• The agricultural impact of the 2015–2016 floods in Ireland as mapped through Sentinel 1 satellite imagery

      O'HAra, Rob; Teagasc Walsh Fellowship Programme (Teagasc, 2019-10-11)
      Irish Journal of Agricultural and Food Research | Volume 58: Issue 1 The agricultural impact of the 2015–2016 floods in Ireland as mapped through Sentinel 1 satellite imagery R. O’Haraemail , S. Green and T. McCarthy DOI: https://doi.org/10.2478/ijafr-2019-0006 | Published online: 11 Oct 2019 PDF       Abstract Article PDF References Recommendations Abstract The capability of Sentinel 1 C-band (5 cm wavelength) synthetic aperture radio detection and ranging (RADAR) (abbreviated as SAR) for flood mapping is demonstrated, and this approach is used to map the extent of the extensive floods that occurred throughout the Republic of Ireland in the winter of 2015–2016. Thirty-three Sentinel 1 images were used to map the area and duration of floods over a 6-mo period from November 2015 to April 2016. Flood maps for 11 separate dates charted the development and persistence of floods nationally. The maximum flood extent during this period was estimated to be ~24,356 ha. The depth of rainfall influenced the magnitude of flood in the preceding 5 d and over more extended periods to a lesser degree. Reduced photosynthetic activity on farms affected by flooding was observed in Landsat 8 vegetation index difference images compared to the previous spring. The accuracy of the flood map was assessed against reports of flooding from affected farms, as well as other satellite-derived maps from Copernicus Emergency Management Service and Sentinel 2. Monte Carlo simulated elevation data (20 m resolution, 2.5 m root mean square error [RMSE]) were used to estimate the flood’s depth and volume. Although the modelled flood height showed a strong correlation with the measured river heights, differences of several metres were observed. Future mapping strategies are discussed, which include high–temporal-resolution soil moisture data, as part of an integrated multisensor approach to flood response over a range of spatial scales.
    • Effect of nitrogen fertiliser application timing on grain yield and grain protein concentration of spring barley

      Hackett, R. (Teagasc, 2019-06-01)
      There is relatively little recent information regarding the effect of timing of fertiliser N application to spring barley on grain yield and grain protein concentration (GPC) under Irish conditions. The objectives of this work were to examine the effects of a) timing of the first N application to spring barley (at sowing or at crop emergence), b) altering the proportion of the total N allocation that is applied in the first of two applications and c) delaying a portion of the total N dose until after the tillering phase on grain yield and GPC of spring barley. Twenty experiments were carried out over four seasons (2011–2014) in the south and south-east of Ireland. Results indicated that there was little consistent difference, in terms of grain yield or GPC between applying the first N at sowing compared to where the initial N application was made at crop emergence. Similarly, altering the proportion of N applied in the first application, irrespective of whether the first application was at sowing or at crop emergence, had little effect on either yield or GPC. Delaying the application of a portion (0.2) of the total N until after the tillering stage also had little consistent effect on either yield or GPC. It is concluded that where the majority of N is applied to spring barley before the end of the tillering stage, altering the timing of applications or the proportion of the total applied in each application will have limited effect on grain yield or GPC.
    • First evidence of retained sexual capacity and survival in the pyrethroid resistant Sitobion avenae (F.) (Hemiptera: Aphididae) SA3 super-clone following exposure to a pyrethroid at current field-rate

      Walsh, L.E.; Gaffney, M.T.; Malloch, G.L.; Foster, S.P.; Williamson, M.S.; Mangan, R.; Purvis, G.; Department of Agriculture, Food and the Marine; Biotechnology and Biological Sciences Council; Rural ̦ Environment Science ̦ Analytical Services Division of the Scottish Government; et al. (Teagasc, 2019-04-17)
      The grain aphid Sitobion avenae is a prolific pest of cereal crops worldwide, controlled effectively with pyrethroid insecticides. However, the classic knock down resistance (kdr) mutation, L1014F on the S. avenae sodium channel gene, has been identified as the cause of the recently observed heterozygous (kdr-SR) resistance in the SA3 grain aphid super-clone. Results indicate that the kdr-SR SA3 clone can survive pyrethroid exposure above twice the normal field rate, continuing to reproduce thereafter. Additionally, the SA3 clone was found to be capable of producing sexual oviparous morphs, able to lay eggs following pyrethroid exposure. This demonstrates that possession of the L1014F mutation does not preclude the capacity to produce sexual morphs. This makes the adoption of an effective resistance management strategy imperative, within a wider integrated pest management (IPM) approach to control grain aphid.
    • First evidence of retained sexual capacity and survival in the pyrethroid resistant Sitobion avenae (F.) (Hemiptera: Aphididae) SA3 super-clone following exposure to a pyrethroid at current field-rate

