• An Analysis of Abatement Potential of Greenhouse Gas Emissions in Irish Agriculture 2021-2030

      Lanigan, Gary; Donnellan, Trevor; Hanrahan, Kevin; Carsten, Paul; Shalloo, Laurence; Krol, Dominika; Forrestal, Patrick J.; Farrelly, Niall; O’Brien, Donal; Ryan, Mary; et al. (Teagasc, 2018-06-10)
      This report has been prepared by the Teagasc Working Group on GHG Emissions, which brings together and integrates the extensive and diverse range of organisational expertise on agricultural greenhouse gases. The previous Teagasc GHG MACC was published in 2012 in response to both the EU Climate and Energy Package and related Effort Sharing Decision and in the context of the establishment of the Food Harvest 2020 production targets.
    • Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions

      Szoboszlay, Márton; Näther, Astrid; Mullins, Ewen; Tebbe, Christoph C.; European Union; 289706 (Public Library of Science (PLoS), 2019-12-17)
      The importance of geographic location and annual variation on the detection of differences in the rhizomicrobiome caused by the genetic modification of maize (Bt-maize, event MON810) was evaluated at experimental field sites across Europe including Sweden, Denmark, Slovakia and Spain. DNA of the rhizomicrobiome was collected at the maize flowering stage in three consecutive years and analyzed for the abundance and diversity of PCR-amplified structural genes of Bacteria, Archaea and Fungi, and functional genes for bacterial nitrite reductases (nirS, nirK). The nirK genes were always more abundant than nirS. Maize MON810 did not significantly alter the abundance of any microbial genetic marker, except for sporadically detected differences at individual sites and years. In contrast, annual variation between sites was often significant and variable depending on the targeted markers. Distinct, site-specific microbial communities were detected but the sites in Denmark and Sweden were similar to each other. A significant effect of the genetic modification of the plant on the community structure in the rhizosphere was detected among the nirK denitrifiers at the Slovakian site in only one year. However, most nirK sequences with opposite response were from the same or related source organisms suggesting that the transient differences in community structure did not translate to the functional level. Our results show a lack of effect of the genetic modification of maize on the rhizosphere microbiome that would be stable and consistent over multiple years. This demonstrates the importance of considering annual variability in assessing environmental effects of genetically modified crops.
    • Assessing populations of the major cereal pathogens for reduced sensitivity to MBC, DMI and Strobilurin fungicides

      O'Sullivan, Eugene (Teagasc, 01/08/2009)
      Studies of eyespot populations in winter wheat crops in the period 2001 to 2003 showed that the R type (Tapesia acuformis) is the dominant strain comprising 77% of isolates. Over 90% of isolates were resistant to MBC fungicides, 53% showed reduced sensitivity to prochloraz and 22% reduced sensitivity to cyprodinil. A study of winter wheat crops in February and March 2003 showed that resistance to strobilurin fungicides was widespread in Mycosphaerella graminicola (Septoria tritici) populations. Resistance was found in all but one of 21 crops sampled, at levels ranging from 9% to 84% with an average of 48%. Subsequent studies of 27 crops over the summer of 2003 showed that strobilunin resistance increased from an average of 31% before the application of the second (T2) spray to an average of 73%, three to four weeks after the application of the final (T3) spray. Strobilurin resistance in M. graminicola remained high in 2004, ranging from 50% to 100% with an average of 83% in populations in winter wheat crops sampled in March. The effect of different fungicide programmes on resistance was studied during summer 2003 at two experimental sites. Levels of strobilurin resistance in M. graminicola populations increased during the summer, in unsprayed plots and plots treated with triazole fungicides as well as in those treated with strobiurin fungicides at both sites. M. graminicola populations in winter wheat crops sampled in 2003 and 2004 were predominantly resistant to MBC-generating fungicides and sensitive to the triazole-based fungicides. Studies of the barley leaf blotch pathogen Rhynchosporium secalis showed that resistance to MBC fungicides occurred in 20% of isolates collected from crops from 2001 to 2003, but all isolates were sensitive to triazole and strobilurin fungicides.
    • Assessing the Impact of Pollen-mediated Gene Flow from GM Herbicide Tolerant Brassica Napus into Common Wild Relatives in Ireland

