Veterinary and Agricultural Sciences Collected Works - Research Publications
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ItemAutomated hyperspectral vegetation index derivation using a hyperparameter optimisation framework for high-throughput plant phenotyping.(Wiley, 2022-03)Hyperspectral vegetation indices (VIs) are widely deployed in agriculture remote sensing and plant phenotyping to estimate plant biophysical and biochemical traits. However, existing VIs consist mainly of simple two-band indices that limit the net performance and often do not generalise well for traits other than those for which they were originally designed. We present an automated hyperspectral vegetation index (AutoVI) system for the rapid generation of novel two- to six-band trait-specific indices in a streamlined process covering model selection, optimisation and evaluation, driven by the tree parzen estimator algorithm. Its performance was tested in generating novel indices to estimate chlorophyll and sugar contents in wheat. Results showed that AutoVI can rapidly generate complex novel VIs (at least a four-band index) that correlated strongly (R2 > 0.8) with measured chlorophyll and sugar contents in wheat. Automated hyperspectral vegetation index-derived indices were used as features in simple and stepwise multiple linear regressions for chlorophyll and sugar content estimation, and outperformed the results achieved with the existing 47 VIs and those provided using partial least squares regression. The AutoVI system can deliver novel trait-specific VIs readily adoptable to high-throughput plant phenotyping platforms and should appeal to plant scientists and breeders. A graphical user interface for the AutoVI is provided here.
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ItemGenome-wide association studies dissect the G × E interaction for agronomic traits in a worldwide collection of safflowers (Carthamus tinctorius L.)(Springer Science and Business Media LLC, 2022-04-01)Abstract Genome-wide association studies were conducted using a globally diverse safflower (Carthamus tinctorius L.) Genebank collection for grain yield (YP), days to flowering (DF), plant height (PH), 500 seed weight (SW), seed oil content (OL), and crude protein content (PR) in four environments (sites) that differed in water availability. Phenotypic variation was observed for all traits. YP exhibited low overall genetic correlations (rGoverall) across sites, while SW and OL had high rGoverall and high pairwise genetic correlations (rGij) across all pairwise sites. In total, 92 marker-trait associations (MTAs) were identified using three methods, single locus genome-wide association studies (GWAS) using a mixed linear model (MLM), the Bayesian multi-locus method (BayesR), and meta-GWAS. MTAs with large effects across all sites were detected for OL, SW, and PR, and MTAs specific for the different water stress sites were identified for all traits. Five MTAs were associated with multiple traits; 4 of 5 MTAs were variously associated with the three traits of SW, OL, and PR. This study provided insights into the phenotypic variability and genetic architecture of important safflower agronomic traits under different environments.
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ItemCBM: An IoT Enabled LiDAR Sensor for In-Field Crop Height and Biomass Measurements.(MDPI AG, 2021-12-29)The phenotypic characterization of crop genotypes is an essential, yet challenging, aspect of crop management and agriculture research. Digital sensing technologies are rapidly advancing plant phenotyping and speeding-up crop breeding outcomes. However, off-the-shelf sensors might not be fully applicable and suitable for agricultural research due to the diversity in crop species and specific needs during plant breeding selections. Customized sensing systems with specialized sensor hardware and software architecture provide a powerful and low-cost solution. This study designed and developed a fully integrated Raspberry Pi-based LiDAR sensor named CropBioMass (CBM), enabled by internet of things to provide a complete end-to-end pipeline. The CBM is a low-cost sensor, provides high-throughput seamless data collection in field, small data footprint, injection of data onto the remote server, and automated data processing. The phenotypic traits of crop fresh biomass, dry biomass, and plant height that were estimated by CBM data had high correlation with ground truth manual measurements in a wheat field trial. The CBM is readily applicable for high-throughput plant phenotyping, crop monitoring, and management for precision agricultural applications.
