of mRNA degradation pathways in response to stress, providing insights into the molecular mechanisms controlling root growth and development in oak seedlings under varying water availability. This research was funded by National Science Center, Poland [grant number 2021/41/N/NZ9/00433].
Project description:Identification of genes involved in the regulation of taproot and lateral root growth in Quercus robur seedlings under drought stress and well-watered conditions. Genes involved in the regulation of taproot and lateral root growth in Quercus robur seedlings were identified using RNA-seq, miRNA-seq, and degradome-seq. The analysis focused on the gene expression, miRNA regulation, and mRNA degradation profiles of taproots and lateral roots under both drought stress and well-watered conditions. Key genes and their regulatory miRNAs were identified, along with the role of mRNA degradation pathways in response to stress, providing insights into the molecular mechanisms controlling root growth and development in oak seedlings under varying water availability. This research was funded by National Science Center, Poland [grant number 2021/41/N/NZ9/00433].
Project description:Development of cereal crops with high nitrogen-use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improve crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse sorghum lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry (GC-MS) were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxa, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low-N stress. This indicates that the shift in the sorghum microbiome due to low-N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low-N stress.
Project description:Pedunculate oak (Quercus robur) is a foundation tree species in European forests and reforestation programs, and forest nurseries represent key phytosanitary bottlenecks where asymptomatic planting stock can disseminate cryptic pathogens. Cadophora luteo-olivacea is frequently associated with grapevine trunk diseases and has been recovered from diverse woody hosts, yet its pathogenic potential on oak and its interactions with antagonistic fungi remain unresolved. Here, we combine pathogenicity testing, dual-culture confrontation assays and time-resolved, spatially resolved contact-zone proteomics and metabolomics to connect detection to causality and mechanism in an oak associated Cadophora–Trichoderma system. We fulfill Koch’s postulates for C. luteo-olivacea on Q. robur seedlings and quantify inhibition of Cadophora by a natural isolate of Trichoderma atroviride. Contact-zone proteomics at 4 and 8 days post-contact reveals a staged, interface-localized antagonistic program dominated by fungal cell-wall targeting hydrolases (including chitinases and β-1,3-glucanases), secreted proteases, oxidoreductases, transporters and small secreted proteins, alongside factors consistent with adhesion and self-protection. Together, these complementary assays provide the first experimental evidence that C. luteo-olivacea is pathogenic on Q. robur and delineate mechanistic signatures of T. atroviride mycoparasitism at the interaction front. This framework links nursery-relevant pathogen screening to mechanistic readouts and informs evaluation of biocontrol potential in a foundation forest species.