      Collier, Marcus J.; Mullins, Ewen; Environmental Protection Agency; Teagasc; ERTDI 2006-B-MS-46; 2007-B-DS-1-S1 (Royal Irish Academy, 30/04/2012)
      Although now we have had many years of research completed on assessing the potential environmental impact of GM crops, concern remains over their potential impact on biodiversity in the rural landscape. In particular, issues have arisen in regards to the modification of crops with traits that could introgress into sexually compatible wild relatives. In contrast to wheat, barley, potato and maize, Brassica napus (oilseed rape) is the only commercial crop grown in Ireland at present with the potential to successfully transfer its DNA, via pollen-mediated gene flow, into inter-related weed species. This review details the species in question and by examining the relevant literature that relates to Irish agronomic conditions, demonstrates that gene flow is likely to occur, especially to an earlier used cultivar, Brassica rapa. However, the critical factor remains not that GM traits will flow from the commercial source but what might the consequences of said gene flow events be. This review indicates that the conferred trait in question (in this case, herbicide tolerance) can only impact on weed diversity in the presence of selecting herbicide action. In the absence of the herbicide, the GM traits will be lost from the wild species over time and will not confer any selective advantage that could facilitate population growth.
    • Assessment of water-limited winter wheat yield potential at spatially contrasting sites in Ireland using a simple growth and development model

      Lynch, J.P.; Fealy, Reamonn; Doyle, D.; Black, L.; Spink, John; Department of Agriculture, Food and the Marine, Ireland (Teagasc (Agriculture and Food Development Authority), Ireland, 19/09/2017)
      Although Irish winter wheat yields are among the highest globally, increases in the profitability of this crop are required to maintain its economic viability. However, in order to determine if efforts to further increase Irish wheat yields are likely to be successful, an accurate estimation of the yield potential is required for different regions within Ireland. A winter wheat yield potential model (WWYPM) was developed, which estimates the maximum water-limited yield achievable, within the confines of current genetic resources and technologies, using parameters for winter wheat growth and development observed recently in Ireland and a minor amount of daily meteorological input (maximum and minimum daily temperature, total daily rainfall and total daily incident radiation). The WWYPM is composed of three processes: (i) an estimation of potential green area index, (ii) an estimation of light interception and biomass accumulation and (iii) an estimation of biomass partitioning to grain yield. Model validation indicated that WWYPM estimations of water-limited yield potential (YPw) were significantly related to maximum yields recorded in variety evaluation trials as well as regional average and maximum farm yields, reflecting the model’s sensitivity to alterations in the climatic environment with spatial and seasonal variations. Simulations of YPw for long-term average weather data at 12 sites located at spatially contrasting regions of Ireland indicated that the typical YPw varied between 15.6 and 17.9 t/ha, with a mean of 16.7 t/ha at 15% moisture content. These results indicate that the majority of sites in Ireland have the potential to grow high-yielding crops of winter wheat when the effects of very high rainfall and other stresses such as disease incidence and nutrient deficits are not considered.
    • Beef production from feedstuffs conserved using new technologies to reduce negative environmental impacts

      O'Kiely, Padraig; Crosson, Paul; Hamilton, William J.; Little, Enda; Stacey, Pamela; Walsh, Karl; Black, Alistair D; Crowley, James C.; Drennan, Michael J; Forristal, Dermot; et al. (Teagasc, 2007-12-01)
      Most (ca. 86%) Irish farms make some silage. Besides directly providing feed for livestock, the provision of grass silage within integrated grassland systems makes an important positive contribution to effective grazing management and improved forage utilisation by grazing animals, and to effective feed budgeting by farmers. It can also contribute to maintaining the content of desirable species in pastures, and to livestock not succumbing to parasites at sensitive times of the year. Furthermore, the optimal recycling of nutrients collected from housed livestock can often be best achieved by spreading the manures on the land used for producing the conserved feed. On most Irish farms, grass silage will remain the main conserved forage for feeding to livestock during winter for the foreseeable future. However, on some farms high yields of whole-crop (i.e. grain + straw) cereals such as wheat, barley and triticale, and of forage maize, will be an alternative option provided that losses during harvesting, storage and feedout are minimised and that input costs are restrained. These alternative forages have the potential to reliably support high levels of animal performance while avoiding the production of effluent. Their production and use however will need to advantageously integrate into ruminant production systems. A range of technologies can be employed for crop production and conservation, and for beef production, and the optimal options need to be identified. Beef cattle being finished indoors are offered concentrate feedstuffs at rates that range from modest inputs through to ad libitum access. Such concentrates frequently contain high levels of cereals such as barley or wheat. These cereals are generally between 14% to 18% moisture content and tend to be rolled shortly before being included in coarse rations or are more finely processed prior to pelleting. Farmers thinking of using ‘high-moisture grain’ techniques for preserving and processing cereal grains destined for feeding to beef cattle need to know how the yield, conservation efficiency and feeding value of such grains compares with grains conserved using more conventional techniques. European Union policy strongly encourages a sustainable and multifunctional agriculture. Therefore, in addition to providing European consumers with quality food produced within approved systems, agriculture must also contribute positively to the conservation of natural resources and the upkeep of the rural landscape. Plastics are widely used in agriculture and their post-use fate on farms must not harm the environment - they must be managed to support the enduring sustainability of farming systems. There is an absence of information on the efficacy of some new options for covering and sealing silage with plastic sheeting and tyres, and an absence of an inventory of the use, re-use and post-use fate of plastic film on farms. Irish cattle farmers operate a large number of beef production systems, half of which use dairy bred calves. In the current, continuously changing production and market conditions, new beef systems must be considered. A computer package is required that will allow the rapid, repeatable simulation and assessment of alternate beef production systems using appropriate, standardised procedures. There is thus a need to construct, evaluate and utilise computer models of components of beef production systems and to develop mathematical relationships to link system components into a network that would support their integration into an optimal system model. This will provide a framework to integrate physical and financial on-farm conditions with models for estimating feed supply and animal growth patterns. Cash flow and profit/loss results will be developed. This will help identify optimal systems, indicate the cause of failure of imperfect systems and identify areas where applied research data are currently lacking, or more basic research is required.
    • Can herbage nitrogen fractionation in Lolium perenne be improved by herbage management?

