Project description:Background: Maize plants developed typical gray leaf spot disease (GLS) symptoms initiating at the lower leaves and progressing to upper leaves through the season. Leaf material was collected at 77 days after planting, at which stage there were a large number of GLS disease necrotic lesions on lower leaves (8% surface area on average determined by digital image analysis), but very few lesions and only at chlorotic stage on leaves above the ear (average of 0.2% lesion surface area). Method:To collect material that reflected a difference between C.zeina infected B73 leaves and control B73 leaf material, samples were collected from two lower GLS infected leaves (second and third leaf internode below ear) , and two upper leaves with minimal GLS symptoms (second and third internode above ear), respectively. The two lower leaves from each plant were pooled prior to RNA extraction, and the two upper leaves from each plant were pooled prior to RNA extraction. Upper and lower leaf samples from three maize B73 plants were subjected to RNA sequencing individually. The three maize plants were selected randomly as one plant per row from three rows of ten B73 plants each. Result: A systems genetics strategy revealed regions on the maize genome underlying co-expression of genes in susceptible and resistance responses, including a set of 100 genes common to the susceptible response of sub-tropical and temperate maize.
Project description:The goal of this study is to investigate differential transcription profiles of leaf material/cells accumulating different levels of alkaloids in the anticancer plant Catharanthus roseus.
Project description:af13_plp2 - plp2 botrytis cinerea 2 - Effects of deregulation of a lipid acyl hydrolase gene (PLP2, At2g26560) on global transcriptome upon infection by Botrytis cinerea. This deregulation affects resistance levels against fungal and bacterial pathogens, likely by perturbing the biosynthesis of oxylipins. Oxylipins are fatty acid-derived compounds (example:jasmonic acid) with diverse signaling or antimicrobial properties. - 5000 spores of Botrytis were pipetted on 4 infection sites per ault leaf. Leaf material was harvested at 0 and 2 days later. 3 plant genotypes were used (Col-0 ecotype): siPLP2 (RNAi-silenced),pBIN (empty pBIN-transformed),PLP2OE (PLP2-overexpressors).
Project description:Effects of deregulation of a lipid acyl hydrolase gene (PLP2, At2g26560) on global transcriptome upon infection by Botrytis cinerea. This deregulation affects resistance levels against fungal and bacterial pathogens, likely by perturbing the biosynthesis of oxylipins. Oxylipins are fatty acid-derived compounds (example:jasmonic acid) with diverse signaling or antimicrobial properties. - 5000 spores of Botrytis were pipetted on 4 infection sites per ault leaf. Leaf material was harvested at 0,1,2,3 days later. 3 plant genotypes were used (Col-0 ecotype): siPLP2 (RNAi-silenced),pBIN (empty pBIN-transformed),PLP2OE (PLP2-overexpressors). Keywords: gene knock in (transgenic),normal vs rnai mutant comparaison,time course
Project description:Effects of deregulation of a lipid acyl hydrolase gene (PLP2, At2g26560) on global transcriptome upon infection by Botrytis cinerea. This deregulation affects resistance levels against fungal and bacterial pathogens, likely by perturbing the biosynthesis of oxylipins. Oxylipins are fatty acid-derived compounds (example:jasmonic acid) with diverse signaling or antimicrobial properties. - 2500 spores of Botrytis cinerea were pipetted on 4 infection sites per adult leaf. Leaf material was harvested at 0, 24 and 48 hours. 3 plant genotypes were used (Col-0) : PLP2- silenced (RNAi), control, PLP2-overexpressors. Keywords: normal vs rnai mutant comparison,time course,treated vs untreated comparison
Project description:Higher-order chromatin structure undergoes dramatic changes in response to various developmental and environmental signals, wherein distinct cell types posses specific chromatin organization. High throughput chromatin conformation capture assays (Hi-C) allows study of higher-order chromatin structure; however, it requires a large number of cells. This requirement has so far limited the establishment of cell type-specific higher-order chromatin structure in the plant. To overcome this limitation, we modified the Hi-C protocol (mHi-C) to be applicable to a limited amount of starting material. For this, mHi-C libraries were generated from INTACT-purified endosperm and leaf nuclei. Correlation plots showed that our mHi-C data from INTACT-leaf accurately reiterate chromatin interaction patterns derived from conventional leaf Hi-C data. We further identified compacted structural domains (CSDs) and loose structural domains (LSDs) in leaf and endosperm and their differential patterns revealed distinct higher-order chromatin organization in leaf and endosperm. Our analysis revealed that DNA methylation and repressive histone marks positively correlate with the chromatin compaction level. We discovered increased chromatin interactions frequencies in the endosperm in comparison to leaf tissue. Using cell-specific Hi-C and INTACT-RNA-seq, on a genome-wide scale higher expression of self-looped interacting genes was observed. It was further identified that interacting intergenic regions act as a negative regulator and influence the gene expression in a specific cells in the plant. Our study provides evidence that the higher-order chromatin structure differs between cell types in plants and these interactions could influence the transcription activity positively as well as negatively.
Project description:Goal:identify the genes regulated by RON2 involved in the delay of floral transitional and those associated with leaf development. The gene expression profile of mature leaf 6 of ron2-1 EMS mutant and the wild-type Ler are compared. The plant material for this experiment was grown in LEPSE-INRA Montpellier, and the microarrays at the MAF-VIB Leuven with PSB-VIB Ghent.