      Walsh, L.E.; Gaffney, M.T.; Malloch, G.L.; Foster, S.P.; Williamson, M.S.; Mangan, R.; Purvis, G.; Department of Agriculture, Food and the Marine; Biotechnology and Biological Sciences Council of the United Kingdom; 14/s/879; et al. (Teagasc, 2019-04-17)
      The grain aphid Sitobion avenae is a prolific pest of cereal crops worldwide, controlled effectively with pyrethroid insecticides. However, the classic knock down resistance (kdr) mutation, L1014F on the S. avenae sodium channel gene, has been identified as the cause of the recently observed heterozygous (kdr-SR) resistance in the SA3 grain aphid super-clone. Results indicate that the kdr-SR SA3 clone can survive pyrethroid exposure above twice the normal field rate, continuing to reproduce thereafter. Additionally, the SA3 clone was found to be capable of producing sexual oviparous morphs, able to lay eggs following pyrethroid exposure. This demonstrates that possession of the L1014F mutation does not preclude the capacity to produce sexual morphs. This makes the adoption of an effective resistance management strategy imperative, within a wider integrated pest management (IPM) approach to control grain aphid.
    • The impact of cattle drinking points on aquatic macroinvertebrates in streams in south-east Ireland

      Madden, D.; Harrison, S.; Finn, J. A.; Ó hUallacháin, D. (Teagasc, 2019-03-25)
      Measures that prevent cattle access to watercourses are commonly implemented through agri-environment schemes, in an effort to address the objectives of the Water Framework Directive. Despite the widespread implementation, few studies have assessed the impact of cattle access to streams on aquatic macroinvertebrates. This study assessed the local-scale impact of cattle drinking points on water quality parameters (i.e. macroinvertebrate and water chemistry metrics) on 39 intensively-managed grassland farms in the south-east of Ireland. The results indicate that sites that were more than or equal to good quality upstream of cattle drinking points, were more susceptible to cattle access impacts than sites where upstream water quality was less than good. The European Court of Auditors (2011) recommended that there should be a higher rate of EU contribution for measures with higher environmental potential, in this instance, for cattle exclusion measures targeted to sites where background quality is more than or equal to good. Appropriate efforts should thus be made to incentivise farmers in good to high status sites to adopt cattle exclusion measures.
    • Low-density genotype panel for both parentage verification and discovery in a multi-breed sheep population

      Berry, D.P.; McHugh, N.; Wall, E.; McDermott, K.; O’Brien, A.C.; Department of Agriculture, Food and the Marine (Teagasc, 2019-03-01)
      The generally low usage of artificial insemination and single-sire mating in sheep, compounded by mob lambing (and lambing outdoors), implies that parentage assignment in sheep is challenging. The objective here was to develop a low-density panel of single nucleotide polymorphisms (SNPs) for accurate parentage verification and discovery in sheep. Of particular interest was where SNP selection was limited to only a subset of chromosomes, thereby eliminating the ability to accurately impute genome-wide denser marker panels. Data used consisted of 10,933 candidate SNPs on 9,390 purebred sheep. These data consisted of 1,876 validated genotyped sire–offspring pairs and 2,784 validated genotyped dam–offspring pairs. The SNP panels developed consisted of 87 SNPs to 500 SNPs. Parentage verification and discovery were undertaken using 1) exclusion, based on the sharing of at least one allele between candidate parent–offspring pairs, and 2) a likelihood-based approach. Based on exclusion, allowing for one discordant offspring–parent genotype, a minimum of 350 SNPs was required when the goal was to unambiguously identify the true sire or dam from all possible candidates. Results suggest that, if selecting SNPs across the entire genome, a minimum of 250 carefully selected SNPs are required to ensure that the most likely selected parent (based on the likelihood approach) was, in fact, the true parent. If restricting the SNPs to just a subset of chromosomes, the recommendation is to use at least a 300-SNP panel from at least six chromosomes, with approximately an equal number of SNPs per chromosome.
    • Prediction of 24-hour milk yield and composition in dairy cows from a single part-day yield and sample

