Now showing items 1-20 of 2787

    • Linear type trait genetic trends in Irish Holstein-Friesian dairy animals

      Berry, D.P.; Ring, S.C.; Kelleher, M.M.; Science Foundation Ireland; Department of Agriculture, Food and Marine; 16/RC/3835 (Teagasc, 2022-11-04)
      The objective of the present study was to investigate the genetic trends of 18 subjectively scored linear type traits describing animal morphology, as well as udder, teat, feet and leg conformation. The analysis was undertaken using 2,932,700 Holstein-Friesian females born in the Republic of Ireland between the years 2000 and 2020, inclusive. The results indicate that Holstein-Friesian females have progressively become shorter in stature as well as shallower (i.e. body depth) and less angular. The reduction in genetic merit for stature score since the year 2004 was, however, only observed in non-herdbook-registered heifers. Furthermore, the reducing score in body depth (i.e. narrower) and angularity (i.e. less angular) was approximately twice as fast in non-herdbook-registered heifers as it was in herdbook-registered heifers. Differences in the genetic merit of the body-related traits for calves born versus those that became cows only existed prior to 2010 with little biological differences thereafter; this observation was common across most of the linear type traits. Genetic merit for locomotion in non-herdbook-registered animals has deteriorated over the 20-yr period, while the foot angle over that period is becoming lower; no such trends were observed for the herdbook-registered animals. Large differences not only in the trends themselves, but also in the mean genetic merit for udder traits existed when comparing herdbook-registered calves versus non-registered calves. In conclusion, genetic merit for many of the traits evaluated has trended relatively consistent in a given direction, albeit the cumulative change in genetic s.d. units per traits over the 20-yr period was very small.
    • Irish cattle farmers’ experiences and perceptions of negative framing of farm animal welfare in the media

      Duley, A.; Connor, M.; Vigors, B. (Teagasc, 2022-11-04)
      RECORDABSTRACTARTICLE Irish cattle farmers’ experiences and perceptions of negative framing of farm animal welfare in the media RESEARCH-ARTICLE Author(s): A. Duley 1 , , M. Connor 1 , B. Vigors 2 Publication date (Electronic): 04 November 2022 Journal: Irish Journal of Agricultural and Food Research Publisher: Compuscript Keywords: Agriculture, farm animal welfare, farmer perception, media framing, rural sociology Abstract Increased urbanisation in recent decades has created a knowledge gap between farming and the Irish public. Mainstream media has begun filling this gap through reports on farm animal welfare (FAW) incidents that sometimes frame farming in a negative way. This negative framing can influence how farmers perceive the information communicated in these media stories and colour their experiences. Furthermore, perceived societal pressures may contribute to farmers feeling overwhelmed or negatively impact their mental health. In the context of FAW, the latter is particularly relevant as poor farmer mental health has been associated with poorer animal welfare. However, little is known about how the negative framing of FAW stories influence farmers’ perceptions and experiences. The aim of this study was to explore how negatively framed media stories about FAW incidents affect cattle farmers’ perceptions of animal welfare. Face-to-face interviews were conducted with seven Irish beef and dairy farmers using vignettes displaying negatively framed FAW incidents presented in the media. Five themes were identified: (1) job satisfaction and motivation, (2) impact on the human–animal relationship, (3) the importance of community, (4) negative portrayal of farmers and (5) need for FAW education. Findings suggest that negative framing of FAW in the media, as well as rural restructuring in Ireland, may negatively affect farmers’ motivation which could have indirect implications for the welfare of their animals.
    • A short survey of key silage-making practices on Northern Ireland dairy farms, and farmer perceptions of factors influencing silage quality

      Ferris, C.P.; Laidlaw, A.S.; Wylie, A.R.G. (Teagasc, 2022-11-07)
      Northern Ireland dairy farmers (n = 174) were surveyed to identify key silage-making practices, and factors perceived to influence the quality of grass silage made on their farms. The majority of farmers (65%) harvested grass for silage three times/year: 62% normally used a contractor, while 47% routinely used a silage additive. Delays to mowing and delays to harvesting due to adverse weather or poor ground conditions were perceived to have a large or very large impact on silage quality (68% and 53% of farmers, respectively). Inadequate wilting, poor-quality swards on owned land, on rented land and “contamination” of first-cut grass with autumn or winter growth herbage were all perceived as having a large or very large impact on silage quality (32%, 27%, 40%, 30% of farmers, respectively). Over the previous decade, 11%, 41% and 37% of farmers claimed a small, moderate or large improvement in silage quality, mainly due to earlier cutting of grass and ensiling better quality swards.
    • Solutions to enteric methane abatement in Ireland

