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A note on the impact of CYP51 alterations and their combination in the wheat pathogen Zymoseptoria tritici on sensitivity to the azole fungicides epoxiconazole and metconazole
Get PDFpeer-reviewedPeer-reviewedSeptoria tritici blotch caused by the fungal pathogen Zymoseptoria tritici is the most economically damaging disease of winter wheat in Ireland. As azoles have been intensively used, Z. tritici has developed different means of resisting their toxic effects with multiple alterations now reported in individual strains. Using previously characterised Irish collections of Z. tritici, the relationships between these different alterations have been examined using conditional inference trees and random forest. The results from this study highlight the importance of specific alterations I381V and S524T, with both contributing most to the reductions in epoxiconazole (EPZ) and metconazole (MTZ) sensitivity. As the azole class of fungicides is an extensive and diverse group, it is possible these alterations do not impact other azoles in a similar manner. Further analysis of these and contemporary collections to additional azoles, including mefentrifluconazole, which continues to provide good field control of Z. tritici, is warranted
A comparative study of thermally and chemically treated dairy waste: Impacts on soil phosphorus turnover and availability using 33P isotope dilution
Get PDFpeer-receivedDairy processing sludge (DPS) and DPS-derived secondary products such as struvite, biochar, hydrochar and ash (collectively known as SRUBIAS) are emerging as alternatives to fertilizers produced from mined rock phosphate. However, little is known about how these products affect soil P availability and daily P turnover rates.. A lack of such information prevents precision nutrient management planning using these products out on farms. This study used a novel isotope dilution technique (IPD) with 33P as a tracer to compare P turnover in soils amended with chemically (alum-treated DPS and struvite) and thermally (biochar, hydrochar, ash) treated DPS. Results showed that thermally treated products exhibited poor agronomic performance as P fertilizers, potentially inhibiting P availability when applied to soils. For example, a P deficient soil amended with hydrochar treatment at the highest application rates did not record a build-up of available P to agronomic target values. In ash and biochar treated P deficient soils, available P increased but only with very high application rates of 150 and 80 mg P kg −1. The application of these products as fertilizers could have negative implications for both environmental and agronomic goals. Conversely, chemically treated fertilisers demonstrated better agronomic performance. The same agronomic target value was reached with application rates of only 20 mg P kg −1 soil for DPS and 50 mg P kg −1 soil for struvite. However, the techniques deployed revealed that these products exhibited slower rates of available and exchangeable P build-up when compared with chemical fertilisers. This suggests that these bio-based alternatives require higher application rates or earlier application times compared to conventional chemical fertilizers. Regulations providing advice on P use in agricultural soils need to account for slower P turnover in soils receiving recycled fertilizers. The IPD technique is transferrable to all wastes to examine their performance as fertilizers.Horizon 202
Barriers and opportunities of soil knowledge to address soil challenges: Stakeholders’ perspectives across Europe
Get PDFpeer-reviewedClimate-smart sustainable management of agricultural soil is critical to improve soil health, enhance food and water security, contribute to climate change mitigation and adaptation, biodiversity preservation, and improve human health and wellbeing. The European Joint Programme for Soil (EJP SOIL) started in 2020 with the aim to significantly improve soil management knowledge and create a sustainable and integrated European soil research system. EJP SOIL involves more than 350 scientists across 24 Countries and has been addressing multiple aspects associated with soil management across different European agroecosystems. This study summarizes the key findings of stakeholder consultations conducted at the national level across 20 countries with the aim to identify important barriers and challenges currently affecting soil knowledge but also assess opportunities to overcome these obstacles. Our findings demonstrate that there is significant room for improvement in terms of knowledge production, dissemination and adoption. Among the most important barriers identified by consulted stakeholders are technical, political, social and economic obstacles, which strongly limit the development and full exploitation of the outcomes of soil research. The main soil challenge across consulted member states remains to improve soil organic matter and peat soil conservation while soil water storage capacity is a key challenge in Southern Europe. Findings from this study clearly suggest that going forward climate-smart sustainable soil management will benefit from (1) increases in research funding, (2) the maintenance and valorisation of long-term (field) experiments, (3) the creation of knowledge sharing networks and interlinked national and European infrastructures, and (4) the development of regionally-tailored soil management strategies. All the above-mentioned interventions can contribute to the creation of healthy, resilient and sustainable soil ecosystems across Europe
Improved representation of cattle herd dynamics for bio-physical modelling of pathways to a climate neutral land sector
Get PDFpeer-reviewedLivestock production contributes to food security and livelihood improvement globally but places a significant burden on the environment. In Ireland, an ongoing transition towards highly profitable dairy production after the phasing out of EU milk quotas has changed the composition of the national cattle herd with more dairy and fewer beef cows. This shift impacts greenhouse gas (GHG) accounting across different cattle cohorts, e.g. increasing the proportion of calves from the dairy herd. Dairy x beef crossbreeds (DxB) increasingly contribute to national beef output, leveraging larger average daily liveweight gain (ADG) traits from beef breeding bulls.
