The rumen microbiota of sheep grazing perennial ryegrass swards with and without companion forages
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ABSTRACT:
PROVIDER: PRJNA1100441 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The changes in the transcriptome of leaves between 0, 9, 13 and 17 days of cold acclimation were analyzed using RNA-Seq in Veyo and Falster genotypes of perennial ryegrass.
2016-04-20 | E-MTAB-2779 | biostudies-arrayexpress
Project description:Knowledge about molecular mechanisms underlying cold and freezing stress responses in perennial ryegrass is scarce. The current study aims to study cold and freezing stress responses of perennial ryegrass genotypes with contrasting cold tolerances. A panel of 160 genotypes were screened for cold tolerances based on electrolyte leakage % measured after 24 hrs at 12 °C and 24 hrs at 14 °C. Among them, 4 genotypes (2 low EL% and 2 high EL%) were selected to study cold and freezing stress responses. Plants were sampled at 6 timepoints; control (T1), beginning of cold acclimation (T2), 2 weeks into cold acclimation (T3), end of cold cold acclimation (T4), -5°C (T5), -10 °C (T6) followed by RNA extraction and sequencing.
2024-08-30 | E-MTAB-14223 | biostudies-arrayexpress
Project description:Transcriptome profiling of leaves of perennial ryegrass genotype Veyo adapted to warmer climates, and ‘Falster’ adapted to cold climates, in response to low-temperature and drought stress conditions, were performed using RNA-Seq approach.
2023-07-01 | E-MTAB-3639 | biostudies-arrayexpress
Project description:Lack of resistance to pink snow mould (Microdochium nivale) is seen as a major constraint for adaptation of perennial ryegrass (Lolium perenne L.) at higher latitudes. Plants generally become more resistant to snow moulds after cold acclimation, and almost all investigations of genetic variation in resistance have been performed using cold acclimated plants. However, there may be variation in resistance mechanisms that are functioning independently of cold acclimation. In this study our aim was to identify candidate genes involved in such resistance mechanisms. We first characterized variation in resistance to M. nivale among non-acclimated plants of eight genotypes from the Norwegian cultivar Fagerlin and selected one resistant and one susceptible genotype for transcriptome analysis. Total RNA was extracted from leaf blade tissue of plants exposed to three different treatments: non-inoculated and non-incubated plants, non-inoculated plants after four days of incubation, and inoculated plants after four days of incubation. cDNA libraries were prepared and paired-end sequencing performed using Illumina Hiseq 2000. Transcriptome profiles, GO enrichment and KEGG pathway analysis indicate that defence response related genes are differentially expressed between incubated non-inoculated and incubated inoculated conditions both within resistant and susceptible genotypes. A significant up-regulation of defence related genes as well as genes involved in cell wall cellulose metabolic processes and aryl-alcohol dehydrogenase (NADP+) activity was observed in the resistant genotype. The candidate genes identified in this study might be potential molecular marker resources for breeding perennial ryegrass cultivars with improved resistance to pink snow mould.
2016-04-29 | E-MTAB-4459 | biostudies-arrayexpress
Project description:Perennial ryegrass (Lolium perenne L.) is a major grass species used for forage and turf throughout the world, and gains by conventional breeding have reached a plateau. Perennial ryegrass is an outcrossing, self-incompatible diploid (2n = 2x = 14) with a relatively large genome (4067 Mbp/diploid genome; Evans, G.M., Rees, H., Snell, C.L. and Sun, S. (1972). The relation between nuclear DNA amount and the duration of the mitotic cycle. Chrom. Today, 3, 24–31). Using tissues sourced from active pastures during the peak of the autumn, winter, spring and summer seasons, we analysed the ryegrass transcriptome employing a Serial Analysis of Gene Expression (SAGE™) protocol, with the dual goals of understanding the seasonal changes in perennial ryegrass gene expression and enhancing our ability to select genes for genetic manipulation. A total of 159 002 14-mer SAGE™ tags was sequenced and mapped to the perennial ryegrass DNA database, comprising methyl-filtered (GeneThresher®) and expressed sequence tag (EST) sequences. The analysis of 14 559 unique SAGE™ tags, which were present more than once in our SAGE™ library, revealed 964, 1331, 346 and 131 exclusive transcripts to autumn, winter, spring and summer, respectively. Intriguingly, our analysis of the SAGE™ tags revealed season-specific expression profiles for the small subunit of ribulose-1,5-bisphosphate carboxylase (Rubisco), LprbcS. The transcript level for LprbcS was highest in spring, and then decreased gradually between summer and winter. Five different copies of LprbcS were revealed in ryegrass, with one possibly producing splice variant transcripts. Two highly expressed LprbcS genes were reported, one of which was