Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
Browse
10 results
Search Results
Item The compounding effects of high pollen limitation, selfing rates and inbreeding depression leave a New Zealand tree with few viable offspring.(2015-10) Van Etten ML; Tate JA; Anderson SH; Kelly D; Ladley JJ; Merrett MF; Peterson PG; Robertson AWBACKGROUND AND AIMS: Interactions between species are especially sensitive to environmental changes. The interaction between plants and pollinators is of particular interest given the potential current global decline in pollinators. Reduced pollinator services can be compensated for in some plant species by self-pollination. However, if inbreeding depression is high, selfed progeny could die prior to reaching adulthood, leading to cryptic recruitment failure. METHODS: To examine this scenario, pollinator abundance, pollen limitation, selfing rates and inbreeding depression were examined in 12 populations of varying disturbance levels in Sophora microphylla (Fabaceae), an endemic New Zealand tree species. KEY RESULTS: High pollen limitation was found in all populations (average of 58 % reduction in seed production, nine populations), together with high selfing rates (61 % of offspring selfed, six populations) and high inbreeding depression (selfed offspring 86 % less fit, six populations). Pollen limitation was associated with lower visitation rates by the two endemic bird pollinators. CONCLUSIONS: The results suggest that for these populations, over half of the seeds produced are genetically doomed. This reduction in the fitness of progeny due to reduced pollinator service is probably important to population dynamics of other New Zealand species. More broadly, the results suggest that measures of seed production or seedling densities may be a gross overestimate of the effective offspring production. This could lead to cryptic recruitment failure, i.e. a decline in successful reproduction despite high progeny production. Given the global extent of pollinator declines, cryptic recruitment failure may be widespread.Item A weight optimization-based transfer learning approach for plant disease detection of New Zealand vegetables(Frontiers Media, 25/10/2022) Saleem MH; Potgieter J; Arif KDeep learning (DL) is an effective approach to identifying plant diseases. Among several DL-based techniques, transfer learning (TL) produces significant results in terms of improved accuracy. However, the usefulness of TL has not yet been explored using weights optimized from agricultural datasets. Furthermore, the detection of plant diseases in different organs of various vegetables has not yet been performed using a trained/optimized DL model. Moreover, the presence/detection of multiple diseases in vegetable organs has not yet been investigated. To address these research gaps, a new dataset named NZDLPlantDisease-v2 has been collected for New Zealand vegetables. The dataset includes 28 healthy and defective organs of beans, broccoli, cabbage, cauliflower, kumara, peas, potato, and tomato. This paper presents a transfer learning method that optimizes weights obtained through agricultural datasets for better outcomes in plant disease identification. First, several DL architectures are compared to obtain the best-suited model, and then, data augmentation techniques are applied. The Faster Region-based Convolutional Neural Network (RCNN) Inception ResNet-v2 attained the highest mean average precision (mAP) compared to the other DL models including different versions of Faster RCNN, Single-Shot Multibox Detector (SSD), Region-based Fully Convolutional Networks (RFCN), RetinaNet, and EfficientDet. Next, weight optimization is performed on datasets including PlantVillage, NZDLPlantDisease-v1, and DeepWeeds using image resizers, interpolators, initializers, batch normalization, and DL optimizers. Updated/optimized weights are then used to retrain the Faster RCNN Inception ResNet-v2 model on the proposed dataset. Finally, the results are compared with the model trained/optimized using a large dataset, such as Common Objects in Context (COCO). The final mAP improves by 9.25% and is found to be 91.33%. Moreover, the robustness of the methodology is demonstrated by testing the final model on an external dataset and using the stratified k-fold cross-validation method.Item Seasonal variation in soil and herbage CO2 efflux for a sheep-grazed alpine meadow on the north-east Qinghai-Tibetan Plateau and estimated net annual CO2 exchange(2/06/2022) Yuan H; Matthew C; He XZ; Sun Y; Liu Y; Zhang T; Gao X; Yan C; Chang S; Hou FThe Qinghai-Tibetan Plateau is a vast geographic area currently subject to climate warming. Improved knowledge of the CO2 respiration dynamics of the Plateau alpine meadows and of the impact of grazing on CO2 fluxes is highly desirable. Such information will assist land use planning. We measured soil and vegetation CO2 efflux of alpine meadows using a closed chamber technique over diurnal cycles in winter, spring and summer. The annual, combined soil and plant respiration on ungrazed plots was 28.0 t CO2 ha-1 a-1, of which 3.7 t ha-1 a-1occurred in winter, when plant respiration was undetectable. This suggests winter respiration was driven mainly by microbial oxidation of soil organic matter. The winter respiration observed in this study was sufficient to offset the growing season CO2 sink reported for similar alpine meadows in other studies. Grazing increased herbage respiration in summer, presumably through stimulation of gross photosynthesis. From limited herbage production data, we estimate the sustainable yield of these meadows for grazing purposes to be about 500 kg herbage dry matter ha-1 a-1. Addition of photosynthesis data and understanding of factors affecting soil carbon sequestration to more precisely determine the CO2 balance of these grasslands is recommended.Item Secreted Glycoside Hydrolase Proteins as Effectors and Invasion Patterns of Plant-Associated Fungi and Oomycetes.