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    The effect of defoliation frequency and height on plantain and chicory-based swards
    (2021) Cranston L; Kenyon P; Morris S; Lopez-Villalobos N; Kemp P
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    New targets acquired: Improving locus recovery from the Angiosperms353 probe set
    (Botanical Society of America, 14/06/2021) McLay T; Birch J; Gunn B; Ning W; Tate J; Nauheimer L; Joyce E; Simpson L; Schmidt-Lebuhn A; Baker W; Forest F; Jackson C
    PREMISE: Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6–18 taxa per locus. Consequently, reads sequenced from on-target DNA molecules may fail to map to references, resulting in fewer on-target reads for assembly, and reducing locus recovery. METHODS: We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a ‘mega353’ target file, with each locus represented by 17–373 taxa. This mega353 file is a drop-in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user-selected taxon groups, and to incorporate other transcriptome or protein-coding gene data sets. RESULTS: Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on-target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%. DISCUSSION: Increasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson-pellicle/NewTargets.
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    Weed Detection by Faster RCNN Model: An Enhanced Anchor Box Approach
    (MDPI AG, 29/06/2022) Saleem MH; Potgieter J; Arif KM
    To apply weed control treatments effectively, the weeds must be accurately detected. Deep learning (DL) has been quite successful in performing the weed identification task. However, various aspects of the DL have not been explored in previous studies. This research aimed to achieve a high average precision (AP) of eight classes of weeds and a negative (non-weed) class, using the DeepWeeds dataset. In this regard, a DL-based two-step methodology has been proposed. This article is the second stage of the research, while the first stage has already been published. The former phase presented a weed detection pipeline and consisted of the evaluation of various neural networks, image resizers, and weight optimization techniques. Although a significant improvement in the mean average precision (mAP) was attained. However, the Chinee apple weed did not reach a high average precision. This result provided a solid ground for the next stage of the study. Hence, this paper presents an in-depth analysis of the Faster Region-based Convolutional Neural Network (RCNN) with ResNet-101, the best-obtained model in the past step. The architectural details of the Faster RCNN model have been thoroughly studied to investigate each class of weeds. It was empirically found that the generation of anchor boxes affects the training and testing performance of the Faster RCNN model. An enhancement to the anchor box scales and aspect ratios has been attempted by various combinations. The final results, with the addition of 64 × 64 scale size, and aspect ratio of 1:3 and 3:1, produced the best classification and localization of all classes of weeds and a negative class. An enhancement of 24.95% AP was obtained in Chinee apple weed. Furthermore, the mAP was improved by 2.58%. The robustness of the approach has been shown by the stratified k-fold cross-validation technique and testing on an external dataset.
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    Genetic susceptibility to Theileria orientalis (Ikeda) in Angus- and Hereford-sired yearling cattle born to dairy cattle on an endemically infected farm in New Zealand
    (Taylor and Francis Group, 5/03/2023) Lawrence K; Fermin L; Gedye K; Hickson R; lawrence B; coleman L; Pomroy W; Natalia M; Lopez- Villalobos N
    Theileria orientalis (Ikeda) was first detected in New Zealand in 2012, becoming endemic in most of the North Island, and can cause incidences of anaemia and death. Research has been performed in New Zealand on the incidence and severity of infection. Through this research anecdotal evidence has been found to suggest a potential genetic susceptibility component in the response of the host to the parasite. To investigate the genetic susceptibility of cattle to T. orientalis (Ikeda), 99 calves born in 2016 as part of a separate experiment and grown in six grazing herds, were examined for their response to the parasite. In addition to measuring live weight, two blood collections were taken in the first four months of life which were used to measure packed cell volume by haematocrit and qPCR to assess parasite load. Heritability was calculated and was low for parasite load, but the result indicates that there is some potential to increase resistance through selective breeding. The mechanisms of the differences in parasite load were not elucidated in this research; however, significant variation was found among herds and sires, indicating that both genetic selection and environmental management could be utilised to reduce parasite load in growing calves.