      Cummins, S.; Lanigan, G.J.; Richards, K.G.; Boland, T.M.; Kirwan, S.F.; Smith, P.E.; Waters, S.M.; Department of Agriculture, Food and the Marine (Teagasc, 2022-11-10)
      The efficiency of Ireland’s grass-based livestock systems can be attributed to high outputs, low production costs and a low carbon footprint relative to housed systems. Methane (CH4) is a potent greenhouse gas (GHG) of which enteric fermentation from livestock production is a key source, being directly responsible for 57% of Irish agricultural GHG emissions. There are a number of strategies including dietary manipulation and breeding initiatives that have shown promising results as potential mitigation solutions for ruminant livestock production. However, the majority of international research has predominantly been conducted on confined systems. Given the economic viability of Irish livestock systems, it is vital that any mitigation methods are assessed at pasture. Such research cannot be completed without access to suitable equipment for measuring CH4 emissions at grazing. This review documents the current knowledge capacity in Ireland (publications and projects) and includes an inventory of equipment currently available to conduct research. A number of strategic research avenues are identified herein that warrant further investigation including breeding initiatives and dietary manipulation. It was notable that enteric CH4 research seems to be lacking in Ireland as it constituted 14% of Irish agricultural GHG research publications from 2016 to 2021. A number of key infrastructural deficits were identified including respiration chambers (there are none currently operational in the Republic of Ireland) and an urgent need for more pasture-based GreenFeed™ systems. These deficits will need to be addressed to enable inventory refinement, research progression and the development of effective solutions to enteric CH4 abatement in Ireland.
    • Evaluating the timing of insecticide application to manage barley yellow dwarf virus and yield in winter barley

      Walsh, L. E.; Lacey, S.; Doyle, D.; Gaffney, M. T.; Mc Namara, L.; Department of Agriculture, Fod and the MArine; 14/s/879 (Teagasc, 2022-11-30)
      Barley yellow dwarf virus (BYDV) is an important viral disease of grain crops worldwide and a major cause of yield loss. The risk periods for BYDV infection coincide with milder temperature that prolongs aphid flight and facilitates viral transmission through primary and secondary aphid movement in the crop. Secondary aphid movement is associated with greater BYDV spread in winter cereals. A critical component of BYDV management is therefore delaying sowing of winter cereals and correctly timing insecticide application to maximise crop protection. Previous research in Ireland considered insecticide timing in early (September) and late (October onwards) sown cereals. Early research did not consider action thresholds around temperature, aphid flight and risk of secondary spread. This research set out to understand the optimal timing of insecticide application in October sown winter barley to reduce BYDV infection and yield impact. A critical temperature of 3°C was used as a threshold for aphid development that leads to movement and BYDV spread, and insecticide treatments were applied to the crop at predictable intervals in relation to temperature. Results show that BYDV symptoms and yield are affected by spray time, location and year, although only significant with regard to the reduction of BYDV symptoms. For both BYDV symptoms and yield, there was a significant difference between untreated (control) plots and “early” and “late” applications of insecticide, again more notable for BYDV symptoms than yield. This work indicates the value of optimising a single insecticide spray for control of October sown cereals and supports decision-making in the management of cereal crops.
    • Yield response of field beans (Vicia faba) to plant population and sowing date in a temperate climate

