Project description:Analysis of barley grains/seedlings representing six well characterized and distinct germination stages over the course of seed germination and seedling growth. Overall design: Three biological replications, six developmental stages.
Project description:small RNA and degradome sequencing was carried out on samples isolated from developing barley grains. The datasets were analysed to identify putative miRNAs and their target mRNAs Samples were whole grain tissue (pericarp, embryo and endosperm) from developing barley grains. Three samples were used that pooled 1 to 5, 6-10 and 11-15 days post anthesis grains. For each sample a small RNA library and a degradome library (using the PARE method) was constructed and sequenced using the Illumina platform
Project description:Analysis of barley grains/seedlings representing six well characterized and distinct germination stages over the course of seed germination and seedling growth. Three biological replications, six developmental stages.
Project description:Gene expression was investigated in response to nitrogen fertilizer in developing grains of field grown barley (Hordeum vulgare L. cv. Barke) at four different time points: 10, 15, 18 and 25 days after pollination (DAP).
Project description:Endosperm transfer cells (ETCs) of barley grains/seeds are located at the maternal-filial boundary in seeds and fascilitate nutrient transfer from the mother plant into the filial endosperm tissue. Due to the difficult accessibility of ETCs inside the seed, signalling and metabolic pathways involved in differentiation processes of ETCs are poorly understood. To analyse ETC differentiation, we applied laser microdissection pressure catapulting (LMPC) coupled to transcriptome analysis at various developmental stages from cellularization to full functionality and ongoing modifications. ETC-specific transcriptome data identified candidate genes and associated pathways involved in distinct differentiation processes. Barley grains were harvested at 5, 7, 10 and 12 days after flowering/pollination (DAF) and immediately frozen in liquid nitrogen. In a cryostat (-20°C), middle parts were cut by a razor blade, glued onto sample plates by Tissue-Tek® O.C.T™ and 20 µm sections were mounted on PEN membrane slides (PALM, Bernried, Germany). Cryosections were stored for 7 days at -20°C until complete dryness. LMPC-based isolation of ETC tissue from cryosections has been done using the PALM® MicroBeam laser system. For each biological replicate, 50-70 sections from three independent grains were collected. Three biological replicates were generated from each time point (total number of samples = 12).
Project description:To investigate the differences in gene expression during germination time course of two elite breeding barley lines (LP104 and LP106), an Agilent oligo microarray was applied. A total of 5320 and 4271 genes were found to be significantly up- and down-regulated, respectively, in LP104 compared to LP106. The highest number of differentially expressed genes (DEGs) was identified after 24h of germination (2260); stages 0h, 2h, 48h, 96h, 120h and 144h were of a lesser magnitude ranging from 929 to 1169 DEGs, and at 72h only 826 DEGs were identified. Analysis of DEGs according to their biological functions revealed that major enriched functional categories among DEGs included RNA, protein, stress, transport and development. Overall design: Gene expression in germinating grains of two barley lines was measured at 0-144 hours after imbibition. Three biological replications, eight germination stages.
Project description:Caves are populated with a diverse fauna of highly adapted species that tend to exhibit a consistent suite of both regressive and constructive trait modifications. Because molecular studies of cave adaptation have largely concentrated on vertebrate models, our ability to recognize universalities in the genetic trajectories underlying cave adaptation remains limited. We have initiated efforts to elucidate the molecular evolution of the flightless small carrion beetle Ptomaphagus hirtus (Ptomaphagus hirtus), which represents one of the highly endemic signature inhabitants of the Mammoth Cave system of Kentucky. Ptomaphagus hirtus has been considered blind despite the presence of lateral eye rudiments. However, analysis of the Ptomaphagus hirtus adult head transcriptome by deep RNA sequencing reveals the conservation and expression of all essential insect phototransduction genes including a single long wavelength-sensitive opsin. Consistent with the preservation of visual ability, Ptomaphagus hirtus expresses all core members of the clock gene network and exhibits a similar degree of negative phototaxis as does a closely related flight-active species in light-dark choice assays. The structural reduction of the peripheral Ptomaphagus hirtus visual system is reflected by the lack of five eye pigmentation specific genes in the head transcriptome. Taken together our data suggest that wavelength contingent and probably also spatial vision have been lost in Ptomaphagus hirtus, while irradiance vision and contingent behavioral modules have remained preserved. We predict that the adaptive state of Ptomaphagus hirtus is representative for a large number of microphthalmic species adapted to the twilight zone of caves and other subterranean habitats Poly(A)+ transcripts were isolated from a pooled sample of 25 adult Ptomaphagus hirtus heads, reverse transcribed and sequenced on the Illumina GAII
Project description:Purpose: The goal of this study was to investigate the mechanisms involved in the initiation and development of crown-roots (CRs) in barley and to estimate the role of cytokines (CKs) in this process. Method: stranded libraries were obtained from RNA extracted from the stem base of 1 day-after-germination (DAG) and 10DAG-seedlings of wild-type (WT) and AtCKX-overexpressing barley lines (OE-CKX). OE-CKX lines have a reduced content of endogenous CKs and are characterized by a higher number of CRs. Libraries were deep sequenced on Illumina HighSeq platform. Each sample was investigated in three independent biological replicates. Results: Using a data analysis workflow optimized for barley, we identified more than 4000 transcripts differentially expressed in the stem base of 1DAG and 10DAG-seedlings. Expression as determined by RNA-seq was validated by real-time PCR. Our data were compared to the transcriptomic profiling obtained from rice and we were able to identify genes potentially involved in the initiation/development of CRs in barley. Also the use of the transgenic line with altered endogenous CK content allowed us to conclude about the role of CKs in the process. Conclusions: Our study represents the first analysis aiming to understand the initiation and development of CRs in barley. Overall design: mRNA profiles of stem base of 1 day-after-germination (DAG) and 10DAG seedling were generated by deep sequencing, in triplicate, using Illumina HighSeq the analysis was performed on wild-type (WT) as well as on AtCKX1-overexpressing lines, accumulating lower amount of cytokinins