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ItemMachine learning regression analysis for estimation of crop emergence using multispectral uav imagery(MDPI AG, 2021-08-01)Optimal crop emergence is an important trait in crop breeding for genotypic screening and for achieving potential growth and yield. Emergence is conventionally quantified manually by counting the sub-sections of field plots or scoring; these are less reliable, laborious and inefficient. Remote sensing technology is being increasingly used for high-throughput estimation of agronomic traits in field crops. This study developed a method for estimating wheat seedlings using multispectral images captured from an unmanned aerial vehicle. A machine learning regression (MLR) analysis was used by combining spectral and morphological information extracted from the multispectral images. The approach was tested on diverse wheat genotypes varying in seedling emergence. In this study, three supervised MLR models including regression trees, support vector regression and Gaussian process regression (GPR) were evaluated for estimating wheat seedling emergence. The GPR model was the most effective compared to the other methods, with R2 = 0.86, RMSE = 4.07 and MAE = 3.21 when correlated to the manual seedling count. In addition, imagery data collected at multiple flight altitudes and different wheat growth stages suggested that 10 m altitude and 20 days after sowing were desirable for optimal spatial resolution and image analysis. The method is deployable on larger field trials and other crops for effective and reliable seedling emergence estimates.
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ItemHigh-throughput phenotyping to dissect genotypic differences in safflower for drought tolerance(PUBLIC LIBRARY SCIENCE, 2021-07-23)Drought is one of the most severe and unpredictable abiotic stresses, occurring at any growth stage and affecting crop yields worldwide. Therefore, it is essential to develop drought tolerant varieties to ensure sustainable crop production in an ever-changing climate. High-throughput digital phenotyping technologies in tandem with robust screening methods enable precise and faster selection of genotypes for breeding. To investigate the use of digital imaging to reliably phenotype for drought tolerance, a genetically diverse safflower population was screened under different drought stresses at Agriculture Victoria's high-throughput, automated phenotyping platform, Plant Phenomics Victoria, Horsham. In the first experiment, four treatments, control (90% field capacity; FC), 40% FC at initial branching, 40% FC at flowering and 50% FC at initial branching and flowering, were applied to assess the performance of four safflower genotypes. Based on these results, drought stress using 50% FC at initial branching and flowering stages was chosen to further screen 200 diverse safflower genotypes. Measured plant traits and dry biomass showed high correlations with derived digital traits including estimated shoot biomass, convex hull area, caliper length and minimum area rectangle, indicating the viability of using digital traits as proxy measures for plant growth. Estimated shoot biomass showed close association having moderately high correlation with drought indices yield index, stress tolerance index, geometric mean productivity, and mean productivity. Diverse genotypes were classified into four clusters of drought tolerance based on their performance (seed yield and digitally estimated shoot biomass) under stress. Overall, results show that rapid and precise image-based, high-throughput phenotyping in controlled environments can be used to effectively differentiate response to drought stress in a large numbers of safflower genotypes.
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ItemDigital Phenotyping to Delineate Salinity Response in Safflower Genotypes(FRONTIERS MEDIA SA, 2021-06-16)Salinity is a major contributing factor to the degradation of arable land, and reductions in crop growth and yield. To overcome these limitations, the breeding of crop varieties with improved salt tolerance is needed. This requires effective and high-throughput phenotyping to optimize germplasm enhancement. Safflower (Carthamus tinctorius L.), is an underappreciated but highly versatile oilseed crop, capable of growing in saline and arid environments. To develop an effective and rapid phenotyping protocol to differentiate salt responses in safflower genotypes, experiments were conducted in the automated imaging facility at Plant Phenomics Victoria, Horsham, focussing on digital phenotyping at early vegetative growth. The initial experiment, at 0, 125, 250, and 350 mM sodium chloride (NaCl), showed that 250 mM NaCl was optimum to differentiate salt sensitive and tolerant genotypes. Phenotyping of a diverse set of 200 safflower genotypes using the developed protocol defined four classes of salt tolerance or sensitivity, based on biomass and ion accumulation. Salt tolerance in safflower was dependent on the exclusion of Na+ from shoot tissue and the maintenance of K+ uptake. Salinity response identified in glasshouse experiments showed some consistency with the performance of representatively selected genotypes tested under sodic field conditions. Overall, our results suggest that digital phenotyping can be an effective high-throughput approach in identifying candidate genotypes for salt tolerance in safflower.