      Murphy, L.C.; Sparkes, D.L.; Spink, J.H.; Alves, S.; Teagasc Walsh Scholarship programme; Irish Farmers Association (Teagasc, 2022-12-23)
      Sowing date and seed rate influence crop establishment, growth, yield and profitability. The growth and yield of field beans (Vicia faba) in response to sowing date and seed rate was examined over three seasons, 2016–2019, in Teagasc, Oak Park, Carlow, Ireland. Early winter sowings (October) established better than late winter sowings in November and January. No significant difference was found in establishment from mid-February to mid-March. Yield was generally highest from October sowings for the winter cultivar. Yields were similar from February, March and April sowings for the spring cultivar, with March generally yielding higher across the three seasons. Yield was also found to increase significantly with seed rate for both winter and spring cultivars. The economic optimum plant population was estimated for the October and March sowing dates, by fitting a standard (linear + exponential) curve. There is no published information on the optimum plant populations for field beans in Ireland and we believe we are the first to report these findings. The estimated economic optimum plant populations varied between 13 and 38 plants/m2 for both varieties, with an average optimum of 25.5 plants/m2. This range falls within the current recommendations for sowing field beans in Ireland, demonstrating that increasing plant populations above the current commercial practice for field beans in Ireland, will not increase yield or profitability.
    • A note on current pyrethroid susceptibility in the bird cherry-oat aphid Rhopalosiphum padi in Ireland

      George, A.; Meally, H.; Foster, S.; Williamson, M.; Walsh, L.; Carroll, J.; Gaffney, M.T.; McNamara, L.; South East Technological University, President’s Fellowship scheme; Teagasc (Teagasc, 2022-12-28)
      The objective of this study was to observe the response of the bird cherry oat aphid, Rhopalosiphum padi (Linnaeus, 1758) to field rate equivalents of insecticides, by using bioassays of vials coated with the pyrethroid, λ-cyhalothrin. The results from the geographically separated Irish R. padi colonies indicated a susceptible response, which was a similar finding to the UK which showed sensitivity in this species of cereal aphids. Monitoring the susceptibility status of aphids using bioassays gives information regarding developments of any tolerance, which could be a precursor, or resistance against the target chemical insecticide, which is an important integrated pest management tool.
    • Identification and distribution of leatherjackets (Tipula spp.) in the Republic of Ireland

      Moffat, A.; Gaffney, M. T.; Brennan, F.; Cole, L.; Jackson, G.; Konkolewska, A.; McNamara, L.; Teagasc (Teagasc, 2022-12-28)
      The soil-dwelling larval stage of crane flies, commonly known as leatherjackets, are classified as agricultural pests in Europe, and pests of turf in North America and Canada. They cause significant damage and yield loss in many cropping systems through their feeding on plant roots and stems at ground level. The effective chemical control for these pests, chlorpyrifos (available since 1965), was prohibited across Europe in 2019. This has left severely restricted control options for growers. Unlike Northern Ireland and Great Britain, no leatherjacket surveys or routine identifications have been conducted across Ireland. Therefore, the leatherjacket species of agronomic importance has not been confirmed. Since lifecycles, feeding behaviour and damage periods differ between species, identifying the most common species is a vital first step in any pest management strategy. Here we report key findings from a 2-yr structured survey of Irish crops, conducted in 2019 and 2021, where 135 sites were sampled. Both grassland and cereal crops were inspected. Soil cores and soil samples were collected and larval abundance determined. The European crane fly, Tipula paludosa Meigen, accounted for approximately 70% of larvae collected and identified (n = 337). In 2019, 40% of grasslands exceeded the threshold of 1 million larvae/ha, while only 3.3% of cereal fields were over the threshold of 600,000 larvae/ha. These results indicate that agricultural grasslands in Ireland have the potential to be significantly impacted by leatherjacket damage, although this may vary temporally and geographically across the island. Without effective control options, yield losses will be highly probable.
    • An in vitro study to assess bioaccessibility and bioavailability of calcium from blue whiting (Micromesistius poutassou) fish bone powder

      Busca, K.; Wu, S.; Miao, S.; Govindan, A.; Strain, C.R.; O’Donnell, S.T.; Whooley, J.; Gite, S.; Paul Ross, R.; Stanton, C.; et al. (Teagasc, 2021-12-21)
      The aim of this study was to determine how well calcium-rich mineral extracts derived from blue whiting fish bone powders compare with existing calcium sources (commercially available fish bone supplement, calcium carbonate and milk powder) in terms of physicochemical properties, in vitro bioaccessibility and bioavailability using simulated gastrointestinal tract treatment and a Caco-2 cell culture model. Blue whiting calcium-rich fish bone powders (A to E) were supplied by Bio-marine Ingredients Ireland (BII) and a commercial calcium-rich fish bone powder was used as the positive control F. The BII calcium-rich fish bone powders analysed through atomic emission spectrometry were shown to have similar levels of mineral content in comparison with powder F. Solubility and rheology tests were performed on the rehydrated powders. The pH of BII calcium-rich fish bone powders in water solution (10% w/v) ranged from 6.96 to 9.09 compared to control F (pH 7.33). Following simulated oral, gastric and duodenal in vitro digestion using the COST INFOGEST standardised static adult digestion method, the fish powders A, E and F showed higher values of soluble ionic calcium than rehydrated milk powder. We compared in vitro bioavailability of the powders using the Caco-2 cell line to test the effects of calcium on human colonic epithelial cells, which confirmed that calcium from blue whiting fish bone was more bioavailable than calcium from milk and calcium carbonate. These data indicate that calcium-rich blue whiting fish bone powder compares well with existing calcium sources, in terms of physicochemical properties, bioaccessibility and bioavailability.
    • Celebrating 60 years of the Irish Journal of Agricultural and Food Research

