ORCID Profile
0000-0003-1195-4478
Current Organisation
University of Adelaide
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Agricultural biotechnology | Genetically modified field crops and pasture | Non-genetically modified uses of biotechnology
ANZSRC Socio-Economic Objective (SEO)
Related Links
Publications
Detecting spikes of wheat plants using neural networks with Laws texture energy
Publisher: Springer Science and Business Media LLC
Date: 13-10-2017
Arbuscular mycorrhizae are important for phosphorus uptake and root biomass, and exudation for nitrogen uptake in tomato plants grown under variable water conditions
Publisher: Springer Science and Business Media LLC
Date: 19-05-2023
Using High-Throughput Phenotyping to Explore Growth Responses to Mycorrhizal Fungi and Zinc in Three Plant Species
Publisher: American Association for the Advancement of Science (AAAS)
Date: 2019
Abstract: There are many reported benefits to plants of arbuscular mycorrhizal fungi (AMF), including positive plant biomass responses however, AMF can also induce biomass depressions in plants, and this response receives little attention in the literature. High-throughput phenotyping (HTP) technology permits repeated measures of an in idual plant’s aboveground biomass. We examined the effect on AMF inoculation on the shoot biomass of three contrasting plant species: a vegetable crop (tomato), a cereal crop (barley), and a pasture legume (Medicago). We also considered the interaction of mycorrhizal growth responses with plant-available soil zinc (Zn) and phosphorus (P) concentrations. The appearance of a depression in shoot biomass due to inoculation with AMF occurred at different times for each plant species depressions appeared earliest in tomato, then Medicago, and then barley. The usually positive-responding Medicago plants were not responsive at the high level of soil available P used. Mycorrhizal growth responsiveness in all three species was also highly interactive with soil Zn supply tomato growth responded negatively to AMF inoculation in all soil Zn treatments except the toxic soil Zn treatment, where it responded positively. Our results illustrate how context-dependent mycorrhizal growth responses are and the value of HTP approaches to exploring the complexity of mycorrhizal responses.
Atlas of Age- and Tissue-Specific DNA Methylation during Early Development of Barley (Hordeum vulgare)
Publisher: IntechOpen
Date: 07-2020
A single nucleotide substitution in TaHKT1;5‐D controls shoot Na+ accumulation in bread wheat
Publisher: Wiley
Date: 22-07-2020
DOI: 10.1111/PCE.13841
Combining field performance with controlled environment plant imaging to identify the genetic control of growth and transpiration underlying yield response to water-deficit stress in wheat
Publisher: Oxford University Press (OUP)
Date: 15-07-2015
DOI: 10.1093/JXB/ERV320
Approaches, applications, and future directions for hyperspectral vegetation studies: An emphasis on yield‐limiting factors in wheat
Publisher: Wiley
Date: 2020
DOI: 10.1002/PPJ2.20007
Dissecting new genetic components of salinity tolerance in two-row spring barley at the vegetative and reproductive stages
Publisher: Public Library of Science (PLoS)
Date: 23-07-2020
Improved Salinity Tolerance-Associated Variables Observed in EMS Mutagenized Wheat Lines
Publisher: MDPI AG
Date: 27-09-2022
Abstract: Salinity tolerance-associated phenotypes of 35 EMS mutagenized wheat lines originating from BARI Gom-25 were compared. Vegetative growth was measured using non-destructive image-based phenotyping. Five different NaCl concentrations (0 to 160 mM) were applied to plants 19 days after planting (DAP 19), and plants were imaged daily until DAP 38. Plant growth, water use, leaf Na+, K+ and Cl− content, and thousand kernel weight (TKW) were measured, and six lines were selected for further analysis. In saline conditions, leaf Na+, K+, and Cl− content variation on a dry weight basis within these six lines were ~9.3, 1.4, and 2.4-fold, respectively. Relative to BARI Gom-25, two (OA6, OA62) lines had greater K+ accumulation, three (OA6, OA10, OA62) had 50–75% lower Na+:K+ ratios, and OA62 had ~30% greater water-use index (WUI). OA23 had ~2.2-fold greater leaf Na+ and maintained TKW relative to BARI Gom-25. Two lines (OA25, OA52) had greater TKW than BARI Gom-25 when grown in 120 mM NaCl but similar Na+:K+, WUI, and biomass accumulation. OA6 had relatively high TKW, high leaf K+, and WUI, and low leaf Na+ and Cl−. Phenotypic variation revealed differing associations between the parameters measured in the lines. Future identification of the genetic basis of these differences, and crossing of lines with phenotypes of interest, is expected to enable the assessment of which combinations of parameters deliver the greatest improvement in salinity tolerance.