OBJECTIVE
Prospective modelling of climate and land consequences arising from alternative cattle production strategies requires more accurate simulation of cohort-specific ADG and associated feed requirements and GHG emissions.
METHODS
A new COHORTS model was developed to improve national climate scenario mitigation modelling. COHORTS is capable of simulating 21 genetics-gender-age cohorts calibrated to Irish performance, using just a few basic input parameters (at minimum dairy- and beef-cow numbers). A cohort specific ADG and average standing liveweight is estimated for each genetic (pure dairy calves, DxB and pure beef calves), gender and age combination, enabling more accurate calculation of energy requirements and enteric fermentation emissions based on IPCC Tier 2 calculations.
RESULTS AND CONCLUSIONS
National simulation of cattle numbers, enteric fermentation emissions and beef outputs were validated against relevant Irish inventories. For the period between 2006 and 2020, simulations resulted in total cattle numbers, emissions and beef production within 4%, 1.8% and 0.5%, respectively, of officially reported data. Our results indicate that climate projections based on average emission factors for pre-adult cattle cohorts may overestimate emissions in scenarios with projected growing dairy calf numbers and declining beef calf numbers.
SIGNIFICANCE
Validation using a 15-year data time series provides a high degree of confidence that COHORTS can be used to represent future herd dynamics in a wide range of scenarios, supporting robust policy regarding GHG mitigation, livestock production and land use – distinguishing between different levels of dairy or beef specialisation and across different levels of performance to predict forage (land) requirements and GHG emissions more accurately. COHORTS can be easily adapted for other countries, even when limited data are available.Department of Agriculture, Food and the Marine, Irelan
Genetic and phenotypic trends for carcass traits in Irish beef cattle
Get PDFpeer-reviewedPeer-reviewedAnimals subjected to intensive genetic selection require continuous monitoring to observe changes in economically important traits. The focus of this research was to estimate genetic and phenotypic trends for carcass traits for three genotypes: dairy dam and dairy sire (D×D), dairy dam and beef sire (D×B) and beef dam and beef sire (B×B). Linear regression models were used to generate genetic and phenotypic trends for carcass weight, conformation and fat score for both cows and prime animals (i.e. never parented an animal). Phenotypic trends for age at slaughter were also estimated in prime animals. Results indicated that carcass weight increased genetically by 1.1 kg per year for B×B animals, but decreased by 0.14 and 0.39 kg per year for D×B and D×D animals, respectively. Phenotypic trends reflected the genetic trends for carcass weight for D×B and B×B animals, but the decline in genetic trends for carcass weight for D×D animals was not replicated in their phenotypic trends. Carcass conformation declined genetically by 0.02 and 0.05 units per year for D×D and D×B animals, respectively, and increased by 0.05 units per year for B×B animals. Phenotypic trends for conformation were similar to genetic trends. Carcass fat showed a decrease genetically for D×D and B×B, but remained constant for D×B animals, although this was not reflected in the phenotypic trends. Age at slaughter decreased phenotypically for all genotypes. Current breeding programmes have a favourable impact on carcass traits for B×B animals, but an unfavourable trend was observed for D×D and D×B animals
Farmers’ knowledge of Johne’s disease and opinions of the Irish Johne’s Control Programme: results of an online survey answered mostly by young farmers
Get PDFpeer-reviewedAbstract
A voluntary control programme for Johne’s disease, the Irish Johne’s Control Programme (IJCP) has been implemented in Ireland since 2017. The objective of this observational study was to assess Irish beef and dairy farmers’ Johne’s disease knowledge, implemented management practices and IJCP opinions. A questionnaire open to dairy and beef farmers was distributed via social media and email. In total 126 responses were used for this study; these responses came from mostly young farmers (18–25 years old) and represent a small proportion of the total number of dairy and beef farmers in Ireland whose average age is 55.