      Hoekstra, Nyncke J.; Struik, Paul; Lantinga, Egbert A.; Van Amburgh, Michael; Schulte, Rogier P.; Teagasc Walsh Fellowship Programme (Elsevier, 2009-08-20)
      The high degradability of grass protein is an important factor in the low nitrogen (N) utilization of grazing bovines in intensive European grassland systems. We tested the hypothesis that protein degradability as measured by the Cornell Net Carbohydrate and Protein System (CNCPS) protein fractionation scheme, can be manipulated by herbage management tools, with the aim to reduce N loss to the environment. A field experiment comprising the factorial combinations of three fertilizer N application rates (0, 90 and 390 kg N ha−1 year−1), three regrowth periods (2–3, 4–5, and 6–7 weeks), two perennial ryegrass (Lolium perenne L.) cultivars [Aberdart (high sugar content) and Respect (low sugar content)] and two cutting heights (approximately 8 and 12 cm) was conducted at Teagasc, Johnstown Castle Research Centre, Wexford, Ireland. The plots were sampled during four seasons [September/October 2002 (late season), April 2003 (early season), May/June 2003 (mid season) and September 2003 (late season)] and protein fractions were determined in both sheath and lamina material. The protein was highly soluble and on average 19% and 28% of total N was in the form of non-protein N, 16% and 19% in the form of buffer-soluble protein, 52% and 40% in the form of buffer-insoluble protein, and 12% and 13% in the form of potentially available cell wall N for lamina and sheath material, respectively. In both materials only 0.9% of total N was present as unavailable cell wall N. In general the herbage management tools investigated did not have much effect on protein fractionation. The effects of regrowth period, cultivar and cutting height were small and inconsistent. High N application rates significantly increased protein degradability, especially during late season. This is relevant, as it has been shown that enhanced protein degradation increases the potential N loss through urine excretion at a time when urine-N excreted onto pasture is prone to leaching. However, the effect was most evident for sheath material, which forms only a small proportion of the animals' intake. It was concluded that there appears to be little scope for manipulating the herbage-N fractionation through herbage management. The consequences for modelling herbage quality could be positive as there does not seem to be a need to model the individual N fractions; in most cases the N fractions can be expressed as a fixed proportion of total N instead.
    • Cereal yield gaps across Europe

      Schils, René; Olesen, Jørgen E.; Kersebaum, Kurt-Christian; Rijk, Bert; Oberforster, Michael; Kalyada, Valery; Khitrykau, Maksim; Gobin, Anne; Kirchev, Hristofor; Manolova, Vanya; et al. (Elsevier, 2018-09-18)
      Europe accounts for around 20% of the global cereal production and is a net exporter of ca. 15% of that production. Increasing global demand for cereals justifies questions as to where and by how much Europe’s production can be increased to meet future global market demands, and how much additional nitrogen (N) crops would require. The latter is important as environmental concern and legislation are equally important as production aims in Europe. Here, we used a country-by-country, bottom-up approach to establish statistical estimates of actual grain yield, and compare these to modelled estimates of potential yields for either irrigated or rainfed conditions. In this way, we identified the yield gaps and the opportunities for increased cereal production for wheat, barley and maize, which represent 90% of the cereals grown in Europe. The combined mean annual yield gap of wheat, barley, maize was 239 Mt, or 42% of the yield potential. The national yield gaps ranged between 10 and 70%, with small gaps in many north-western European countries, and large gaps in eastern and south-western Europe. Yield gaps for rainfed and irrigated maize were consistently lower than those of wheat and barley. If the yield gaps of maize, wheat and barley would be reduced from 42% to 20% of potential yields, this would increase annual cereal production by 128 Mt (39%). Potential for higher cereal production exists predominantly in Eastern Europe, and half of Europe’s potential increase is located in Ukraine, Romania and Poland. Unlocking the identified potential for production growth requires a substantial increase of the crop N uptake of 4.8 Mt. Across Europe, the average N uptake gaps, to achieve 80% of the yield potential, were 87, 77 and 43 kg N ha−1 for wheat, barley and maize, respectively. Emphasis on increasing the N use efficiency is necessary to minimize the need for additional N inputs. Whether yield gap reduction is desirable and feasible is a matter of balancing Europe’s role in global food security, farm economic objectives and environmental targets.
    • Changes in yield and composition of barley, wheat and triticale grains harvested during advancing stages of ripening