The R2R3‐MYB transcription factor HAG1/MYB28 is a regulator of methionine‐derived glucosinolate biosynthesis in Arabidopsis thaliana
Publisher: Wiley
Date: 08-06-2007
Variation in shoot tolerance mechanisms not related to ion toxicity in barley
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/FP17049
Abstract: Soil salinity can severely reduce crop growth and yield. Many studies have investigated salinity tolerance mechanisms in cereals using phenotypes that are relatively easy to measure. The majority of these studies measured the accumulation of shoot Na+ and the effect this has on plant growth. However, plant growth is reduced immediately after exposure to NaCl before Na+ accumulates to toxic concentrations in the shoot. In this study, nondestructive and destructive measurements are used to evaluate the responses of 24 predominately Australian barley (Hordeum vulgare L.) lines at 0, 150 and 250 mM NaCl. Considerable variation for shoot tolerance mechanisms not related to ion toxicity (shoot ion-independent tolerance) was found, with some lines being able to maintain substantial growth rates under salt stress, whereas others stopped growing. Hordeum vulgare spp. spontaneum accessions and barley landraces predominantly had the best shoot ion independent tolerance, although two commercial cultivars, Fathom and Skiff, also had high tolerance. The tolerance of cv. Fathom may be caused by a recent introgression from H. vulgare L. spp. spontaneum. This study shows that the most salt-tolerant barley lines are those that contain both shoot ion-independent tolerance and the ability to exclude Na+ from the shoot (and thus maintain high K+ : Na+ ratios).
Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare)
Publisher: MDPI AG
Date: 20-06-2018
High-throughput shoot imaging to study drought responses
Publisher: Oxford University Press (OUP)
Date: 26-07-2010
DOI: 10.1093/JXB/ERQ201
Abstract: Drought is a complex stress which elicits a wide variety of plant responses. As such, genetic studies of drought are particularly difficult. Elucidation of the genetic basis of components contributing to drought tolerance is likely to be more tractable than that of overall drought tolerance. Certain of the traits which contribute to drought tolerance in plants and the high-throughput phenotyping techniques available to measure those traits are described in this paper. On the basis of the dynamic nature of drought, plant development, and the resulting stress response, the focus is on non-destructive imaging techniques which allow a temporal resolution and monitoring of the same plants throughout the experiment. Information on the physiological changes in response to drought over time is vital in order to identify and characterize different drought-tolerance mechanisms. High-throughput imaging provides a valuable new tool which allows the dissection of plant responses to drought into a series of component traits.
The Development of Hyperspectral Distribution Maps to Predict the Content and Distribution of Nitrogen and Water in Wheat (Triticum aestivum)
Publisher: Frontiers Media SA
Date: 30-10-2019
Utilization of a high-throughput shoot imaging system to examine the dynamic phenotypic responses of a C4 cereal crop plant to nitrogen and water deficiency over time
Publisher: Oxford University Press (OUP)
Date: 19-02-2015
DOI: 10.1093/JXB/ERU526
The Performances of Hyperspectral Sensors for Proximal Sensing of Nitrogen Levels in Wheat
Publisher: MDPI AG
Date: 13-08-2020
DOI: 10.3390/S20164550
Abstract: The accurate and high throughput quantification of nitrogen (N) content in wheat using non-destructive methods is an important step towards identifying wheat lines with high nitrogen use efficiency and informing agronomic management practices. Among various plant phenotyping methods, hyperspectral sensing has shown promise in providing accurate measurements in a fast and non-destructive manner. Past applications have utilised non-imaging instruments, such as spectrometers, while more recent approaches have expanded to hyperspectral cameras operating in different wavelength ranges and at various spectral resolutions. However, despite the success of previous hyperspectral applications, some important research questions regarding hyperspectral sensors with different wavelength centres and bandwidths remain unanswered, limiting wide application of this technology. This study evaluated the capability of hyperspectral imaging and non-imaging sensors to estimate N content in wheat leaves by comparing three hyperspectral cameras and a non-imaging spectrometer. This study answered the following questions: (1) How do hyperspectral sensors with different system setups perform when conducting proximal sensing of N in wheat leaves and what aspects have to be considered for optimal results? (2) What types of photonic detectors are most sensitive to N in wheat leaves? (3) How do the spectral resolutions of different instruments affect N measurement in wheat leaves? (4) What are the key-wavelengths with the highest correlation to N in wheat? Our study demonstrated that hyperspectral imaging systems with satisfactory system setups can be used to conduct proximal sensing of N content in wheat with sufficient accuracy. The proposed approach could reduce the need for chemical analysis of leaf tissue and lead to high-throughput estimation of N in wheat. The methodologies here could also be validated on other plants with different characteristics. The results can provide a reference for users wishing to measure N content at either plant- or leaf-scales using hyperspectral sensors.