Most respondents claimed to know what Johne’s disease was (73%; 92/126) and associated the disease to loss of body condition (68%; 78/114) and diarrhoea (59%; 67/114). Twenty-eight respondents (mostly dairy farmers; 22/28) reported positive cases in their premises. And 38% reported to implement management practices to prevent Johne’s disease transmission within or into their herd (i.e. management of milk for calf consumption and isolation of Johne’s test-positive or newly purchased stock; 47/124).
Eighteen percent (22/125) of respondents were, at the time of questionnaire or previously, members of the IJCP. The main benefits reported by some of the participating farmers were identification of positive cases (29%; 4/14), and management of milk for calf consumption (21%; 3/14). While the main disadvantage was inaccurate testing methods (50%; 10/20). The main reasons reported for the lack of participation in the IJCP were not being aware of the programme (52%; 53/102) and not having a Johne’s disease problem on the farm (48%; 49/102).
In conclusion, this study suggests that while young farmers are aware of Johne’s disease, their participation in the IJCP is limited and could benefit from further promotion. Studies representing the wider farming community in Ireland are warranted to gather non-biased input and contribute to Johne’s disease control in Ireland
Datafile: Effects of multispecies and monoculture forages on nutrient digestibility and fermentation responses using an in vitro rumen simulation technique (RUSITEC)
No full textDatasetEnteric methane (CH4) emissions are a major contributor to global greenhouse gas emissions. A number of different CH4 mitigation strategies have been proposed, and the inclusion of alternative forages into grazing systems would be a more practical and feasible option. Multispecies swards (MSS) comprise a mixture of forage species, and can increase grassland productivity, reduce nitrogen fertilizer requirements, and reducing fertilizer-associated nitrous-oxide (N2O) emissions. This study investigated the potential benefit of MSS in reducing ruminal CH4 production. Using an in vitro RUSITEC experiment, we compared the effects of different forages (perennial ryegrass, timothy, red clover, white clover, chicory, ribwort plantain and their equi-proportional mixture) on CH4 and gas production, ruminal fermentation parameters and nutrient digestibility. We also compared these responses to perennial ryegrass produced with higher (300N) nitrogen application rate. The experiment was conducted over 21 d, with the initial 14 d allowed for dietary adaptation. Over the subsequent 7 d, there were significant effects of forage type on CH4 production, ruminal fermentation and digestibility. Ribwort plantain, chicory and white clover showed lower CH4 production; chicory incubation produced 73 and 57% less CH4 (mmol d-1) compared to 300N perennial ryegrass and 150N perennial ryegrass incubation respectively. Chicory had 72% lower CH4 produced per unit of organic matter digested (mmol g-1 OMD) than that of 300N perennial ryegrass. Chicory and 300N perennial ryegrass had greater (P < 0.01) nutrient digestibility (DM, OM, CP, NDF, and ADF) than other forages. Greater ammonia nitrogen (NH3-N) concentration was observed in chicory and both clover species, compared to the other forage species (P < 0.01). In general, the response of the six-species mixture was not significantly different to the average response of the six component monocultures. These results show that different grassland forages, especially chicory and white clover, have the potential to reduce ruminal CH4 emissions and could be a promising anti-methanogenic alternative to chemical CH4 inhibitors and feed additives. More generally, the relatively wide variation in CH4 abatement potential across a small sample of plant species suggests the merit of wider screening to identify grassland species with high CH4 abatement potential in vitro
Low temperature microfiltration of skim milk: Impact of membrane type, configuration and concentration factor on serum protein permeation efficiency
