• Alley coppice—a new system with ancient roots

      Morhart, Christopher D.; Douglas, Gerry C.; Dupraz, Christian; Graves, Anil R.; Nahm, Michael; Paris, Perluigi; Sauter, Udo H.; Sheppard, Jonathan; Spiecker, Heinrich; European Commission (Springer, 2014-05)
      Context: Current production from natural forests will not satisfy future world demand for timber and fuel wood, and new land management options are required. Aims: We explore an innovative production system that combines the production of short rotation coppice in wide alleys with the production of high-value trees on narrow strips of land; it is an alternative form of alley cropping which we propose to call ‘alley coppice’. The aim is to describe this alley coppice system and to illustrate its potential for producing two diverse products, namely high-value timber and energy wood on the same land unit. Methods: Based on a comprehensive literature review, we compare the advantages and disadvantages of the alley coppice system and contrast the features with well-known existing or past systems of biomass and wood production. Results: We describe and discuss the basic aspects of alley coppice, its design and dynamics, the processes of competition and facilitation, issues of ecology, and areas that are open for future research. Conclusion: Based on existing knowledge, a solid foundation for the implementation of alley coppice on suitable land is presented, and the high potential of this system could be shown.
    • The challenge of managing soil functions at multiple scales: An optimisation study of the synergistic and antagonistic trade-offs between soil functions in Ireland

      Valujeva, Kristine; O’Sullivan, Lilian; Gutzler, Carsten; Fealy, Reamonn; Schulte, Rogier P.; European Commission (Elsevier, 2016-08-09)
      Recent forecasts show a need to increase agricultural production globally by 60% from 2005 to 2050, in order to meet a rising demand from a growing population. This poses challenges for scientists and policy makers to formulate solutions on how to increase food production and simultaneously meet environmental targets such as the conservation and protection of water, the conservation of biodiversity, and the mitigation of greenhouse gas emissions. As soil and land are subject to growing pressure to meet both agronomic and environmental targets, there is an urgent need to understand to what extent these diverging targets can be met simultaneously. Previously, the concept of Functional Land Management (FLM) was developed as a framework for managing the multifunctionality of land. In this paper, we deploy and evaluate the concept of FLM, using a real case-study of Irish agriculture. We investigate a number of scenarios, encompassing combinations of intensification, expansion and land drainage, for managing three soil functions, namely primary productivity, water purification and carbon sequestration. We use proxy-indicators (milk production, nitrate concentrations and area of new afforestation) to quantify the ‘supply’ of these three soil functions, and identify the relevant policy targets to frame the ‘demand’ for these soil functions. Specifically, this paper assesses how soil management and land use management interact in meeting these multiple targets simultaneously, by employing a non-spatial land use model for livestock production in Ireland that assesses the supply of soil functions for contrasting soil drainage and land use categories. Our results show that, in principle, it is possible to manage these three soil functions to meet both agronomic and environmental objectives, but as we add more soil functions, the management requirements become increasingly complex. In theory, an expansion scenario could meet all of the objectives simultaneously. However, this scenario is highly unlikely to materialise due to farm fragmentation, low land mobility rates and the challenging afforestation rates required for achieving the greenhouse gas reduction targets. In the absence of targeted policy interventions, an unmanaged combination of scenarios is more likely to emerge. The challenge for policy formation on future land use is how to move from an unmanaged combination scenario towards a managed combination scenario, in which the soil functions are purposefully managed to meet current and future agronomic and environmental targets, through a targeted combination of intensification, expansion and land drainage. Such purposeful management requires that the supply of each soil function is managed at the spatial scale at which the corresponding demand manifests itself. This spatial scale may differ between the soil functions, and may range from farm scale to national scale. Finally, our research identifies the need for future research to also consider and address the misalignment of temporal scales between the supply and demand of soil functions.
    • A disease resistance locus on potato and tomato chromosome 4 exhibits a conserved multipartite structure displaying different rates of evolution in different lineages