      Stacey, Pamela; O'Kiely, Padraig; Hackett, Richard; Rice, B.; O'Mara, Frank P.; Teagasc Walsh Fellowship Programme (Teagasc, Oak Park, Carlow, Ireland, 2006)
      This study involved an evaluation of the changes in grain yield, nutritive value, ensilability and harvesting losses of intensively managed winter cereals harvested during the advancing stages of ripening. Five cereal crops (barley cv. Regina and wheat cv. Madrigal in 2001; barley cv. Regina, wheat cv. Falstaff and triticale cv. Fidelio in 2002) were assessed. Twenty plots per crop were arranged in a randomised complete block design, with five times of harvest (four for barley in 2002) and four replicate blocks per harvest. Dry matter (DM) yields changed relatively little between harvest dates, but fresh yields declined (P < 0.001) over time due to the moisture loss associated with ripening. Time-course changes in indices of nutritive value, such as concentrations of crude protein, starch and ash, and organic matter digestibility, were relatively small and did not follow a consistent pattern. Ensilability indices, such as DM and watersoluble carbohydrate concentrations and buffering capacity, indicated that satisfactory fermentations were likely if such crops were ensiled; buffering capacity, generally declining with advancing maturity. Harvesting losses were not clearly related to growth stage at harvest. It is concluded that winter cereal grain (barley, wheat and triticale) DM yields and quality were relatively constant as ripening progressed from DM concentrations of around 550 to >800 g/kg.
    • The Characterisation of Genetic Diversity of a Collection of Perennial Ryegrass (Lolium perenne L.).

      McGrath, Sarah Katherine; Teagasc Walsh Fellowship Programme (2008)
      Perennial ryegrass (Lolium perenne L.) is a member of the Poaceae family, is native to Europe, the Near East and North Africa and is grown in all the temperate climate areas of the world as a forage and turf grass. Due to its persistence, palatability and nutritive value for ruminants, it is a principal component of pastures, and the most important forage species in Ireland. The primary aim of this thesis was to characterise the level of diversity in a large genetic resource collection of L. perenne germplasm held at Teagasc, Oak Park. Molecular markers, both chloroplast and nuclear SSRs, biochemical characters (water soluble carbohydrate, crude protein, and dry matter), and morphological characters (vegetative and flowering) were used to characterise this diversity, as well as population differentiation, and geographic patterns. Levels of diversity in all systems were found to be high in this collection. Primers to amplify microsatellite markers from the chloroplast genome of Lolium perenne were designed and optimized using de novo sequencing and in silico sequences. With one exception, each locus was polymorphic with a range from two to nine alleles in L. perenne. The newly developed primer pairs cross-amplified in different species of Lolium and in 50 other grass species representing nine grass subfamilies. These markers were then used to characterise chloroplast genetic diversity at allelic and haplotypic level in 104 accessions of Lolium perenne, other Lolium species, Festuca species and ´Festulolium cultivars. Furthermore, genetic relationships between the accessions and biogeographic distribution of haplotypes were investigated using a range of population genetic diversity measures and an Analysis of Molecular Variance (AMOVA). An extremely high number of 511 haplotypes was detected in 1,575 individuals possibly attributable to natural and anthropogenic migration. Much of the L. perenne European ecotype diversity (61%) could be attributed to within population variance. Plastid gene pools and maternal lineages for L. perenne could be clearly identified. Evidence was found showing a most likely migration route of L. perenne into Ireland from southern regions of Europe northwards. 5 Morphological variation of 13 vegetative and reproductive traits was characterised for 2,481 individuals from 50 L. perenne accessions, a mixture of Irish and European ecotypes and cultivars. Considerable levels of among and within population variation was found across traits. Principal component analysis and UPGMA dendrograms were able to separate ecotypes from cultivars. Cultivars generally had later dates of ear emergence, better spring and summer growth, longer rachis length and more spikelets per spike than ecotypes. Correlation and regression analysis were used to assess relationships between traits and strong positive relationships were seen between reproductive characters, i.e. rachis length with spikelets per spike, florets per spikelet and glume length. The strong relationship between rachis length and the other reproductive characters suggested that rachis length could be used as a predictor for reproductive performance. Later flowering was correlated with improved spring and summer growth. Water soluble carbohydrate (WSC; glucose and fructose determined by HPLC), crude protein (determined via LECO analysis), and dry matter contents were recorded for 1,320 individuals, pooled into 132 samples from 33 L. perenne ecotypes and cultivars at five different harvest time points across the 2004 growing season. While, in general, the cultivars had higher WSC contents than the ecotypes, individual ecotypes did show potential to be used in breeding programmes, as they showed higher values than all other accessions at particular cutting points. In correlation analyses, positive relationships were shown between dry matter and glucose both early and late in the growing season, and this was in agreement with the amount of leaves compared to stem at these times in the growing season. PCA analysis allowed the separation either between cultivars and ecotypes, or between tetraploid cultivars and the rest of the accessions at four out of five cutting points. In the ANOVA analysis, cutting point was the most significant factor influencing the variation in the traits. Eight nuclear SSR markers were used to characterize genetic diversity in 928 individuals from 40 diploid ecotypes and cultivars of L. perenne. High levels of genetic diversity (0.82, Nei’s gene diversity, over all accessions) and high numbers of alleles (22.25 average number of alleles per locus) was found. An average polymorphic information content (PIC) value of 0.81 across all loci was found. When deviations from Hardy-Weinberg equilibrium were tested, the majority of populations 6 had an excess of homozygotes. Very low levels of linkage disequilibrium were found between pairs of loci tested. AMOVA analysis and F statistics were used to test partitioning of variation, and most variation was found within populations (e.g. 31% for glume length in ecotypes). UPGMA, PCA and STRUCTURE analysis all gave similar patterns of relationships between populations, where relationships with high bootstrap support on the UPGMA dendrogram were also seen in the other analyses. The overall results of the thesis are discussed in the context of plant breeding programmes and natural population genetic variation. Strategies for incorporation of the results of the thesis (and the novel markers developed within) into plant breeding programmes are suggested.
    • Characterisation of Miscanthus genetic resources: a combined analysis of plastid and nuclear microsatellites, nrDNA sequences, flow cytometry and morphology.