not active in autumn. Another LprbcS gene showed an inverse expression profile to the autumn inactive LprbcS in a manner to compensate the expression level. Keywords: paddock samples, pasture, perennial ryegrass, Serial Analysis of Gene Expression (SAGE™), season specific expression, monocot Ryegrass tissue Perennial ryegrass (Lolium perenne L.) cv. Bronsyn was used throughout this study. Field-grown samples, comprising mainly viable leaves and pseudostems, were collected at midday from livestock-active monocultural paddocks at Dexcel, Hamilton, New Zealand during the peak of each season, and frozen immediately in liquid nitrogen. Samples were transported in dry-ice and stored at ?80 oC until use. During spring and summer, care was taken not to include any floral stems in the tissue sample. Grass samples were collected from pregrazed (15–60 days post-grazing) and post-grazed (1 day post-grazing) ryegrass swards, which were visibly healthy and free of any pests. Construction of SAGE™ libraries RNA was extracted using TRIZOL® reagent (Invitrogen, Carlsbad,CA, USA). For each SAGE™ library, 100 ug of pre- and post-grazed sample-derived total RNA was employed, and the libraries were created using an I-SAGE™ or I-SAGE™Long Kit (Invitrogen) according to the manufacturer’s protocol. Pre- and post-grazed SAGE™ libraries were sequenced at the Australian Genome Research Facility (Brisbane, Australia), and the tags were extracted using SAGE2000 software and combined to produce the transcript profile for the season.
2006-11-08 | E-GEOD-5211 | biostudies-arrayexpress
Project description:The rumen is a major the site of digestion and absorption of energy predominantly in the form of short chain fatty acids as well as amino acids and simple carbohydrates. The value of crops such as perennial wheat (PW) for grain and grazing compared to conventional wheat (W), or the addition of lucerne to PW (PWL) is still being determined. The research sought to determine if these diets representing high potassium (K): low sodium (Na) ratio (W, PW and PWL) was associated with changes in the membrane bound proteins that transport nutrients in the rumen epithelium (RE). Information about these proteins and the influence of different diets is scarce due to difficulties developing a procedure to examine them using quantitative proteomics. The research focuses on proteins extracted using an enzymatic procedure (Bond et al. 2019) from the rumen epithelium layer of the sheep’s’ forestomach. A membrane protein enriched fraction was then extracted and prepared for TMT-MS. The comprehensive assignment of proteins (>4000) to cellular location and quantification of differences in protein abundance will progress the annotation and understanding of protein functions in the ruminant genomes.
2023-10-24 | PXD044135 | Pride
Project description:Global transcriptome changes in perennial ryegrass during early infection by pink snow mould
| PRJEB12774 | ENA
Project description:Transcriptome profiling of leaves in two genotypes of perennial ryegrass during cold acclimation
| PRJEB6903 | ENA
Project description:Perennial ryegrass (Lolium perenne L.) is a major grass species used for forage and turf throughout the world, and gains by conventional breeding have reached a plateau. Perennial ryegrass is an outcrossing, self-incompatible diploid (2n = 2x = 14) with a relatively large genome (4067 Mbp/diploid genome; Evans, G.M., Rees, H., Snell, C.L. and Sun, S. (1972). The relation between nuclear DNA amount and the duration of the mitotic cycle. Chrom. Today, 3, 24–31). Using tissues sourced from active pastures during the peak of the autumn, winter, spring and summer seasons, we analysed the ryegrass transcriptome employing a Serial Analysis of Gene Expression (SAGE™) protocol, with the dual goals of understanding the seasonal changes in perennial ryegrass gene expression and enhancing our ability to select genes for genetic manipulation. A total of 159 002 14-mer SAGE™ tags was sequenced and mapped to the perennial ryegrass DNA database, comprising methyl-filtered (GeneThresher®) and expressed sequence tag (EST) sequences. The analysis of 14 559 unique SAGE™ tags, which were present more than once in our SAGE™ library, revealed 964, 1331, 346 and 131 exclusive transcripts to autumn, winter, spring and summer, respectively. Intriguingly, our analysis of the SAGE™ tags revealed season-specific expression profiles for the small subunit of ribulose-1,5-bisphosphate carboxylase (Rubisco), LprbcS. The transcript level for LprbcS was highest in spring, and then decreased gradually between summer and winter. Five different copies of LprbcS were revealed in ryegrass, with one possibly producing splice variant transcripts. Two highly expressed LprbcS genes were reported, one of which was not active in autumn. Another LprbcS gene showed an inverse expression profile to the autumn inactive LprbcS in a manner to compensate the expression level. Keywords: paddock samples, pasture, perennial ryegrass, Serial Analysis of Gene Expression (SAGE™), season specific expression, monocot
2006-11-09 | GSE5211 | GEO