(2022) Bradley EL; Ökmen B; Doehlemann G; Henrissat B; Bradshaw RE; Mesarich CHDuring host colonization, plant-associated microbes, including fungi and oomycetes, deliver a collection of glycoside hydrolases (GHs) to their cell surfaces and surrounding extracellular environments. The number and type of GHs secreted by each organism is typically associated with their lifestyle or mode of nutrient acquisition. Secreted GHs of plant-associated fungi and oomycetes serve a number of different functions, with many of them acting as virulence factors (effectors) to promote microbial host colonization. Specific functions involve, for example, nutrient acquisition, the detoxification of antimicrobial compounds, the manipulation of plant microbiota, and the suppression or prevention of plant immune responses. In contrast, secreted GHs of plant-associated fungi and oomycetes can also activate the plant immune system, either by acting as microbe-associated molecular patterns (MAMPs), or through the release of damage-associated molecular patterns (DAMPs) as a consequence of their enzymatic activity. In this review, we highlight the critical roles that secreted GHs from plant-associated fungi and oomycetes play in plant-microbe interactions, provide an overview of existing knowledge gaps and summarize future directions.Item Polyploidy on Islands: Its Emergence and Importance for Diversification(Frontiers Media, 4/03/2021) Meudt H; Dirk A; Tanentzap A; Igea J; Newmarch S; Brandt A; Lee W; Tate JWhole genome duplication or polyploidy is widespread among floras globally, but traditionally has been thought to have played a minor role in the evolution of island biodiversity, based on the low proportion of polyploid taxa present. We investigate five island systems (Juan Fernández, Galápagos, Canary Islands, Hawaiian Islands, and New Zealand) to test whether polyploidy (i) enhances or hinders diversification on islands and (ii) is an intrinsic feature of a lineage or an attribute that emerges in island environments. These island systems are diverse in their origins, geographic and latitudinal distributions, levels of plant species endemism (37% in the Galapagos to 88% in the Hawaiian Islands), and ploidy levels, and taken together are representative of islands more generally. We compiled data for vascular plants and summarized information for each genus on each island system, including the total number of species (native and endemic), generic endemicity, chromosome numbers, genome size, and ploidy levels. Dated phylogenies were used to infer lineage age, number of colonization events, and change in ploidy level relative to the non-island sister lineage. Using phylogenetic path analysis, we then tested how the diversification of endemic lineages varied with the direct and indirect effects of polyploidy (presence of polyploidy, time on island, polyploidization near colonization, colonizer pool size) and other lineage traits not associated with polyploidy (time on island, colonizer pool size, repeat colonization). Diploid and tetraploid were the most common ploidy levels across all islands, with the highest ploidy levels (>8x) recorded for the Canary Islands (12x) and New Zealand (20x). Overall, we found that endemic diversification of our focal island floras was shaped by polyploidy in many cases and certainly others still to be detected considering the lack of data in many lineages. Polyploid speciation on the islands was enhanced by a larger source of potential congeneric colonists and a change in ploidy level compared to overseas sister taxa.Item THE SHORT-TERM EFFECT OF IRRADIANCE ON THE PHOTOSYNTHETIC PROPERTIES OF ANTARCTIC FAST-ICE MICROALGAL COMMUNITIES(1).(WILEY-BLACKWELL PUBLISHING, INC, 2009-12) Ryan KG; Cowie ROM; Liggins E; McNaughtan D; Martin A; Davy SKAlthough sea-ice represents a harsh physicochemical environment with steep gradients in temperature, light, and salinity, diverse microbial communities are present within the ice matrix. We describe here the photosynthetic responses of sea-ice microalgae to varying irradiances. Rapid light curves (RLCs) were generated using pulse amplitude fluorometry and used to derive photosynthetic yield (ΦPSII ), photosynthetic efficiency (α), and the irradiance (Ek ) at which relative electron transport rate (rETR) saturates. Surface brine algae from near the surface and bottom-ice algae were exposed to a range of irradiances from 7 to 262 μmol photons · m(-2) · s(-1) . In surface brine algae, ΦPSII and α remained constant at all irradiances, and rETRmax peaked at 151 μmol photons · m(-2) · s(-1) , indicating these algae are well acclimated to the irradiances to which they are normally exposed. In contrast, ΦPSII , α, and rETRmax in bottom-ice algae reduced when exposed to irradiances >26 μmol photons · m(-2) · s(-1) , indicating a high degree of shade acclimation. In addition, the previous light history had no significant effect on the photosynthetic capacity of bottom-ice algae whether cells were gradually exposed to target irradiances over a 12 h period or were exposed immediately (light shocked). These findings indicate that bottom-ice algae are photoinhibited in a dose-dependent manner, while surface brine algae tolerate higher irradiances. Our study shows that sea-ice algae are able to adjust to changes in irradiance rapidly, and this ability to acclimate may facilitate survival and subsequent long-term acclimation to the postmelt light regime of the Southern Ocean.Item Weed Identification by Single-Stage and Two-Stage