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    Predator- and killed prey-induced fears bear significant cost to an invasive spider mite: implications in pest management
    (Wiley, 5/09/2022) Ristyadi D; He XZ; Wang Q
    BACKGROUND: The success of biological control using predators is normally assumed to be achieved through direct predation. Yet it is largely unknown how the predator- and killed prey-induced stress to prey may contribute to biological control effectiveness. Here, we investigate variations in life-history traits and offspring fitness of the spider mite Tetranychus ludeni in response to cues from the predatory mite Phytoseiulus persimilis and killed T. ludeni, providing knowledge for evaluation of the nonconsumptive contribution to the biological control of T. ludeni and for future development of novel spider mite control measures using these cues. RESULTS: Cues from predators and killed prey shortened longevity by 23-25% and oviposition period by 35-40%, and reduced fecundity by 31-37% in T. ludeni females. These cues significantly reduced the intrinsic rate of increase (rm ) and net population growth rate (R0 ), and extended time to double the population size (Dt ). Predator cues significantly delayed lifetime production of daughters. Mothers exposed to predator cues laid significantly smaller eggs and their offspring developed significantly more slowly but these eggs had significantly higher hatch rate. CONCLUSION: Predator- and killed prey-induced fears significantly lower the fitness of T. ludeni, suggesting that these nonconsumptive effects can contribute to the effectiveness of biological control to a great extent. Our study provides critical information for evaluation of biological control effectiveness using predators and paves the way for identification of chemical odors from the predator and killed prey, and development of new materials and methods for the control of spider mite pests. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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    The growth response of Pasture Brome (Bromus valdivianus Phil.) to defoliation frequency under two soil water restriction levels
    (MDPI AG, 15/02/2021) Cranston L
    Pasture brome (Bromus valdivianus Phil.) has the potential to increase current levels of herbage production and pasture persistence in New Zealand dryland, well-drained soils. However, there is little literature on the effect of defoliation management on growth of this grass under contrasting soil-water restriction levels. The growth physiology and performance of pasture brome were evaluated in pots in a glasshouse. Defoliation frequency (DF) treatments were applied based on three different accumulated growing degree-days (AGDD): 250, 500 and 1000 AGDD (high, medium, and low DF). At end of the first growing cycle (1000 AGDD), water availability was restricted to 20–25% of field capacity (FC) in half of the pots, while the other pots were maintained between 80–85% FC. Total accumulated herbage mass was positively related with the low DF and well-watered conditions (p < 0.05). At the final harvest, plants subjected to low DF had greater root mass than high and medium DF (p < 0.05). At each harvest, the leaf regrowth stage (LS) for low DF was 3.5, while for high and medium DF, the LS was 1.5 and 2.0; respectively. Tiller water-soluble carbohydrates were highest at the low DF and under 20–25% FC. Regardless of soil-water conditions, defoliation at 3.5 LS supports production, enhancing survival during a drought.
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    Characterization of the Volatile Profiles of Six Industrial Hemp (Cannabis sativa L.) Cultivars
    (American Society of Agronomy, 27/10/2022) Sofkova-Bobcheva S
    Volatile organic compounds (VOCs) play an important role in plant ecology and can be useful in pest management. This work characterises, for the first time, the VOC emissions of six industrial hemp (Cannabis sativa L.) cultivars grown in New Zealand: CFX-2, CRS-1, Ferimon 12, Katani, Futura 75, and Finola. Volatiles emitted from flowers and foliage of eight-week-old plants were collected using a dynamic headspace sampling method and analysed using gas chromatography coupled to mass spectrometry. We assessed the effect of cultivar, sex (monoecious, male, and female), and site (i.e., two sites differing in soil types, maintained under irrigation and rain-fed conditions) on VOC emissions. Thirty-five volatile compounds were tentatively identified from the headspace samples of hemp plants, but none of the cultivars emitted all 35 compounds. β-Myrcene was the most abundant compound in most cultivars. Overall, there was a significant effect of sex, and the interaction of sex and cultivar on the volatile profiles, but no effect of site. Female plants typically emitted more volatiles than their male counterparts and monoecious cultivars. The main compounds driving the difference between cultivars and sexes were (Z)- and (E)-β-ocimene. We hypothesize that differences in emission emerged as a defence strategy to protect costly female flowers from herbivores (since C. sativa is wind pollinated), but this hypothesis needs further testing. We recommend additional studies exploring how biotic and abiotic factors influence hemp VOC emissions, changes in VOCs throughout the crop cycle, the role of VOCs in plant-insect interactions and their use in pest management.
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    Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics
    (Botanical Society of America, 26/07/2021) McDonnell A; Baker WJ; Dodsworth S; Forest F; Graham SW; Johnson MG; Pokorny L; Tate J; Wicke S; Wickett NJ