      De Cesare, Mariateresa; Teagasc Walsh Fellowship Programme; National Development Plan (2012)
      Miscanthus is a highly important forage and horticultural genus of perennial grasses (Poaceae) primarily native to South East Asia. Miscanthus is under intense global investigation as a biomass source for renewable energy production and several breeding initiatives are underway to develop new genotypes optimized for improved biomass and tolerance to a range of environmental stress conditions. A collection of 128 accessions belonging to the genus Miscanthus was established in Oak Park, Teagasc, Carlow, in 2008 and was investigated for morphological and molecular variation. Morphological traits were measured at the end of the second growing season and were compared with herbarium specimens of Miscanthus. Vegetative and inflorescence traits were scored and analysed using basic summary statistics, tests of normality and Principal Components Analysis (PCA). A large degree of morphological variation was recorded in the collections. The PCA of herbarium specimens was able to separate some species from others but there was also considerable overlap among species in the ordination, especially M. sacchariflorus, M. sinensis, M. condensatus and M. floridulus. These are known to be closely related and can interbreed. The PCA of the specimens from the Oak Park collection was less informative because of missing data due to lack of inflorescences (accessions did not flower). It was clear that morphology alone is often insufficient to distinguish taxa especially when inflorescence characters and ploidy information is lacking. The ploidy level of the accessions in the collection was evaluated through flow cytometry. The ploidy included di-, tri- and tetraploids. All individuals labelled as M. ×giganteus showed a triploid status, together with the newly bred M. sacchariflorus×M. sinensis hybrids. Most M. sinensis were diploids. Miscanthus sinensis Tea-62 was triploid and comparable to the value of the M. ×giganteus. A different situation was found for other non-diploid M. sinensis, in particular four M. sinensis ‘Goliath’ and the M. sinensis ‘Zebrinus’ Tea-33. In these the ratio measured by the flowcytometer was in between the values of the triploid M. giganteus and tetraploid M. sacchariflorus standards. The ‘Goliath-like’ hybrid is likely an autotriploid with three M. sinensis haploid sets, whereas M. ×giganteus is an allotriploid that is supposed to have two genomes from M. sinensis and one from M. sacchariflorus, which has a lower amount of DNA per haploid genome. DNA sequences of the internal transcribed spacer of the nrDNA were obtained for 76 genotypes in the collection and compared for polymorphism. The SNPs were particularly VI useful for differentiating M. sinensis, M. sacchariflorus and M. ×giganteus accessions and in combination with ploidy and morphology offer high potential for taxon identification. To gather more markers for population level diversity and differentiation studies, new microsatellite markers for both plastid and nuclear genomes were developed. For the development of plastid markers the chloroplast genome information of Saccharum officinarum was used. The nuclear SSRs (nSSRs) were developed from the sequences of 192 clones obtained from microsatellite enriched library. New primer pairs for the amplification of nineteen nuclear loci and six chloroplast loci were developed. Both chloroplast (cpSSR) and nSSR primers were used to characterise DNA variation, to help establish gene pools and to better understand hybridization and introgression. Huge genotypic variation was found within the genus, mostly in the species M. sinensis. The markers showed wide utility across a large number of Miscanthus species and also some closely related genera. The analysis of the cpSSRs showed a high number of different haplotypes but with a clear bias in allele composition between M. sinensis and the two species M. sacchariflorus and M. ×giganteus, thus confirming M. sacchariflorus as the maternal lineage of the hybrid M. xgiganteus. The nSSRs were found to be highly polymorphic across the collection and transferable to closely related genera such as Saccharum. The new markers were also used in UPGMA clustering and Bayesian structuring analysis to group individuals according to their similarity. Three major clusters of individuals were defined using the Bayesian STRUCTURE analysis with nuclear markers (nSSRs) and two with plastid markers (cpSSRs). In conclusion, the morphological, ploidy, sequence and microsatellite results highlighted the high level of diversity still unexplored in the genus and have clarified taxon identity of many accessions in the collection. A large set of new markers have been developed for the plant breeding and systematics community. The newly developed markers will be useful to further explore this diversity and to select useful traits for breeding of new and improved genotypes for biomass production.
    • Characteristaion of the initial generations of recombinant inbred lines in perennial ryegrass (lolium perenne L.) using molecular markers and cytogenetics