      Destefanis, M.; Nagy, Istvan; Rigney, Brian; Bryan, Glenn J; McLean, Karen; Hein, Ingo; Griffin, Denis; Milbourne, Dan; Teagasc Walsh Fellowship Programme; Department of Agriculture, Food and the Marine, Ireland; et al. (Biomed Central, 24/10/2015)
      Background In plant genomes, NB-LRR based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions. R-gene sequences mostly differentiate by accumulating point mutations and gene conversion events. Potato and tomato chromosome 4 harbours a syntenic R-gene locus (known as the R2 locus in potato) that has mainly been examined in central American/Mexican wild potato species on the basis of its contribution to resistance to late blight, caused by the oomycete pathogen Phytophthora infestans. Evidence to date indicates the occurrence of a fast evolutionary mode characterized by gene conversion events at the locus in these genotypes. Results A physical map of the R2 locus was developed for three Solanum tuberosum genotypes and used to identify the tomato syntenic sequence. Functional annotation of the locus revealed the presence of numerous resistance gene homologs (RGHs) belonging to the R2 gene family (R2GHs) organized into a total of 4 discrete physical clusters, three of which were conserved across S. tuberosum and tomato. Phylogenetic analysis showed clear orthology/paralogy relationships between S. tuberosum R2GHs but not in R2GHs cloned from Solanum wild species. This study confirmed that, in contrast to the wild species R2GHs, which have evolved through extensive sequence exchanges between paralogs, gene conversion was not a major force for differentiation in S. tuberosum R2GHs, and orthology/paralogy relationships have been maintained via a slow accumulation of point mutations in these genotypes. Conclusions S. tuberosum and Solanum lycopersicum R2GHs evolved mostly through duplication and deletion events, followed by gradual accumulation of mutations. Conversely, widespread gene conversion is the major evolutionary force that has shaped the locus in Mexican wild potato species. We conclude that different selective forces shaped the evolution of the R2 locus in these lineages and that co-evolution with a pathogen steered selection on different evolutionary paths.
    • The Irish Forest Soils Project and its Potential Contribution to the Assessment of Biodiversity

      Loftus, M; Bulfin, Michael; Farrelly, Niall; Fealy, Reamonn; green, stuart; Meehan, R; Radford, Toddy; National Development Plan; European Commission (Royal Irish Academy, 2002)
      The United Nations Environment Programme (UNEP) has proposed methods and thematic areas for data collection that are appropriate to the evaluation of biodiversity. The Heritage Council has identified a paucity of data on habitats in Ireland. Within this context, we outline the Irish Forest Soils (IFS) element of the Forest Inventory and Planning System (FIPS) and present a detailed account of land-cover mapping, which is an important aspect of the project. The IFS project aims to produce a national thematic map of land cover using soft-copy photogrammetry, combined with satellite-image classification and field survey. This aspect of the IFS project generates data on land cover at different spatial and classification resolutions. We report on the progress made to date and present illustrative examples of the data sets. The UNEP proposals provide a useful framework within which to discuss the potential contribution of IFS data to the assessment of biodiversity.
    • Multiple factors control the environmental effectiveness of agri-environment schemes: implications for design and evaluation

      Finn, John; Kurz, Isabelle; Bourke, David; European Union; European Commission; SSPE-CT-2003-502070 (School of Agriculture, Food Science and Veterinary Medicine, University College Dublin in association with Teagasc, 2008)
      Achieving and evaluating the environmental effectiveness of agri-environment schemes (AESs) has proven difficult. The design and ex ante evaluation of AESs is a crucial phase for ensuring effectiveness, but seems to receive relatively little attention. We propose a programme theory (a structured description of the various cause-and-effect relationships that underpin and achieve a policy initiative) for AESs that considers multiple factors that drive environmental performance at farm-scale (appropriate farm-level objectives, farmer compliance, implementation by institutions, and cause-and-effect relationship between management prescriptions and environmental objectives), and factors that determine how farm-scale performance aggregates to produce scheme-scale performance (participation rate, targeting, and threshold effects). These factors can be used as assessment criteria with which to pinpoint specific causes of AES failure, and thereby offer a practical approach to complement the design and evaluation of the environmental effects of AESs.
    • Multiple viral infections in Agaricus bisporus - Characterisation of 18 unique RNA viruses and 8 ORFans identified by deep sequencing

      Deakin, Gregory; Dobbs, Edward; Bennett, Julie M.; Jones, Ian M.; Grogan, Helen; Burton, Kerry S.; Teagasc Walsh Fellowship Programme; European Commission; 201043; 286836 (Nature Publishing Group, 26/05/2017)
      Thirty unique non-host RNAs were sequenced in the cultivated fungus, Agaricus bisporus, comprising 18 viruses each encoding an RdRp domain with an additional 8 ORFans (non-host RNAs with no similarity to known sequences). Two viruses were multipartite with component RNAs showing correlative abundances and common 3′ motifs. The viruses, all positive sense single-stranded, were classified into diverse orders/families. Multiple infections of Agaricus may represent a diverse, dynamic and interactive viral ecosystem with sequence variability ranging over 2 orders of magnitude and evidence of recombination, horizontal gene transfer and variable fragment numbers. Large numbers of viral RNAs were detected in multiple Agaricus samples; up to 24 in samples symptomatic for disease and 8–17 in asymptomatic samples, suggesting adaptive strategies for co-existence. The viral composition of growing cultures was dynamic, with evidence of gains and losses depending on the environment and included new hypothetical viruses when compared with the current transcriptome and EST databases. As the non-cellular transmission of mycoviruses is rare, the founding infections may be ancient, preserved in wild Agaricus populations, which act as reservoirs for subsequent cell-to-cell infection when host populations are expanded massively through fungiculture.