The health status of Irish honeybee colonies in 2006

peer-reviewedThis study assessed the health status of Irish honeybee colonies and provides a snapshot of the incidence of a number of important colony parasites/pathogens including: the mite Varroa destructor; three associated viruses (deformed wing virus (DWV), acute bee paralysis virus (ABPV) and Kashmir virus (KBV)); the tracheal mite Acarapis woodi; the microsporidian Nosema spp., and the insect Braula coeca. During June/July 2006, 135 samples of adult bees were collected from productive colonies throughout Ireland and standard techniques were used to determine the presence and absence of the parasites and pathogens. Varroa destructor was positively identified in 72.6% of the samples and was widely distributed. Although the samples were analysed for three viruses, DWV, ABPV and KBV, only DWV was detected (frequency = 12.5%). Acarapis woodi and Nosema spp. occurred in approximately 11% and 22% of the samples, respectively, while B. coeca, a wingless dipteran that was once common in Irish honeybee colonies, was very rare (3.7%). Samples where all the pathogens/parasites were jointly absent were statistically under-represented in Leinster and DWV was statistically over-represented in Munster. In Ulster, there was over-representation of the categories where all parasites/pathogens were jointly absent and for A. woodi, and underrepresentation of V. destructor.The project was funded by EU FEOGA and the National Apiculture Programme 2007–2010 of the Department of Agriculture, Food and the Marine

Muttergebundene Aufzucht in der Milchviehhaltung - langfristige Auswirkungen auf Verhalten und Wohlbefinden

The integration of dairy heifers into the cow herd shortly before their first parturition is a common management practice also in organic farming and is associated with stress. In this study we investigated whether the ability to cope with such challenges is affected by experiences during early age. Three groups of heifers which differed with respect to the contact to their mother during the first 12 weeks of life were compared. At the age of 25+/-0.2 months heifers were integrated individually into the cow herd and observed for 33 hours. Heifers reared with contact to their mother used the cubicles quicker and more consistently and also tended to differ in the social behaviour compared to the heifers reared without mother. These preliminary results suggest some positive long-term effects of mother-bonded rearing on later challenge response and welfare of dairy cattle

Plastid genome sequencing reveals biogeographical structure and extensive population genetic variation in wild populations of Phalaris arundinacea L. in north‐western Europe

peer-reviewedNew and comprehensive collections of the perennial rhizomatous reed canary grass (Phalaris arundinacea) were made in NW Europe along north‐to‐south and east‐to‐west clines from Denmark, Germany, Ireland, Poland, Sweden and the United Kingdom. Rhizome, seed and leaf samples were taken for analysis and genetic resource conservation. A subsample covering the geographical range was characterized using plastid genome sequencing and SNP discovery generated using a long‐read PCR and MiSeq sequencing approach. Samples were also subject to flow cytometry and all found to be tetraploid. New sequences were assembled against a Lolium perenne (perennial ryegrass) reference genome, and an average of approximately 60% of each genome was aligned (81 064 bp). Genetic variation was high among the 48 sequenced genotypes with a total of 1793 SNPs, equating to 23 SNPs per kbp. SNPs were subject to principal coordinate and Structure analyses to detect population genetic groupings and to examine phylogeographical pattern. Results indicate substantial genetic variation and population genetic structuring of this allogamous species at a broad geographical scale in NW Europe with plastid genetic diversity organized more across an east‐to‐west than a north‐to‐south cline

Transcriptomic response of maize primary roots to low temperatures at seedling emergence

peer-reviewedBackground Maize (Zea mays) is a C4 tropical cereal and its adaptation to temperate climates can be problematic due to low soil temperatures at early stages of establishment. Methods In the current study we have firstly investigated the physiological response of twelve maize varieties, from a chilling condition adapted gene pool, to sub-optimal growth temperature during seedling emergence. To identify transcriptomic markers of cold tolerance in already adapted maize genotypes, temperature conditions were set below the optimal growth range in both control and low temperature groups. The conditions were as follows; control (18 °C for 16 h and 12 °C for 8 h) and low temperature (12 °C for 16 h and 6 °C for 8 h). Four genotypes were identified from the condition adapted gene pool with significant contrasting chilling tolerance. Results Picker and PR39B29 were the more cold-tolerant lines and Fergus and Codisco were the less cold-tolerant lines. These four varieties were subjected to microarray analysis to identify differentially expressed genes under chilling conditions. Exposure to low temperature during establishment in the maize varieties Picker, PR39B29, Fergus and Codisco, was reflected at the transcriptomic level in the varieties Picker and PR39B29. No significant changes in expression were observed in Fergus and Codisco following chilling stress. A total number of 64 genes were differentially expressed in the two chilling tolerant varieties. These two varieties exhibited contrasting transcriptomic profiles, in which only four genes overlapped. Discussion We observed that maize varieties possessing an enhanced root growth ratio under low temperature were more tolerant, which could be an early and inexpensive measure for germplasm screening under controlled conditions. We have identified novel cold inducible genes in an already adapted maize breeding gene pool. This illustrates that further varietal selection for enhanced chilling tolerance is possible in an already preselected gene pool