Deciphering Salt Stress Responses inSolanum pimpinellifoliumthrough High-Throughput Phenotyping
Publisher: Cold Spring Harbor Laboratory
Date: 17-08-2023
DOI: 10.1101/2023.08.15.553433
Abstract: Soil salinity is a major environmental stressor affecting agricultural productivity worldwide. Understanding plant responses to salt stress is crucial for developing resilient crop varieties. Wild relatives of cultivated crops, such as wild tomato, Solanum pimpinellifolium , can serve as a useful resource to further expand the resilience potential of the cultivated germplasm, S. lycopersicum . In this study, we employed high-throughput phenotyping in the greenhouse and field conditions to explore salt stress responses of a S. pimpinellifolium ersity panel. Our study revealed extensive phenotypic variations in response to salt stress, with traits such as transpiration rate, shoot mass, and ion accumulation showing significant correlations with plant performance. We found that while transpiration was a key determinant of plant performance in the greenhouse, shoot mass strongly correlated with yield under field conditions. Conversely, ion accumulation was the least influential factor under greenhouse conditions. Through a Genome Wide Association Study, we identified candidate genes not previously associated with salt stress, highlighting the power of high-throughput phenotyping in uncovering novel aspects of plant stress responses. This study contributes to our understanding of salt stress tolerance in S. pimpinellifolium and lays the groundwork for further investigations into the genetic basis of these traits, ultimately informing breeding efforts for salinity tolerance in tomato and other crops.
Investigating the effects of elevated temperature on salinity tolerance traits in grapevine rootstocks using high‐throughput phenotyping
Publisher: Hindawi Limited
Date: 22-02-2022
DOI: 10.1111/AJGW.12549
Hyperspectral imaging predicts yield and nitrogen content in grass–legume polycultures
Publisher: Springer Science and Business Media LLC
Date: 02-07-2022
Study on spike detection on cereal plants
Publisher: IEEE
Date: 12-2014
Smoothing and extraction of traits in the growth analysis of noninvasive phenotypic data
Publisher: Springer Science and Business Media LLC
Date: 10-03-2020
DOI: 10.1186/S13007-020-00577-6
Abstract: Non-destructive high-throughput plant phenotyping is becoming increasingly used and various methods for growth analysis have been proposed. Traditional longitudinal or repeated measures analyses that model growth using statistical models are common. However, often the variation in the data is inappropriately modelled, in part because the required models are complicated and difficult to fit. We provide a novel, computationally efficient technique that is based on smoothing and extraction of traits (SET), which we compare with the alternative traditional longitudinal analysis methods. The SET-based and longitudinal analyses were applied to a tomato experiment to investigate the effects on plant growth of zinc (Zn) addition and growing plants in soil inoculated with arbuscular mycorrhizal fungi (AMF). Conclusions from the SET-based and longitudinal analyses are similar, although the former analysis results in more significant differences. They showed that added Zn had little effect on plants grown in inoculated soils, but that growth depended on the amount of added Zn for plants grown in uninoculated soils. The longitudinal analysis of the unsmoothed data fitted a mixed model that involved both fixed and random regression modelling with splines, as well as allowing for unequal variances and autocorrelation between time points. A SET-based analysis can be used in any situation in which a traditional longitudinal analysis might be applied, especially when there are many observed time points. Two reasons for deploying the SET-based method are (i) biologically relevant growth parameters are required that parsimoniously describe growth, usually focussing on a small number of intervals, and/or (ii) a computationally efficient method is required for which a valid analysis is easier to achieve, while still capturing the essential features of the exhibited growth dynamics. Also discussed are the statistical models that need to be considered for traditional longitudinal analyses and it is demonstrated that the oft-omitted unequal variances and autocorrelation may be required for a valid longitudinal analysis. With respect to the separate issue of the subjective choice of mathematical growth functions or splines to characterize growth, it is recommended that, for both SET-based and longitudinal analyses, an evidence-based procedure is adopted.