Neural Networks: A Study on the Impact of Image Resizers and Weights Optimization Algorithms(Frontiers Media, 25/04/2022) Saleem MH; Velayudhan KK; Potgieter J; Arif KThe accurate identification of weeds is an essential step for a site-specific weed management system. In recent years, deep learning (DL) has got rapid advancements to perform complex agricultural tasks. The previous studies emphasized the evaluation of advanced training techniques or modifying the well-known DL models to improve the overall accuracy. In contrast, this research attempted to improve the mean average precision (mAP) for the detection and classification of eight classes of weeds by proposing a novel DL-based methodology. First, a comprehensive analysis of single-stage and two-stage neural networks including Single-shot MultiBox Detector (SSD), You look only Once (YOLO-v4), EfficientDet, CenterNet, RetinaNet, Faster Region-based Convolutional Neural Network (RCNN), and Region-based Fully Convolutional Network (RFCN), has been performed. Next, the effects of image resizing techniques along with four image interpolation methods have been studied. It led to the final stage of the research through optimization of the weights of the best-acquired model by initialization techniques, batch normalization, and DL optimization algorithms. The effectiveness of the proposed work is proven due to a high mAP of 93.44% and validated by the stratified k-fold cross-validation technique. It was 5.8% improved as compared to the results obtained by the default settings of the best-suited DL architecture (Faster RCNN ResNet-101). The presented pipeline would be a baseline study for the research community to explore several tasks such as real-time detection and reducing the computation/training time. All the relevant data including the annotated dataset, configuration files, and inference graph of the final model are provided with this article. Furthermore, the selection of the DeepWeeds dataset shows the robustness/practicality of the study because it contains images collected in a real/complex agricultural environment. Therefore, this research would be a considerable step toward an efficient and automatic weed control system.Item 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 NTheileria 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.Item An improved method for monitoring multiscale plant species diversity of alpine grassland using UAVs: A case study in the source region of the Yellow River, China(Frontiers Media, 9/06/2022) Sun Y; Yuan Y; Luo Y; Ji W; Bian Q; Zhu Z; Wang J; Qin Y; He XZ; Li M; Yi SPlant species diversity (PSD) is essential in evaluating the function and developing the management and conservation strategies of grassland. However, over a large region, an efficient and high precision method to monitor multiscale PSD (α-, β-, and γ-diversity) is lacking. In this study, we proposed and improved an unmanned aerial vehicle (UAV)-based PSD monitoring method (UAVB) and tested the feasibility, and meanwhile, explored the potential relationship between multiscale PSD and precipitation on the alpine grassland of the source region of the Yellow River (SRYR), China. Our findings showed that: (1) UAVB was more representative (larger monitoring areas and more species identified with higher α- and γ-diversity) than the traditional ground-based monitoring method, though a few specific species (small in size) were difficult to identify; (2) UAVB is suitable for monitoring the multiscale PSD over a large region (the SRYR in this study), and the improvement by weighing the dominance of species improved the precision of α-diversity (higher R 2 and lower P values of the linear regressions); and (3) the species diversity indices (α- and β-diversity) increased first and then they tended to be stable with the increase of precipitation in SRYR. These findings conclude that UAVB is suitable for monitoring multiscale PSD of an alpine grassland community over a large region, which will be useful for revealing the relationship of diversity-function, and helpful for conservation and sustainable management of the alpine grassland.Item Potential for bioenergy generation and nutrient recycling in horticultural production systems in New Zealand(International Society for Horticultural Science, 20/08/2014) Kerckhoffs LHJ; Renquist RRenewable energy can be produced from a number of sources, including plant biomass. One of the most efficient technologies to generate bioenergy from plant biomass is on-farm anaerobic digestion (AD) producing biogas. Biogas can be used as an equal substitute to natural gas for industrial, commercial and residential use, and/or can be converted to electricity, heat or vehicle fuel using established technologies. Using purified biogas for transport is a highly effective greenhouse gas mitigation strategy. Various organic feed stocks can be converted into biogas: we have identified a large variety of purpose-grown bioenergy crop species (such as Jerusalem artichoke, forage sorghum, whole triticale) under New Zealand conditions, but feedstocks can also include farm and orchard waste streams (reject fruit, clippings, thinning and so on), groundcover biomass and other locally sourced organic municipal and industrial bio-waste as well. A novel biofuel cropping system was developed based on AD technology. It makes full use of the nutrients in the digestate with a unique closed-loop nutrient supply feature that conserves nutrients in the feedstock and recycles them back to the farm and orchard as bio-fertiliser. This eliminates the need for external fertilizer. This paper will explore the considerable potential for bioenergy generation and nutrient recycling in horticultural production systems in New Zealand.