A metabolomics-based approach to study abiotic stress in Lolium perenne

In the United Kingdom and Ireland, a major percentage of fertilized agricultural area is devoted to grasslands, which helps to support the associated milk and beef production industries. In temperate grasslands, perennial ryegrass (L. perenne) is the major forage grass and this species is particularly suitable as a forage grass due to its high yield and digestibility, when compared with other species. However, perennial ryegrass is not well adapted to abiotic stress conditions which are likely to occur in its natural environment. Some of the abiotic stress factors which have significant impacts on plant growth and development include water and nutrient availability. Therefore, this project set out to unravel some of the mechanisms involved in the adaptation of perennial ryegrass to limited water, phosphorous and nitrogen. In order to understand the metabolic mechanisms acting in response to these stresses, metabolite profiling was performed using GC-MS. Furthermore, for the water- and phosphorous-limitation studies this approach was complemented with transcript analysis.In order to study water-limitation a hydroponics system supplemented with polyethyleneglycol (PEG) was used to induce water-limitation for a period of one-week. A clear difference in the metabolic profiles of the leaves of plants grown under water stress was observed. Differences were principally due to a reduction in fatty acid levels in the more water stress-susceptible genotype Cashel and an increase in sugars and compatible solutes in the drought-tolerant PI 462336 genotype. Sugars exhibiting a significant increase included, raffinose, trehalose, glucose, fructose and maltose. Raffinose was identified as the metabolite exhibiting the largest accumulation under water-stress in the more tolerant genotype and may represent a target for engineering superior drought tolerance or form the basis of marker-assisted breeding in perennial ryegrass. The metabolomics approach was combined with a transcriptomics approach in the water stress tolerant genotype PI 462336 which identified genes in perennial ryegrass that were regulated by this stress.The characterization of the response to phosphorus-limitation was performed in a hydroponics system containing two solutions with different levels of phosphorus. Samples were collected from the roots and leaves of two genotypes 24 hours after being exposed to stress. Internal phosphate concentrations were reduced and significant alterations were detected in the metabolome and transcriptome of two perennial ryegrass genotypes. Results indicated a replacement of phospholipids with sulfolipids in response to P deficiency and that this occurs at the very early stages of P deficiency in perennial ryegrass. Additionally, the results suggested the role of glycolytic bypasses and the re-allocation of carbohydrates in response to P deficiency The characterization of the metabolic response of L. perenne leaves to different levels of nitrogen supply was performed for seven different genotypes with variability in the regrowth response rate to nitrogen supply in a hydroponics system. This facilitated the identification of common mechanisms of response between genotypes to nitrogen. The metabolic response observed included modifications of the lipid metabolism, as well as alterations of secondary aromatic metabolite precursors in plants exposed to nitrogendeficit. In contrast, plants grown in a nitrogen saturated media appeared to modify to some extent the metabolism of ascorbate. Additionally, it was found that amino acid levels increased with increasing concentrations of nitrogen supplied. This study suggested that the involvement of secondary metabolism, together with lipid and ascorbate metabolism, is of crucial importance in the early-adaptation of perennial ryegrass plants to different levels of nitrogen supply.EThOS - Electronic Theses Online ServiceIrish Department of Agriculture, Fisheries and Food (DAFF) (RSF 06 346)GBUnited Kingdo

Exploring the potential of grass feedstock from marginal land in Ireland: Does marginal mean lower yield?