      O'Mara, Frank (Teagasc, 2022-12-23)
      This special issue consists of 12 papers, compiled in 2021 — the journal’s anniversary year, providing an overview of the wide range of research undertaken by Teagasc. These papers provide a great source of reference for those interested in Irish agricultural and food research. Topics include forestry, potato breeding and production, pig production, milk quality and processing, meat processing, ruminant nutrition, ruminant breeding, the Agricultural Catchments Programme, grassland, animal health and welfare, and the role of social science in agri food research.
    • Ruminant health research – progress to date and future prospects, with an emphasis on Irish research

      Mee, J.F.; Barrett, D.; Boloña, P. Silva; Conneely, M.; Earley, B.; Fagan, S.; Keane, O.M.; Lane, E.A. (Teagasc, 2022-05-20)
      This review addresses the progress that has been made in ruminant health research over the last 60 yr, with an emphasis on Irish research. The review focuses on the economically important infectious diseases of dairy and beef cattle and of sheep, calf diseases, regulated and non-regulated infectious diseases, lameness, mastitis and parasitoses. The progress to date, current knowledge and future challenges are all addressed. Paradigm shifts have occurred in many of these diseases, the most profound of which is the change from increasing antimicrobial usage (AMU) to the realisation of the challenge of antimicrobial resistance (AMR) and the current reduction in AMU. Another major change in thinking is the move away from focus on the pathogen exclusively towards a more holistic view of the roles of host immunity and adequacy of management. In the last 60 yr, many new diseases have emerged but in parallel many new technologies have rapidly evolved to monitor and control these threats to animal health. Irish research has contributed substantially to improved current ruminant health. The major future challenge is how to manage ruminant health in a OneHealth world where animal, human and environmental health and sustainability are intimately intertwined and interdependent.
    • ‘Come aboard’ the systems-based approach: the role of social science in agri-food research and innovation

      Macken-Walsh, Á.; Henchion, M.M.; Regan, Á. (Teagasc, 2022-05-20)
      Increasingly, systems-based approaches are taken in agri-food research and innovation (R&I). Such approaches also align with changes in science governance and new policies related to research impact and responsible research and innovation. However, taking a holistic view of food systems to maximise impact from R&I in a societally acceptable manner poses theoretical and methodological challenges. How can diverse actors come to occupy roles in forming and pursuing common visions towards more sustainable food systems? This paper focuses on how social science can activate, mediate and add rigour to systems-based approaches. An overview is presented of the policy context in which greater attention is paid to systems-based approaches and we present a framework to theoretically and practically support systems-based approaches: transdisciplinarity and the “multi-actor approach” (MAA). These approaches explain practically how different scientific contributions and non-scientific actors can be engaged and unified in creatively addressing R&I challenges. Overall, because social science is used to inform and deliver R&I outcomes that take into account the whole system of actors, their different values and expectations and their interactions and knowledge exchange, it is a crucial source of knowledge for advancing and meeting the challenges of systems-based approaches. Illustrating this, we present a profile of projects where social science has been applied to enhance R&I within a systems-based approach. However, we also signal caveats, qualifications and provisos in applying such approaches. This paper will be of interest to researchers and practitioners planning to incorporate social science to systems-based R&I initiatives to avoid pitfalls and add rigour.
    • Effect of passive transfer status on response to a glycoprotein E (gE)-negative bovine herpesvirus type 1 (BoHV-1) and bovine respiratory syncytial virus (BRSV) vaccine and weaning stress in pre-weaned dairy calves

