Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
Browse
15 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 Multi-scale spatial heterogeneity of pectic rhamnogalacturonan I (RG-I) structural features in tobacco seed endosperm cell walls(Wiley, 3/09/2013) Lee KJD; Cornuault VRG; Manfield IW; Ralet MC; Knox JPPlant cell walls are complex configurations of polysaccharides that fulfil a diversity of roles during plant growth and development. They also provide sets of biomaterials that are widely exploited in food, fibre and fuel applications. The pectic polysaccharides, which comprise approximately a third of primary cell walls, form complex supramolecular structures with distinct glycan domains. Rhamnogalacturonan I (RG-I) is a highly structurally heterogeneous branched glycan domain within the pectic supramolecule that contains rhamnogalacturonan, arabinan and galactan as structural elements. Heterogeneous RG-I polymers are implicated in generating the mechanical properties of cell walls during cell development and plant growth, but are poorly understood in architectural, biochemical and functional terms. Using specific monoclonal antibodies to the three major RG-I structural elements (arabinan, galactan and the rhamnogalacturonan backbone) for in situ analyses and chromatographic detection analyses, the relative occurrences of RG-I structures were studied within a single tissue: the tobacco seed endosperm. The analyses indicate that the features of the RG-I polymer display spatial heterogeneity at the level of the tissue and the level of single cell walls, and also heterogeneity at the biochemical level. This work has implications for understanding RG-I glycan complexity in the context of cell-wall architectures and in relation to cell-wall functions in cell and tissue development.Item The deconstruction of pectic rhamnogalacturonan I unmasks the occurrence of a novel arabinogalactan oligosaccharide epitope(Oxford University Press (OUP), 1/11/2015) Buffetto F; Cornuault VRG; Rydahl MG; Ropartz D; Alvarado C; Echasserieau V; Le Gall S; Bouchet B; Tranquet O; Verhertbruggen Y; Willats WGT; Knox JP; Ralet MC; Guillon FRhamnogalacturonan I (RGI) is a pectic polysaccharide composed of a backbone of alternating rhamnose and galacturonic acid residues with side chains containing galactose and/or arabinose residues. The structure of these side chains and the degree of substitution of rhamnose residues are extremely variable and depend on species, organs, cell types and developmental stages. Deciphering RGI function requires extending the current set of monoclonal antibodies (mAbs) directed to this polymer. Here, we describe the generation of a new mAb that recognizes a heterogeneous subdomain of RGI. The mAb, INRA-AGI-1, was produced by immunization of mice with RGI oligosaccharides isolated from potato tubers. These oligomers consisted of highly branched RGI backbones substituted with short side chains. INRA-AGI-1 bound specifically to RGI isolated from galactan-rich cell walls and displayed no binding to other pectic domains. In order to identify its RGI-related epitope, potato RGI oligosaccharides were fractionated by anion-exchange chromatography. Antibody recognition was assessed for each chromatographic fraction. INRA-AGI-1 recognizes a linear chain of (1→4)-linked galactose and (1→5)-linked arabinose residues. By combining the use of INRA-AGI-1 with LM5, LM6 and INRA-RU1 mAbs and enzymatic pre-treatments, evidence is presented of spatial differences in RGI motif distribution within individual cell walls of potato tubers and carrot roots. These observations raise questions about the biosynthesis and assembly of pectin structural domains and their integration and remodeling in cell walls.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 Comparative in situ analyses of cell wall matrix polysaccharide dynamics in developing rice and wheat grain(Springer Verlag, 1/03/2015) Palmer R; Cornuault VRG; Marcus SE; Knox JP; Shewry PR; Tosi PCell wall polysaccharides of wheat and rice endosperm are an important source of dietary fibre. Monoclonal antibodies specific to cell wall polysaccharides were used to determine polysaccharide dynamics during the development of both wheat and rice grain. Wheat and rice grain present near synchronous developmental processes and significantly different endosperm cell wall compositions, allowing the localisation of these polysaccharides to be related to developmental changes. Arabinoxylan (AX) and mixed-linkage glucan (MLG) have analogous cellular locations in both species, with deposition of AX and MLG coinciding with the start of grain filling. A glucuronoxylan (GUX) epitope was detected in rice, but not wheat endosperm cell walls. Callose has been reported to be associated with the formation of cell wall outgrowths during endosperm cellularisation and xyloglucan is here shown to be a component of these anticlinal extensions, occurring transiently in both species. Pectic homogalacturonan (HG) was abundant in cell walls of maternal tissues of wheat and rice grain, but only detected in endosperm cell walls of rice in an unesterified HG form. A rhamnogalacturonan-I (RG-I) backbone epitope was observed to be temporally regulated in both species, detected in endosperm cell walls from 12 DAA in rice and 20 DAA in wheat grain. Detection of the LM5 galactan epitope showed a clear distinction between wheat and rice, being detected at the earliest stages of development in rice endosperm cell walls, but not detected in wheat endosperm cell walls, only in maternal tissues. In contrast, the LM6 arabinan epitope was detected in both species around 8 DAA and was transient in wheat grain, but persisted in rice until maturity.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.