      Anhalt, Ulrike C. M.; Teagasc Walsh Fellowship Programme; National Development Plan (2009)
      In this study three early generations of a recombinant inbred line (RIL) breeding programme have been characterised by cytogenetic methods, metabolite profiling and a biomass quantitative trait loci (QTL) study. In situ hybridization was used to analyse recombination and the structure of the parental and the F1 genomes. A metabolite profiling study via GC/MS was conducted to characterise the metabolite activity of the parental inbred lines and the F1 hybrid. Total metabolites were compared across a growth season in a replicated field design. A genetic map was constructed with 75 nuclear DNA markers in the F2 generation, which consisted of 360 individuals. 63% of the markers in the F2 population did not fit the expected Mendelian ratios and showed significant (p<0.05) segregation distortion. Fresh weight, dry weight, and dry matter were analysed with an alpha lattice design throughout the greenhouse and field experiments. Additionally, leaf width was recorded in the greenhouse experiment. Heritablities ranged for the biomass related traits between 78 and 95%. This study provides an insight into the recombination of the parental and the F1 genotypes. Different levels of metabolite activities could be found among the two parental inbred lines across three harvest dates. The QTL study indicates the position of biomass QTL related traits. Major QTL with log of odds scores >3 were identified on linkage groups 2, 3, 4, 5 and 7. About 30% of overall variation could be explained. Increased biomass yield is still one of the most important traits in any Lolium perenne breeding programme. The present QTL study can be used for fine mapping of biomass yield related traits in L. perenne. In the long term biomass yield can be eventually monitored and predicted with marker assisted selection for some of the QTL identified in the present study.
    • Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses

      Della Bartola, Michele; Byrne, Stephen; Mullins, Ewen; Department of Agriculture, Food and the Marine; 15/S/618 SCOPE (MDPI AG, 2020-04-23)
      Potato virus Y (PVY) is the most economically important virus infecting cultivated potato (Solanum tuberosum L.). Accurate diagnosis is crucial to regulate the trade of tubers and for the sanitary selection of plant material for propagation. However, high genetic diversity of PVY represents a challenge for the detection and classification of isolates. Here, the diversity of Irish PVY isolates from a germplasm collection and commercial sites was investigated using conventional molecular and serological techniques. Recombinant PVY isolates were prevalent, with PVYNTNa being the predominant genotype. In addition, we evaluated Nanopore sequencing to detect and reconstruct the whole genome sequence of four viruses (PVY, PVX, PVS, PLRV) and five PVY genotypes in a subset of eight potato plants. De novo assembly of Nanopore sequencing reads produced single contigs covering greater than 90% of the viral genome and sharing greater than 99.5% identity to the consensus sequences obtained with Illumina sequencing. Interestingly, single near full genome contigs were obtained for different isolates of PVY co-infecting the same plant. Mapping reads to available reference viral genomes enabled us to generate near complete genome sequences sharing greater than 99.90% identity to the Illumina-derived consensus. This is the first report describing the use of Oxford Nanopore’s MinION to detect and genotype potato viruses. We reconstructed the genome of PVY and other RNA viruses; indicating the technologies potential for virus detection in potato production systems, and for the study of genetic diversity of highly heterogeneous viruses such as PVY.
    • Chemical composition of lamina and sheath of Lolium perenne as affected by herbage management