      Dunn, Amanda; Welsh, Michael; Gordon, Alan; Arguello, Anastasio; Morrison, Steven J.; Earley, Bernadette; Department of Agriculture, Food and the Marine; Department of Agriculture and Rural Development in Northern Ireland; AgriSearch (farmer levy (Informa UK Limited, 2018-01-09)
      The study objectives were to: 1) examine how calves of divergent immune status respond to BRSV vaccination at 3 weeks of age; 2) trace glycoprotein E negative BoHV-1 antibodies from vaccinated dams to calf sera and to investigate how passive transfer affects response to live BoHV-1 vaccine at 6 weeks of age; 3) explore the impact of passive transfer status on blood metabolites around weaning. Thirty seven Holstein cows and their calves were included in the study. All cows were immunised with a commercial marker vaccine against BoHV-1(gE-) administered intra-muscularly at 4 month prior to the start of calving. Calves were assigned to 1 of 2 colostrum treatment groups: 1) 5% of BW in colostrum fed at birth, or 2) 10% of BW in colostrum fed at birth. Calves were also immunised at 3 weeks of age with a respiratory commercial vaccine, and a booster administered 4 weeks later. Calves were also immunised against BoHV-1 at 6 weeks of age, using one dose of a live commercial vaccine. The results demonstrated that level of passive immunity had no effect on immune response to vaccination and the importance of feeding colostrum from vaccinated BoHV-1 gE- dams to provide calves with passive protection against IBRV.
    • Comparison of single radial immunodiffusion and ELISA for the quantification of immunoglobulin G in bovine colostrum, milk and calf sera

      Dunn, Amanda; Duffy, Catherine; Gordon, Alan; Morrison, Steven; Argűello, Anastasio; Welsh, Michael; Earley, Bernadette; Department of Agriculture and Rural Development in Northern Ireland; AgriSearch (farmer levy); Department of Agriculture, Food and Marine, Ireland; et al. (Informa UK Limited, 2017-11-02)
      The overall objective was to compare immunoglobulin G (IgG) concentrations measured by single radial immunodiffusion (sRID) and ELISA-based methods in samples of bovine colostrum and transition milk from contrasting breed types (Limousin × Friesian (n = 10) and Holstein (n = 10)). Jugular blood samples were collected at 48 h post-birth from beef (n = 10) and dairy (n = 10) calves and sera harvested subsequent to colostrum consumption. Absolute colostrum IgG values determined by ELISA showed poor agreement with mean (SD) IgG values measured using sRID, fixed bias (sRID – ELISA) was 31.89 (±9.84) mg/mL; having wide limits of agreement (12.61–51.17) and a low concordance coefficient (0.26). The agreement between ELISA and sRID when measuring serum IgG was greater than that of colostrum, fixed bias (sRID – ELISA) was 12.36 (±6.60) mg/mL; having narrower limits of agreement (−0.58 to 25.30) and serum IgG concentrations had a greater concordance coefficient (0.44) between samples. Calf sera IgG measured using the indirect zinc sulphate turbidity test showed a strong correlation with the sRID and ELISA methods (P < .001), R2 = 0.78 and R2 = 0.77 respectively. Overall, the ELISA and sRID methodologies had a strong positive association with almost a twofold (1.8) difference between values; therefore, they provide diverse absolute values of IgG concentration.
    • Isolation and characterization of an exopolysaccharide‐producing Leuconostoc citreum strain from artisanal cheese