peer-reviewedThe production of biomass feedstock from marginal land has attracted much attention as a means of avoiding conflict between the production of food and fuel. Yield potentials from marginal lands have generally not been quantified although it is generally assumed that lower biomass yields can be expected from marginal lands. A three year study was conducted in Ireland in order to determine if grass yields of perennial rhizomatous grasses (cocksfoot, tall fescue, reed canary grass, festulolium) for anaerobic digestion from three marginal land sites (very wet site, very dry site, site prone to flooding) could match yields from better soils. Randomised complete block designs were established on each site in 2012 with two varieties of each grass species as treatments. Three grass harvests were taken from each site in 2013 and in 2014. There was no significant difference between yields from the control site and those from the very dry site and the site prone to flooding. Biomass yields from the very wet site were 85% of those from the control site. Highest yields were obtained from festulolium which were significantly higher than yields from perennial ryegrass. An energy analysis showed that maximising the production of grass from low lying mineral marginal grassland in Ireland could provide enough energy to meet the energy requirements of both the private car fleet and the heavy goods vehicle fleet while avoiding conflict with food production which could be concentrated on conventional land

Computer literacy systematic literature review method

Although there have been many attempts to define the concept ‘computer literacy’, no consensus has been reached: many variations of the concept exist within litera-ture. The majority of papers does not explicitly define the concept at all, insteadusing an unjustified subset of elements related to computers to assess a subject’slevel of computer literacy. This can limit the generalizability of research and canlead to fallacious conclusions. This is an internal report listing the method by whichthe research was conducted

A metabolomics-based approach to study abiotic stress in Lolium perenne

In the United Kingdom and Ireland, a major percentage of fertilized agricultural area is devoted to grasslands, which helps to support the associated milk and beef production industries. In temperate grasslands, perennial ryegrass (L. perenne) is the major forage grass and this species is particularly suitable as a forage grass due to its high yield and digestibility, when compared with other species. However, perennial ryegrass is not well adapted to abiotic stress conditions which are likely to occur in its natural environment. Some of the abiotic stress factors which have significant impacts on plant growth and development include water and nutrient availability. Therefore, this project set out to unravel some of the mechanisms involved in the adaptation of perennial ryegrass to limited water, phosphorous and nitrogen. In order to understand the metabolic mechanisms acting in response to these stresses, metabolite profiling was performed using GC-MS. Furthermore, for the water- and phosphorous-limitation studies this approach was complemented with transcript analysis.In order to study water-limitation a hydroponics system supplemented with polyethyleneglycol (PEG) was used to induce water-limitation for a period of one-week. A clear difference in the metabolic profiles of the leaves of plants grown under water stress was observed. Differences were principally due to a reduction in fatty acid levels in the more water stress-susceptible genotype Cashel and an increase in sugars and compatible solutes in the drought-tolerant PI 462336 genotype. Sugars exhibiting a significant increase included, raffinose, trehalose, glucose, fructose and maltose. Raffinose was identified as the metabolite exhibiting the largest accumulation under water-stress in the more tolerant genotype and may represent a target for engineering superior drought tolerance or form the basis of marker-assisted breeding in perennial ryegrass. The metabolomics approach was combined with a transcriptomics approach in the water stress tolerant genotype PI 462336 which identified genes in perennial ryegrass that were regulated by this stress.The characterization of the response to phosphorus-limitation was performed in a hydroponics system containing two solutions with different levels of phosphorus. Samples were collected from the roots and leaves of two genotypes 24 hours after being exposed to stress. Internal phosphate concentrations were reduced and significant alterations were detected in the metabolome and transcriptome of two perennial ryegrass genotypes. Results indicated a replacement of phospholipids with sulfolipids in response to P deficiency and that this occurs at the very early stages of P deficiency in perennial ryegrass. Additionally, the results suggested the role of glycolytic bypasses and the re-allocation of carbohydrates in response to P deficiency The characterization of the metabolic response of L. perenne leaves to different levels of nitrogen supply was performed for seven different genotypes with variability in the regrowth response rate to nitrogen supply in a hydroponics system. This facilitated the identification of common mechanisms of response between genotypes to nitrogen. The metabolic response observed included modifications of the lipid metabolism, as well as alterations of secondary aromatic metabolite precursors in plants exposed to nitrogendeficit. In contrast, plants grown in a nitrogen saturated media appeared to modify to some extent the metabolism of ascorbate. Additionally, it was found that amino acid levels increased with increasing concentrations of nitrogen supplied. This study suggested that the involvement of secondary metabolism, together with lipid and ascorbate metabolism, is of crucial importance in the early-adaptation of perennial ryegrass plants to different levels of nitrogen supply.EThOS - Electronic Theses Online ServiceIrish Department of Agriculture, Fisheries and Food (DAFF) (RSF 06 346)GBUnited Kingdo