      Hoekstra, Nyncke J.; Struik, Paul C.; Lantinga, E. A.; Schulte, Rogier P.; Teagasc Walsh Fellowship Programme (Elsevier, 2009-08-20)
      The quality of grass in terms of form and relative amounts of energy and protein affects both animal production per unit of intake and nitrogen (N) utilization. Quality can be manipulated by herbage management and choice of cultivar. The effects of N application rate (0, 90 or 390 kg N ha−1 year−1), duration of regrowth period (2–3, 4–5, or 6–7 weeks), and cutting height (8 or 12 cm) on the mass fractions of nitrogen (N), water-soluble carbohydrates (WSC), neutral detergent fibre (NDF), acid detergent fibre (ADF), lignin and ash in lamina and sheath material of a high-sugar (Aberdart) and a low-sugar (Respect) perennial ryegrass (Lolium perenne) cultivar, were studied in a factorial field experiment during four seasons in 2002 and 2003. Expressing NDF and ADF mass fractions in g per kg WSC-free dry matter (DM) increased the consistency of treatment effects. The high-sugar cultivar had generally higher WSC mass fractions than the low-sugar cultivar, especially during the late season. Moreover, the relative difference in WSC mass fraction between the two cultivars tended to be higher for the lamina material than for the sheath material, which suggests that the high-sugar trait may be more important under grazing conditions, when lamina forms the bulk of the intake, than under mowing regimes. Longer regrowth periods and lower N application rates increased WSC mass fractions and decreased N mass fractions; interactions between regrowth period and N application rate were highly significant. The mass fractions of NDF and ADF were much less influenced. The NDF mass fraction in terms of g per kg WSC-free DM tended to be higher at lower N application rates and at longer regrowth periods. The effect of cutting height on herbage chemical composition was unclear. In conclusion, high-sugar cultivars, N application rate and length of the regrowth period are important tools for manipulating herbage quality.
    • A comparison of husked and naked oats under Irish conditions

      Hackett, Richard (Teagasc (Agriculture and Food Development Authority), Ireland, 2018-02-22)
      During the harvesting of husked oats (Avena sativa L.), the kernel remains tightly enclosed by a lignified lemma and palea, collectively termed the husk or hull. In naked oats, which are the same species as husked oats, the lemma is much less lignified and the kernel threshes free during harvesting. The absence of the largely indigestible husk increases the nutritive value of naked oats compared to that of husked oats, particularly for non-ruminants and poultry. There is little information regarding the potential of naked oats as an arable crop in Ireland. The objective of this study was to determine the productivity of naked oats under Irish conditions. Field experiments were carried out in the south east of Ireland to compare the grain yield and grain quality of both autumn-sown and spring-sown naked and husked oat cultivars. Grain yield of naked oat cultivars was significantly lower than that of husked oat cultivars, irrespective of whether they were autumn sown or spring sown. However, when the kernel yield of husked oat cultivars was estimated, differences in yield between the two types were much smaller, and in some cases, kernel yield of naked oat cultivars exceeded that of husked oat cultivars. Grain quality, as indicated by hectolitre weight and grain N concentration, was generally greater for naked oat cultivars than for husked oat cultivars. It is concluded that under Irish conditions, naked oats have the potential to produce kernel yields equivalent to husked oats. The grain produced is of high quality and may be particularly suited for the nutrition of non-ruminants.
    • Conservation characteristics of baled grass silages differing in duration of wilting, bale density and number of layers of plastic stretch-film

      Keles, G.; O'Kiely, Padraig; Lenehan, J.J.; Forristal, P.D. (Teagasc, Oak Park, Carlow, Ireland, 2009)
      The effects of duration of wilting, bale density and number of layers of plastic stretchfilm used to wrap bales on the conservation characteristics of baled grass silage was investigated. Grass from the primary growth of a Lolium perenne dominant sward was wilted for 24, 48 or 72 h. For each duration of wilting, 54 cylindrical bales (1.2 m nominal diameter) were made with the baler at a high or low density setting for alternate bales. Bales were wrapped with 2, 4 or 6 layers of plastic stretch-film and stored outdoors for 295 days. Two layers of plastic stretch-film resulted in inferior preservation, lower digestibility and extensive mould growth and deteriorated silage. Substantial improvement occurred to each of these characteristics from applying four layers of stretch-film (P<0.05), while six layers of stretch-film brought little further improvement. When four or six layers of stretch-film were used, extensive wilting restricted fermentation and improved the standard of preservation with the apparently difficult-to-preserve herbage used in this experiment. However, under the anaerobic conditions provided by four or six layers of stretch-film neither progressive wilting nor bale density had a major effect on digestibility, or the extent of surface mould growth or deteriorated silage. It can be concluded that a minimum of four layers of conventional black plastic stretch-film were required to achieve suitably anaerobic conditions, and that the additional benefits from six layers were small. Once anaerobic conditions were achieved, extensive wilting improved the conservation characteristics of baled grass silage made from a difficult-to-preserve crop, whereas bale density had little impact.
    • A critical review of integrated grass weed management in Ireland