Image-based phenotyping for non-destructive screening of different salinity tolerance traits in rice
Publisher: Springer Science and Business Media LLC
Date: 14-08-2014
DOI: 10.1186/S12284-014-0016-3
Abstract: Soil salinity is an abiotic stress wide spread in rice producing areas, limiting both plant growth and yield. The development of salt-tolerant rice requires efficient and high-throughput screening techniques to identify promising lines for salt affected areas. Advances made in image-based phenotyping techniques provide an opportunity to use non-destructive imaging to screen for salinity tolerance traits in a wide range of germplasm in a reliable, quantitative and efficient way. However, the application of image-based phenotyping in the development of salt-tolerant rice remains limited. A non-destructive image-based phenotyping protocol to assess salinity tolerance traits of two rice cultivars (IR64 and Fatmawati) has been established in this study. The response of rice to different levels of salt stress was quantified over time based on total shoot area and senescent shoot area, calculated from visible red-green-blue (RGB) and fluorescence images. The response of rice to salt stress (50, 75 and 100 mM NaCl) could be clearly distinguished from the control as indicated by the reduced increase of shoot area. The salt concentrations used had only a small effect on the growth of rice during the initial phase of stress, the shoot Na + accumulation independent phase termed the ‘osmotic stress’ phase. However, after 20 d of treatment, the shoot area of salt stressed plants was reduced compared with non-stressed plants. This was accompanied by a significant increase in the concentration of Na + in the shoot. Variation in the senescent area of the cultivars IR64 and Fatmawati in response to a high concentration of Na + in the shoot indicates variation in tissue tolerance mechanisms between the cultivars. Image analysis has the potential to be used for high-throughput screening procedures in the development of salt-tolerant rice. The ability of image analysis to discriminate between the different aspects of salt stress (shoot ion-independent stress and shoot ion dependent stress) makes it a useful tool for genetic and physiological studies to elucidate processes that contribute to salinity tolerance in rice. The technique has the potential for identifying the genetic basis of these mechanisms and assisting in pyramiding different tolerance mechanisms into breeding lines.
Trait dissection of salinity tolerance with plant phenomics
Publisher: Humana Press
Date: 2012
DOI: 10.1007/978-1-61779-986-0_27
Abstract: The phenotypic response of plants to high external levels of NaCl is very dynamic so the methods used for phenotyping should be able to capture those dynamics. Non-destructive high-throughput plant imaging enables researchers to measure salt stress-induced changes in plant growth over time. In addition, the color information of the digital images allows the quantification of leaf senescence induced through long-term exposure to NaCl. In combination with destructive leaf s ling to measure leaf [Na(+)], this approach allows dissection of salinity tolerance into its in idual components.
Tackling Nitrogen Use Efficiency in Cereal Crops Using High-Throughput Phenotyping
Publisher: Springer International Publishing
Date: 2018
Accounting for variation in designing greenhouse experiments with special reference to greenhouses containing plants on conveyor systems
Publisher: Springer Science and Business Media LLC
Date: 2013
A Comprehensive Image‐based Phenomic Analysis Reveals the Complex Genetic Architecture of Shoot Growth Dynamics in Rice (Oryza sativa)
Publisher: Wiley
Date: 07-2017
DOI: 10.3835/PLANTGENOME2016.07.0064
Abstract: Early vigor is an important trait for many rice ( Oryza sativa L.)‐growing environments. However, genetic characterization and improvement for early vigor is hindered by the temporal nature of the trait and strong genotype × environment effects. We explored the genetic architecture of shoot growth dynamics during the early and active tillering stages by applying a functional modeling and genomewide association (GWAS) mapping approach on a ersity panel of ∼360 rice accessions. Multiple loci with small effects on shoot growth trajectory were identified, indicating a complex polygenic architecture. Natural variation for shoot growth dynamics was assessed in a subset of 31 accessions using RNA sequencing and hormone quantification. These analyses yielded a gibberellic acid (GA) catabolic gene, OsGA2ox7 , which could influence GA levels to regulate vigor in the early tillering stage. Given the complex genetic architecture of shoot growth dynamics, the potential of genomic selection (GS) for improving early vigor was explored using all 36,901 single‐nucleotide polymorphisms (SNPs) as well as several subsets of the most significant SNPs from GWAS. Shoot growth trajectories could be predicted with reasonable accuracy using the 50 most significant SNPs from GWAS (0.37–0.53) however, the accuracy of prediction was improved by including more markers, which indicates that GS may be an effective strategy for improving shoot growth dynamics during the vegetative growth stage. This study provides insights into the complex genetic architecture and molecular mechanisms underlying early shoot growth dynamics and provides a foundation for improving this complex trait in rice.