Get PDFpeer-reviewedProtein transmission, permeate flux and energy consumption during MF of skim milk was evaluated at 7 °C using two discrete 800 kDa polymeric MF membranes. Filtration trials determined optimum process parameters (i.e., transmembrane pressure and volume concentration factor) and membrane configuration (in-series or in-parallel) to maximise serum protein permeation. This study demonstrated that a combination of higher VCF (3) and lower TMP (75 kPa), with an in-parallel membrane configuration resulted in the most efficient rate of permeation of serum protein per kg of permeate produced. However, from an energy perspective, an in-parallel configuration with a TMP of 75 kPa and a lower VCF2 was the most efficient process, consuming between 1.28 and 1.57 kW h kg−1 of crude protein permeated. Additionally, the permeation of serum β-casein at low temperature was governed by the uniformity of the pore size distribution in discrete MF membranes with the same nominal molecular mass cut-off
Integrated molecular approaches for fermented food microbiome research
Get PDFpeer-reviewedMolecular technologies, including high-throughput sequencing, have expanded our perception of the microbial world. Unprecedented insights into the composition and function of microbial communities have generated large interest, with numerous landmark studies published in recent years relating the important roles of microbiomes and the environment—especially diet and nutrition—in human, animal, and global health. As such, food microbiomes represent an important cross-over between the environment and host. This is especially true of fermented food microbiomes, which actively introduce microbial metabolites and, to a lesser extent, live microbes into the human gut. Here, we discuss the history of fermented foods, and examine how molecular approaches have advanced research of these fermented foods over the past decade. We highlight how various molecular approaches have helped us to understand the ways in which microbes shape the qualities of these products, and we summarize the impacts of consuming fermented foods on the gut. Finally, we explore how advances in bioinformatics could be leveraged to enhance our understanding of fermented foods. This review highlights how integrated molecular approaches are changing our understanding of the microbial communities associated with food fermentation, the creation of unique food products, and their influences on the human microbiome and health.Horizon 202
Understanding the underlying genetic mechanisms for age at first calving, inter-calving period and scrotal circumference in Bonsmara cattle
Get PDFpeer-reviewedBackground
Reproduction is a key feature of the sustainability of a species and thus represents an important component in livestock genetic improvement programs. Most reproductive traits are lowly heritable. In order to gain a better understanding of the underlying genetic basis of these traits, a genome-wide association was conducted for age at first calving (AFC), first inter-calving period (ICP) and scrotal circumference (SC) within the South African Bonsmara breed. Phenotypes and genotypes (120,692 single nucleotide polymorphisms (SNPs) post editing) were available on 7,128 South African Bonsmara cattle; the association analyses were undertaken using linear mixed models.
Results
Genomic restricted maximum likelihood analysis of the 7,128 SA Bonsmara cattle yielded genomic heritability’s of 0.183 (SE = 0.021) for AFC, 0.207 (SE = 0.022) for ICP and 0.209 (SE = 0.019) for SC. A total of 16, 23 and 51 suggestive (P ≤ 4 × 10-6) SNPs were associated with AFC, ICP and SC, while 11, 11 and 44 significant (P ≤ 4 × 10-7) SNPs were associated with AFC, ICP and SC respectively. A total of 11 quantitative trait loci (QTL) and 11 candidate genes were co-located with these associated SNPs for AFC, with 10 QTL harbouring 11 candidate genes for ICP and 41 QTL containing 40 candidate genes for SC. The QTL identified were close to genes previously associated with carcass, fertility, growth and milk-related traits. The biological pathways influenced by these genes include carbohydrate catabolic processes, cellular development, iron homeostasis, lipid metabolism and storage, immune response, ovarian follicle development and the regulation of DNA transcription and RNA translation.
Conclusions
This was the first attempt to study the underlying polymorphisms associated with reproduction in South African beef cattle. Genes previously reported in cattle breeds for numerous traits bar AFC, ICP or SC were detected in this study. Over 20 different genes have not been previously reported in beef cattle populations and may have been associated due to the unique genetic composite background of the SA Bonsmara breed