      Byrne, Ricky; Spink, John; Freckleton, R.; Neve, Paul; Barth, Susanne; Teagasc Walsh Fellowship Programme (Teagasc (Agriculture and Food Development Authority), Ireland, 2018-04-10)
      Grass weeds affect arable crops throughout the world, inflicting yield penalties, reducing crop quality and taking available nutrients away from the growing crop. Recently in Ireland, the presence of herbicide resistance in grass weeds has been noted. In order to preserve the sustainability of crop production in Ireland, an integrated pest management approach must be implemented. How this applies to control grass weeds was the focus of this review. Here we examined the state of current research into grass weed biology and the nature of herbicide resistance, identifying gaps in research in the Irish context. We identified a number of cultural grass weed control techniques, as being relevant to the Irish mode of crop production. Crop rotation, cultivation techniques, manipulation of sowing dates and increased crop competition were recognised as useful strategies. Combining these strategies to provide effective grass weed control may be key to reduce dependence on herbicides.
    • Crop Establishment Practices Are a Driver of the Plant Microbiota in Winter Oilseed Rape (Brassica napus)

      Rathore, Ridhdhi; Dowling, David N.; Forristal, P.D.; Spink, John; Cotter, Paul D.; Bulgarelli, Davide; Germaine, Kieran J.; Teagasc Walsh Fellowship Programme; Marie Curie Actions; Royal Society of Edinburgh/Scottish Government Personal Research Fellowship (Frontiers, 2017-08-09)
      Gaining a greater understanding of the plant microbiota and its interactions with its host plant heralds a new era of scientific discovery in agriculture. Different agricultural management practices influence soil microbial populations by changing a soil’s physical, chemical and biological properties. However, the impact of these practices on the microbiota associated with economically important crops such as oilseed rape, are still understudied. In this work we investigated the impact of two contrasting crop establishment practices, conventional (plow based) and conservation (strip–tillage) systems, on the microbiota inhabiting different plant microhabitats, namely rhizosphere, root and shoot, of winter oilseed rape under Irish agronomic conditions. Illumina 16S rRNA gene sequence profiling showed that the plant associated microhabitats (root and shoot), are dominated by members of the bacterial phyla Proteobacteria, Actinobacteria and Bacteroidetes. The root and shoot associated bacterial communities displayed markedly distinct profiles as a result of tillage practices. We observed a very limited ‘rhizosphere effect’ in the root zone of WOSR, i.e., there was little or no increase in bacterial community richness and abundance in the WOSR rhizosphere compared to the bulk soil. The two tillage systems investigated did not appear to lead to any major long term differences on the bulk soil or rhizosphere bacterial communities. Our data suggests that the WOSR root and shoot microbiota can be impacted by management practices and is an important mechanism that could allow us to understand how plants respond to different management practices and environments.
    • Crop Establishment Practices Are a Driver of the Plant Microbiota in Winter Oilseed Rape (Brassica napus)

      Rathore, Ridhdhi; Dowling, David N.; Forristal, P.D.; Spink, John; Cotter, Paul D.; Bulgarelli, Davide; Germaine, Kieran J.; Teagasc Walsh Fellowship Programme; Royal Society of Edinburgh/Scottish Government Personal Research Fellowship (Frontiers, 2017-08-09)
      Gaining a greater understanding of the plant microbiota and its interactions with its host plant heralds a new era of scientific discovery in agriculture. Different agricultural management practices influence soil microbial populations by changing a soil’s physical, chemical and biological properties. However, the impact of these practices on the microbiota associated with economically important crops such as oilseed rape, are still understudied. In this work we investigated the impact of two contrasting crop establishment practices, conventional (plow based) and conservation (strip–tillage) systems, on the microbiota inhabiting different plant microhabitats, namely rhizosphere, root and shoot, of winter oilseed rape under Irish agronomic conditions. Illumina 16S rRNA gene sequence profiling showed that the plant associated microhabitats (root and shoot), are dominated by members of the bacterial phyla Proteobacteria, Actinobacteria and Bacteroidetes. The root and shoot associated bacterial communities displayed markedly distinct profiles as a result of tillage practices. We observed a very limited ‘rhizosphere effect’ in the root zone of WOSR, i.e., there was little or no increase in bacterial community richness and abundance in the WOSR rhizosphere compared to the bulk soil. The two tillage systems investigated did not appear to lead to any major long term differences on the bulk soil or rhizosphere bacterial communities. Our data suggests that the WOSR root and shoot microbiota can be impacted by management practices and is an important mechanism that could allow us to understand how plants respond to different management practices and environments.
    • CropQuest: Minor Crops Report

      Zahoor, Faisal; Forristal, Dermot; Gillespie, Gary; Department of Agriculture, Food and the Marine; 11/S/119 (Teagasc, 2015)
      In this report as part of the DAFM funded CROPQUEST desk study, a brief description outlining the characteristics of a range of minor crops, their uses/markets and their potential, if known, for production in Ireland is presented. The crops include: Amaranth, Borage, Calendula, Camelina, Crambe, Echium, Flax / Linseed, Hemp, Hops, Lentils, Lupins, Oats, Poppy, Quinoa