Accurate inference of shoot biomass from high-throughput images of cereal plants
Publisher: Springer Science and Business Media LLC
Date: 02-2011
Abstract: With the establishment of advanced technology facilities for high throughput plant phenotyping, the problem of estimating plant biomass of in idual plants from their two dimensional images is becoming increasingly important. The approach predominantly cited in literature is to estimate the biomass of a plant as a linear function of the projected shoot area of plants in the images. However, the estimation error from this model, which is solely a function of projected shoot area, is large, prohibiting accurate estimation of the biomass of plants, particularly for the salt-stressed plants. In this paper, we propose a method based on plant specific weight for improving the accuracy of the linear model and reducing the estimation bias (the difference between actual shoot dry weight and the value of the shoot dry weight estimated with a predictive model). For the proposed method in this study, we modeled the plant shoot dry weight as a function of plant area and plant age. The data used for developing our model and comparing the results with the linear model were collected from a completely randomized block design experiment. A total of 320 plants from two bread wheat varieties were grown in a supported hydroponics system in a greenhouse. The plants were exposed to two levels of hydroponic salt treatments (NaCl at 0 and 100 mM) for 6 weeks. Five harvests were carried out. Each time 64 randomly selected plants were imaged and then harvested to measure the shoot fresh weight and shoot dry weight. The results of statistical analysis showed that with our proposed method, most of the observed variance can be explained, and moreover only a small difference between actual and estimated shoot dry weight was obtained. The low estimation bias indicates that our proposed method can be used to estimate biomass of in idual plants regardless of what variety the plant is and what salt treatment has been applied. We validated this model on an independent set of barley data. The technique presented in this paper may extend to other plants and types of stresses.
GWAS reveals the genetic complexity of fructan accumulation patterns in barley grain
Publisher: Cold Spring Harbor Laboratory
Date: 29-06-2020
DOI: 10.1101/2020.06.29.177881
Abstract: We profiled the grain oligosaccharide content of 154 two-row spring barley genotypes and quantified 27 compounds, mainly fructans, that exhibited differential abundance. Clustering revealed two major profile groups where the ‘high’ set contained greater amounts of sugar monomers, sucrose and overall fructans, but lower fructosylraffinose. GWAS identified a significant association for the variability of two fructan types neoseries-DP7 and inulin-DP9 which showed increased strength when a compound-ratio GWAS was applied. Gene models within this region included five fructan biosynthesis genes, of which three ( fructan:fructan 1-fructosyltransferase , s ucrose:sucrose 1-fructosyltransferase , and s ucrose:fructan 6-fructosyltransferase) have already been described. The remaining two, 6(G)-fructosyltransferase and vacuolar invertase1 have not previously been linked to fructan biosynthesis in barley and showed expression patterns distinct from those of the other three genes, including exclusive expression of 6(G)-fructosyltransferase in outer grain tissues at the storage phase. From exome capture data several SNPs related to inulin- and neoseries-type fructan variability were identified in fructan:fructan 1-fructosyltransferase and 6(G)-fructosyltransferase genes Co-expression analyses uncovered potential regulators of fructan biosynthesis including transcription factors. Our results provide evidence for the distinct biosynthesis of neoseries-type fructans during barley grain maturation plus new gene candidates likely involved in the differential biosynthesis of the various fructan types. Grain fructan profiles in barley are more complex than previously expected and variations in a ersity panel relate to a genomic region where fructan biosynthesis genes cluster.