      McParland, S.; Coughlan, B.; Enright, B.; O’Keeffe, M.; O’Connor, R.; Feeney, L.; Berry, D.P.; Department of Agriculture, Food and Marine; Science Foundation Ireland; 16/RC/3835 (Teagasc, 2019-08-09)
      Irish Journal of Agricultural and Food Research | Volume 58: Issue 1 Prediction of 24-hour milk yield and composition in dairy cows from a single part-day yield and sample S. McParlandemail , B. Coughlan , B. Enright , M. O’Keeffe , R. O’Connor , L. Feeney and D.P. Berry DOI: https://doi.org/10.2478/ijafr-2019-0007 | Published online: 09 Aug 2019 PDF       Abstract Article PDF References Recommendations Abstract The objective was to evaluate the accuracy of predicting 24-hour milk yield and composition from a single morning (AM) or evening (PM) milk weight and composition. A calibration dataset of 37,481 test-day records with both AM and PM yields and composition was used to generate the prediction equations; equations were validated using 4,644 test-day records. Prediction models were developed within stage of lactation and parity while accounting for the inter-milking time interval. The mean correlation between the predicted 24-hour yields and composition of milk, fat and protein and the respective actual values was 0.97 when based on just an AM milk yield and composition with a mean correlation of 0.95 when based on just a PM milk yield and composition. The regression of predicted 24-hour yield and composition on the respective actual values varied from 0.97 to 1.01 with the exception of 24-hour fat percentage predicted from a PM sample (1.06). A single AM sample is useful to predict 24-hour milk yield and composition when the milking interval is known.
    • Prevalence of QoI resistance and mtDNA diversity in the Irish Zymoseptoria tritici population

      Kildea, S.; Bucar, D.E.; Hutton, F.; Rosa, S. de la; Welch, T.E.; Phelan, S.; Department of Agriculture, Food and the Marine; Erasmus+ programme; Mexican National Council of Science and Technology (CONACYT); 11S113 (Teagasc, 2019-06-15)
      The emergence and spread of Quinone outside Inhibitor (QoI) fungicide resistance in the Irish Zymoseptoria tritici population in the early 2000s had immediate impacts on the efficacy of the entire group of fungicides for the control of septoria tritici blotch. As a result, a dramatic reduction in the quantities applied to winter wheat occurred in the following seasons. Even in the absence of these fungicides, the frequency of the resistance allele, G143A in the pathogens mtDNA has remained exceptionally high (>97%), and as such, it can be anticipated that continued poor efficacy of current QoI fungicides will be observed. Amongst the isolates with G143A, differences in sensitivity to the QoI pyraclostrobin were observed in vitro. The addition of the alternative oxidase (AOX) inhibitor salicylhydroxamic acid increased sensitivity in these isolates, suggesting some continued impairment of respiration by the QoI fungicides, albeit weak. Interestingly, amongst those tested, the strains from a site with a high frequency of inserts in the MFS1 transporter gene known to enhance QoI efflux did not exhibit this increase in sensitivity. A total of 19 mtDNA haplotypes were detected amongst the 2017 strain collection. Phylogenetic analysis confirmed the suggestion of a common ancestry of all the haplotypes, even though three of the haplotypes contained at least one sensitive strain.
    • Sensory and ATP derivative-based indicators for assessing the freshness of Atlantic salmon (Salmo salar) and cod (Gadus morhua)

      Fogarty, Colin; Smyth, Conor; Whyte, Paul; Brunton, Nigel; Bolton, Declan; Department of Agriculture, Food and the Marine; 13F458, (Teagasc, 2019-10-31)
      Irish Journal of Agricultural and Food Research | Volume 58: Issue 1 Sensory and ATP derivative-based indicators for assessing the freshness of Atlantic salmon (Salmo salar) and cod (Gadus morhua) Colin Fogarty , Conor Smyth , Paul Whyte , Nigel Brunton and Declan Boltonemail DOI: https://doi.org/10.2478/ijafr-2019-0008 | Published online: 31 Oct 2019 PDF       Abstract Article PDF References Recommendations Abstract To estimate the shelf life of fresh fish, the processor must know the period of time between catch/harvest and arrival at the processing plant. This information is not always available, necessitating the provision of methods to estimate the time since catch or harvest. The objectives of this study were therefore to develop and/or validate sensory and ATP derivative-based methods for rapidly assessing the freshness of fish. A quality index method (QIM; raw fish) and a quantitative descriptive analysis (QDA; cooked fish) were developed and validated (against bacterial count [total viable count (TVC)] and time) for salmon (Salmo salar) and cod (Gadus morhua). The production of inosine monophosphate (IMP), inosine and hypoxanthine (Hx) and associated ratios (IMP/Hx, K1-value or H-value) were also investigated for use as freshness markers. There was a linear relationship between QIM and TVC (R2 = 0.93 for salmon and R2 = 0.89 for cod), QIM and time (R2 = 0.96 for salmon and R2 = 0.98 for cod), QDA and TVC (R2 = 0.93 for salmon and R2 = 0.77 for cod) and QDA and time (R2 = 0.94 for salmon and R2 = 0.87 for cod), suggesting that the QIM and QDA schemes developed could be used to monitor/assess freshness. The H-value also increased linearly with TVC (R2 = 0.88 for salmon and R2 = 0.89 for cod) and time (R2 = 0.93 for salmon and R2 = 0.84 for cod). It was therefore concluded that both the QIM/QDA approach and monitoring ATP degradation, specifically expressed as the H-value, could be used as rapid methods to assess the freshness of salmon and cod arriving at the processing plant