      Domingos‐Lopes, M.F.P.; Lamosa, P.; Stanton, C.; Ross, R.P.; Silva, C.C.G.; FCT; FRCT; PTDC/AGR-ALI/104385/ 2008; M3.1.2/F/009/2011 (Wiley, 2018-10-18)
      High molar mass exopolysaccharides (EPS) produced from sucrose by lactic acid bacteria (LAB) are of great interest as natural additives to use in foods, medical and pharmaceutical industry. This study aimed to identify the EPS produced by Leuconostoc citreum L3C1E7 isolated from Pico cheese and characterize the strain for technological and probiotic potential. Purified EPS was isolated from the culture of L. citreum L3C1E7 by ethanol precipitation, with a yield of 520 mg ml−1. The EPS-producing strain had a mucoid phenotype and average molecular weight of 5·88 × 106 Da. The structural characterization of the purified EPS was determined by 1H, 13C and two-dimensional NMR spectroscopy. EPS was composed of alternating α-(1→6)-linked and α-(1→3)-linked D-glucopyranyl units, suggesting the existence of an alternan. The strain was slow acidifying, produced diacetyl and displayed high esterase/lipase and aminopeptidase activities, which promote the desirable flavours in dairy products. Moreover, L. citreum showed moderate resistance to the adverse conditions of the gastrointestinal (GI) tract and high adhesion to GI cells. This work provides a better understanding of EPS produced by L. citreum and the potential application of EPS-producing strain in food and/or as a probiotic culture.
    • Editorial, International Bull Fertility Conference – Theory to Practice, Westport, Ireland, 2018

      Diskin, MichaelG; Lonergan, Pat; Kenny, David A.; Fair, Sean (Elsevier, 2018)
      This supplement to Animal contains the papers associated with the keynote lectures delivered at the International Bull Fertility Conference – Theory to Practice held in Westport, Ireland from May 27th to 30th 2018. The conference was organised under the auspices of the British Society of Animal Science (BSAS) in close collaboration with Teagasc, University College Dublin, University of Limerick, the Cattle Association of Veterinary Ireland (CAVI), XL Vets, the British Cattle Veterinary Association (BCVA) and the Department of Agriculture Food and the Marine.
    • A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults

      Cronin, Owen; Barton, Wiley; Skuse, Peter; Penney, Nicholas C.; Garcia-Perez, Isabel; Murphy, Eileen F.; Woods, Trevor; Nugent, Helena; Fanning, Aine; Melgar, Silvia; et al. (American Society for Microbiology, 2018-06-26)
      Many components of modern living exert influence on the resident intestinal microbiota of humans with resultant impact on host health. For example, exercise-associated changes in the diversity, composition, and functional profiles of microbial populations in the gut have been described in cross-sectional studies of habitual athletes. However, this relationship is also affected by changes in diet, such as changes in dietary and supplementary protein consumption, that coincide with exercise. To determine whether increasing physical activity and/or increased protein intake modulates gut microbial composition and function, we prospectively challenged healthy but sedentary adults with a short-term exercise regime, with and without concurrent daily whey protein consumption. Metagenomics- and metabolomics-based assessments demonstrated modest changes in gut microbial composition and function following increases in physical activity. Significant changes in the diversity of the gut virome were evident in participants receiving daily whey protein supplementation. Results indicate that improved body composition with exercise is not dependent on major changes in the diversity of microbial populations in the gut. The diverse microbial characteristics previously observed in long-term habitual athletes may be a later response to exercise and fitness improvement. IMPORTANCE The gut microbiota of humans is a critical component of functional development and subsequent health. It is important to understand the lifestyle and dietary factors that affect the gut microbiome and what impact these factors may have. Animal studies suggest that exercise can directly affect the gut microbiota, and elite athletes demonstrate unique beneficial and diverse gut microbiome characteristics. These characteristics are associated with levels of protein consumption and levels of physical activity. The results of this study show that increasing the fitness levels of physically inactive humans leads to modest but detectable changes in gut microbiota characteristics. For the first time, we show that regular whey protein intake leads to significant alterations to the composition of the gut virome.
    • Complete Genome Sequences of Sequence Type 71 (ST71) and ST97 Staphylococcus aureus Isolates from Bovine Milk

      Cormican, Paul; Keane, Orla M.; Department of Agriculture Food and the Marine; 14/S/802 (American Society for Microbiology, 2018-08-09)
      This is the announcement of draft genome sequences for Staphylococcus aureus strains belonging to sequence type 97 (ST97) and ST71. These sequence types are commonly associated with bovine mastitis, and the strains were isolated in Ireland in 2010 from the milk of cows with clinical mastitis.
    • Weed suppression greatly increased by plant diversity in intensively managed grasslands: A continental-scale experiment