Greenhouse spatial effects detected in the barley (Hordeum vulgareL.) epigenome underlie stochasticity of DNA methylation
Publisher: Cold Spring Harbor Laboratory
Date: 21-04-2020
DOI: 10.1101/2020.04.20.051326
Abstract: Environmental cues are known to alter the methylation profile of genomic DNA, and thereby change the expression of some genes. A proportion of such modifications may become adaptive by adjusting expression of stress response genes but others been shown to be highly stochastic, even under controlled conditions. The influence of environmental flux on plants adds an additional layer of complexity that has potential to confound attempts to interpret interactions between environment, methylome and plant form. We therefore adopt a positional and longitudinal approach to study progressive changes to barley DNA methylation patterns in response to salt exposure during development under greenhouse conditions. Methylation-Sensitive Amplified Polymorphism (MSAP) and phenotypic analyses of nine erse barley varieties were grown in a randomized plot design, under two salt treatments (0 mM and 75 mM NaCl). Combining environmental, phenotypic and epigenetic data analyses, we show that at least part of the epigenetic variability, previously described as stochastic, is linked to environmental micro-variations during plant growth. Additionally, we show that differences in methylation increase with time of exposure to micro-variations in environment. We propose that subsequent epigenetic studies take into account microclimate-induced epigenetic variability.
Specific and coordinated control of indolic and aliphatic glucosinolate biosynthesis by R2R3-MYB transcription factors in Arabidopsis thaliana
Publisher: Springer Science and Business Media LLC
Date: 15-11-2008
Identification of salt tolerance QTL in a wheat RIL mapping population using destructive and non-destructive phenotyping
Publisher: CSIRO Publishing
Date: 2021
DOI: 10.1071/FP20167
Abstract: Bread wheat (Triticum aestivum L.) is one of the most important food crops, however it is only moderately tolerant to salinity stress. To improve wheat yield under saline conditions, breeding for improved salinity tolerance of wheat is needed. We have identified nine quantitative trail loci (QTL) for different salt tolerance sub-traits in a recombinant inbred line (RIL) population, derived from the bi-parental cross of Excalibur × Kukri. This population was screened for salinity tolerance subtraits using a combination of both destructive and non-destructive phenotyping. Genotyping by sequencing (GBS) was used to construct a high-density genetic linkage map, consisting of 3236 markers, and utilised for mapping QTL. Of the nine mapped QTL, six were detected under salt stress, including QTL for maintenance of shoot growth under salinity (QG(1-5).asl-5A, QG(1-5).asl-7B) sodium accumulation (QNa.asl-2A), chloride accumulation (QCl.asl-2A, QCl.asl-3A) and potassium:sodium ratio (QK:Na.asl-2DS2). Potential candidate genes within these QTL intervals were shortlisted using bioinformatics tools. These findings are expected to facilitate the breeding of new salt tolerant wheat cultivars.
A Model-Based Approach to Recovering the Structure of a Plant from Images
Publisher: Springer International Publishing
Date: 2015
High‐throughput 3D modelling to dissect the genetic control of leaf elongation in barley (Hordeum vulgare)
Publisher: Wiley
Date: 22-02-2019
DOI: 10.1111/TPJ.14225
Expression of the Arabidopsis vacuolar H+-pyrophosphatase gene (AVP1) improves the shoot biomass of transgenic barley and increases grain yield in a saline field
Publisher: Wiley
Date: 22-11-2014
DOI: 10.1111/PBI.12145
Abstract: Cereal varieties with improved salinity tolerance are needed to achieve profitable grain yields in saline soils. The expression of AVP1, an Arabidopsis gene encoding a vacuolar proton pumping pyrophosphatase (H⁺-PPase), has been shown to improve the salinity tolerance of transgenic plants in greenhouse conditions. However, the potential for this gene to improve the grain yield of cereal crops in a saline field has yet to be evaluated. Recent advances in high-throughput nondestructive phenotyping technologies also offer an opportunity to quantitatively evaluate the growth of transgenic plants under abiotic stress through time. In this study, the growth of transgenic barley expressing AVP1 was evaluated under saline conditions in a pot experiment using nondestructive plant imaging and in a saline field trial. Greenhouse-grown transgenic barley expressing AVP1 produced a larger shoot biomass compared to null segregants, as determined by an increase in projected shoot area, when grown in soil with 150 mM NaCl. This increase in shoot biomass of transgenic AVP1 barley occurred from an early growth stage and also in nonsaline conditions. In a saline field, the transgenic barley expressing AVP1 also showed an increase in shoot biomass and, importantly, produced a greater grain yield per plant compared to wild-type plants. Interestingly, the expression of AVP1 did not alter barley leaf sodium concentrations in either greenhouse- or field-grown plants. This study validates our greenhouse-based experiments and indicates that transgenic barley expressing AVP1 is a promising option for increasing cereal crop productivity in saline fields.