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ItemAutomated Machine Learning for High-Throughput Image-Based Plant Phenotyping(MDPI, 2021-03-01)Automated machine learning (AutoML) has been heralded as the next wave in artificial intelligence with its promise to deliver high-performance end-to-end machine learning pipelines with minimal effort from the user. However, despite AutoML showing great promise for computer vision tasks, to the best of our knowledge, no study has used AutoML for image-based plant phenotyping. To address this gap in knowledge, we examined the application of AutoML for image-based plant phenotyping using wheat lodging assessment with unmanned aerial vehicle (UAV) imagery as an example. The performance of an open-source AutoML framework, AutoKeras, in image classification and regression tasks was compared to transfer learning using modern convolutional neural network (CNN) architectures. For image classification, which classified plot images as lodged or non-lodged, transfer learning with Xception and DenseNet-201 achieved the best classification accuracy of 93.2%, whereas AutoKeras had a 92.4% accuracy. For image regression, which predicted lodging scores from plot images, transfer learning with DenseNet-201 had the best performance (R2 = 0.8303, root mean-squared error (RMSE) = 9.55, mean absolute error (MAE) = 7.03, mean absolute percentage error (MAPE) = 12.54%), followed closely by AutoKeras (R2 = 0.8273, RMSE = 10.65, MAE = 8.24, MAPE = 13.87%). In both tasks, AutoKeras models had up to 40-fold faster inference times compared to the pretrained CNNs. AutoML has significant potential to enhance plant phenotyping capabilities applicable in crop breeding and precision agriculture.
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ItemFusion of Spectral and Structural Information from Aerial Images for Improved Biomass Estimation(MDPI, 2020-10-01)Efficient, precise and timely measurement of plant traits is important in the assessment of a breeding population. Estimating crop biomass in breeding trials using high-throughput technologies is difficult, as reproductive and senescence stages do not relate to reflectance spectra, and multiple growth stages occur concurrently in diverse genotypes. Additionally, vegetation indices (VIs) saturate at high canopy coverage, and vertical growth profiles are difficult to capture using VIs. A novel approach was implemented involving a fusion of complementary spectral and structural information, to calculate intermediate metrics such as crop height model (CHM), crop coverage (CC) and crop volume (CV), which were finally used to calculate dry (DW) and fresh (FW) weight of above-ground biomass in wheat. The intermediate metrics, CHM (R2 = 0.81, SEE = 4.19 cm) and CC (OA = 99.2%, Κ = 0.98) were found to be accurate against equivalent ground truth measurements. The metrics CV and CV×VIs were used to develop an effective and accurate linear regression model relationship with DW (R2 = 0.96 and SEE = 69.2 g/m2) and FW (R2 = 0.89 and SEE = 333.54 g/m2). The implemented approach outperformed commonly used VIs for estimation of biomass at all growth stages in wheat. The achieved results strongly support the applicability of the proposed approach for high-throughput phenotyping of germplasm in wheat and other crop species.
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ItemGenomic prediction and genomic heritability of grain yield and its related traits in a safflower genebank collection(WILEY, 2020-11-02)Safflower, a minor oilseed crop, is gaining increased attention for food and industrial uses. Safflower genebank collections are an important genetic resource for crop enhancement and future breeding programs. In this study, we investigated the population structure of a safflower collection sourced from the Australian Grain Genebank and assessed the potential of genomic prediction (GP) to evaluate grain yield and related traits using single and multi-site models. Prediction accuracies (PA) of genomic best linear unbiased prediction (GBLUP) from single site models ranged from 0.21 to 0.86 for all traits examined and were consistent with estimated genomic heritability (h2 ), which varied from low to moderate across traits. We generally observed a low level of genome × environment interactions (g × E). Multi-site g × E GBLUP models only improved PA for accessions with at least some phenotypes in the training set. We observed that relaxing quality filtering parameters for genotype-by-sequencing (GBS), such as missing genotype call rate, did not affect PA but upwardly biased h2 estimation. Our results indicate that GP is feasible in safflower evaluation and is potentially a cost-effective tool to facilitate fast introgression of desired safflower trait variation from genebank germplasm into breeding lines.