      Connolly, John; Sebastià, Maria-Teresa; Kirwan, Laura; Finn, John Anthony; Llurba, Rosa; Suter, Matthias; Collins, Rosemary P.; Porqueddu, Claudio; Helgadóttir, Áslaug; Baadshaug, Ole H.; et al. (Wiley, 2017-09-27)
      Grassland diversity can support sustainable intensification of grassland production through increased yields, reduced inputs and limited weed invasion. We report the effects of diversity on weed suppression from 3 years of a 31-site continental-scale field experiment.At each site, 15 grassland communities comprising four monocultures and 11 four-species mixtures based on a wide range of species' proportions were sown at two densities and managed by cutting. Forage species were selected according to two crossed functional traits, "method of nitrogen acquisition" and "pattern of temporal development".Across sites, years and sown densities, annual weed biomass in mixtures and monocultures was 0.5 and 2.0 t DM ha-1 (7% and 33% of total biomass respectively). Over 95% of mixtures had weed biomass lower than the average of monocultures, and in two-thirds of cases, lower than in the most suppressive monoculture (transgressive suppression). Suppression was significantly transgressive for 58% of site-years. Transgressive suppression by mixtures was maintained across years, independent of site productivity.Based on models, average weed biomass in mixture over the whole experiment was 52% less (95% confidence interval: 30%-75%) than in the most suppressive monoculture. Transgressive suppression of weed biomass was significant at each year across all mixtures and for each mixture.Weed biomass was consistently low across all mixtures and years and was in some cases significantly but not largely different from that in the equiproportional mixture. The average variability (standard deviation) of annual weed biomass within a site was much lower for mixtures (0.42) than for monocultures (1.77). Synthesis and applications. Weed invasion can be diminished through a combination of forage species selected for complementarity and persistence traits in systems designed to reduce reliance on fertiliser nitrogen. In this study, effects of diversity on weed suppression were consistently strong across mixtures varying widely in species' proportions and over time. The level of weed biomass did not vary greatly across mixtures varying widely in proportions of sown species. These diversity benefits in intensively managed grasslands are relevant for the sustainable intensification of agriculture and, importantly, are achievable through practical farm-scale actions.
    • Optimized Use of Low-Depth Genotyping-by-Sequencing for Genomic Prediction Among Multi-Parental Family Pools and Single Plants in Perennial Ryegrass (Lolium perenne L.)

      Cericola, Fabio; Lenk, Ingo; Fè, Dario; Byrne, Stephen; Jensen, Christian S.; Pedersen, Morten G.; Asp, Torben; Jensen, Just; Janss, Luc; Danish Ministry of Food, Agriculture and Fisheries; et al. (Frontiers Media SA, 2018-03-21)
      Ryegrass single plants, bi-parental family pools, and multi-parental family pools are often genotyped, based on allele-frequencies using genotyping-by-sequencing (GBS) assays. GBS assays can be performed at low-coverage depth to reduce costs. However, reducing the coverage depth leads to a higher proportion of missing data, and leads to a reduction in accuracy when identifying the allele-frequency at each locus. As a consequence of the latter, genomic relationship matrices (GRMs) will be biased. This bias in GRMs affects variance estimates and the accuracy of GBLUP for genomic prediction (GBLUP-GP). We derived equations that describe the bias from low-coverage sequencing as an effect of binomial sampling of sequence reads, and allowed for any ploidy level of the sample considered. This allowed us to combine individual and pool genotypes in one GRM, treating pool-genotypes as a polyploid genotype, equal to the total ploidy-level of the parents of the pool. Using simulated data, we verified the magnitude of the GRM bias at different coverage depths for three different kinds of ryegrass breeding material: individual genotypes from single plants, pool-genotypes from F2 families, and pool-genotypes from synthetic varieties. To better handle missing data, we also tested imputation procedures, which are suited for analyzing allele-frequency genomic data. The relative advantages of the bias-correction and the imputation of missing data were evaluated using real data. We examined a large dataset, including single plants, F2 families, and synthetic varieties genotyped in three GBS assays, each with a different coverage depth, and evaluated them for heading date, crown rust resistance, and seed yield. Cross validations were used to test the accuracy using GBLUP approaches, demonstrating the feasibility of predicting among different breeding material. Bias-corrected GRMs proved to increase predictive accuracies when compared with standard approaches to construct GRMs. Among the imputation methods we tested, the random forest method yielded the highest predictive accuracy. The combinations of these two methods resulted in a meaningful increase of predictive ability (up to 0.09). The possibility of predicting across individuals and pools provides new opportunities for improving ryegrass breeding schemes.