Effect of Rice GDP-L-Galactose Phosphorylase Constitutive Overexpression on Ascorbate Concentration, Stress Tolerance, and Iron Bioavailability in Rice
Publisher: Frontiers Media SA
Date: 03-12-2020
Abstract: Ascorbate (vitamin C) is an essential multifunctional molecule for both plants and mammals. In plants, ascorbate is the most abundant water-soluble antioxidant that supports stress tolerance. In humans, ascorbate is an essential micronutrient and promotes iron (Fe) absorption in the gut. Engineering crops with increased ascorbate levels have the potential to improve both crop stress tolerance and human health. Here, rice ( Oryza sativa L.) plants were engineered to constitutively overexpress the rice GDP-L-galactose phosphorylase coding sequence (35S- OsGGP ), which encodes the rate-limiting enzymatic step of the L-galactose pathway. Ascorbate concentrations were negligible in both null segregant (NS) and 35S- OsGGP brown rice (BR, unpolished grain), but significantly increased in 35S- OsGGP germinated brown rice (GBR) relative to NS. Foliar ascorbate concentrations were significantly increased in 35S- OsGGP plants in the vegetative growth phase relative to NS, but significantly reduced at the reproductive growth phase and were associated with reduced OsGGP transcript levels. The 35S- OsGGP plants did not display altered salt tolerance at the vegetative growth phase despite having elevated ascorbate concentrations. Ascorbate concentrations were positively correlated with ferritin concentrations in Caco-2 cells – an accurate predictor of Fe bioavailability in human digestion – exposed to in vitro digests of NS and 35S- OsGGP BR and GBR s les.
The transcription factor HIG1/MYB51 regulates indolic glucosinolate biosynthesis in Arabidopsis thaliana
Publisher: Wiley
Date: 25-04-2007
Greenhouse Spatial Effects Detected in the Barley (Hordeum vulgare L.) Epigenome Underlie Stochasticity of DNA Methylation
Publisher: Frontiers Media SA
Date: 10-09-2020
Identifying the genetic control of salinity tolerance in the bread wheat landrace Mocho de Espiga Branca
Publisher: CSIRO Publishing
Date: 04-10-2021
DOI: 10.1071/FP21140
Abstract: Salinity tolerance in bread wheat is frequently reported to be associated with low leaf sodium (Na+) concentrations. However, the Portuguese landrace, Mocho de Espiga Branca, accumulates significantly higher leaf Na+ but has comparable salinity tolerance to commercial bread wheat cultivars. To determine the genetic loci associated with the salinity tolerance of this landrace, an F2 mapping population was developed by crossing Mocho de Espiga Branca with the Australian cultivar Gladius. The population was phenotyped for 19 salinity tolerance subtraits using both non-destructive and destructive techniques. Genotyping was performed using genotyping-by-sequencing (GBS). Genomic regions associated with salinity tolerance were detected on chromosomes 1A, 1D, 4B and 5A for the subtraits of relative and absolute growth rate (RGR, AGR respectively), and on chromosome 2A, 2B, 4D and 5D for Na+, potassium (K+) and chloride (Cl−) accumulation. Candidate genes that encode proteins associated with salinity tolerance were identified within the loci including Na+/H+ antiporters, K+ channels, H+-ATPase, calcineurin B-like proteins (CBLs), CBL-interacting protein kinases (CIPKs), calcium dependent protein kinases (CDPKs) and calcium-transporting ATPase. This study provides a new insight into the genetic control of salinity tolerance in a Na+ accumulating bread wheat to assist with the future development of salt tolerant cultivars.
Different NaCl-Induced Calcium Signatures in the Arabidopsis thaliana Ecotypes Col-0 and C24
Publisher: Public Library of Science (PLoS)
Date: 27-02-2015
Genetic Determinants of Salinity Tolerance in Crop Plants
Publisher: Wiley
Date: 20-10-2009
Integrating Image-Based Phenomics and Association Analysis to Dissect the Genetic Architecture of Temporal Salinity Responses in Rice
Publisher: Oxford University Press (OUP)
Date: 25-06-2015
DOI: 10.1104/PP.15.00450
Exploring genetic variation for salinity tolerance in chickpea using image-based phenotyping
Publisher: Springer Science and Business Media LLC
Date: 02-05-2017
DOI: 10.1038/S41598-017-01211-7
Abstract: Soil salinity results in reduced productivity in chickpea. However, breeding for salinity tolerance is challenging because of limited knowledge of the key traits affecting performance under elevated salt and the difficulty of high-throughput phenotyping for large, erse germplasm collections. This study utilised image-based phenotyping to study genetic variation in chickpea for salinity tolerance in 245 erse accessions. On average salinity reduced plant growth rate (obtained from tracking leaf expansion through time) by 20%, plant height by 15% and shoot biomass by 28%. Additionally, salinity induced pod abortion and inhibited pod filling, which consequently reduced seed number and seed yield by 16% and 32%, respectively. Importantly, moderate to strong correlation was observed for different traits measured between glasshouse and two field sites indicating that the glasshouse assays are relevant to field performance. Using image-based phenotyping, we measured plant growth rate under salinity and subsequently elucidated the role of shoot ion independent stress (resulting from hydraulic resistance and osmotic stress) in chickpea. Broad genetic variation for salinity tolerance was observed in the ersity panel with seed number being the major determinant for salinity tolerance measured as yield. This study proposes seed number as a selection trait in breeding salt tolerant chickpea cultivars.
Meeting the Challenges Facing Wheat Production: The Strategic Research Agenda of the Global Wheat Initiative
Publisher: MDPI AG
Date: 07-11-2022
Abstract: Wheat occupies a special role in global food security since, in addition to providing 20% of our carbohydrates and protein, almost 25% of the global production is traded internationally. The importance of wheat for food security was recognised by the Chief Agricultural Scientists of the G20 group of countries when they endorsed the establishment of the Wheat Initiative in 2011. The Wheat Initiative was tasked with supporting the wheat research community by facilitating collaboration, information and resource sharing and helping to build the capacity to address challenges facing production in an increasingly variable environment. Many countries invest in wheat research. Innovations in wheat breeding and agronomy have delivered enormous gains over the past few decades, with the average global yield increasing from just over 1 tonne per hectare in the early 1960s to around 3.5 tonnes in the past decade. These gains are threatened by climate change, the rapidly rising financial and environmental costs of fertilizer, and pesticides, combined with declines in water availability for irrigation in many regions. The international wheat research community has worked to identify major opportunities to help ensure that global wheat production can meet demand. The outcomes of these discussions are presented in this paper.
Evaluation of commercial composts and potting mixes and their ability to support arbuscular mycorrhizal fungi with maize (Zea mays) as host plant
Publisher: Elsevier BV
Date: 10-2021
Comparison of Leaf Sheath Transcriptome Profiles with Physiological Traits of Bread Wheat Cultivars under Salinity Stress
Publisher: Public Library of Science (PLoS)
Date: 05-08-2015
High-throughput, image-based phenotyping reveals nutrient-dependent growth facilitation in a grass-legume mixture
Publisher: Public Library of Science (PLoS)
Date: 07-10-2020
Enhancement of sorghum grain yield and nutrition: A role for arbuscular mycorrhizal fungi regardless of soil phosphorus availability
Publisher: Wiley
Date: 14-10-2021
DOI: 10.1002/PPP3.10224
Abstract: Sorghum is an important cereal crop that provides calories and nutrients for much of the world's population, and it is often grown with low fertiliser input. Optimising the yield, nutritive content and bioavailability of sorghum grain with minimal input is of importance for human nutrition, and arbuscular mycorrhizal (AM) fungi have previously shown potential to assist in this. Across sorghum genetic ersity, AM fungi improved the yield, nutrition and zinc and iron bioavailability of grain in a low phosphorus soil. Thus, food production systems that effectively manage AM fungi may improve consumer outcomes. Sorghum is a C 4 cereal crop that is an important source of calories and nutrition across the world, predominantly cultivated and consumed in low‐ and middle‐income countries. Sorghum can be highly colonised by arbuscular mycorrhizal (AM) fungi, and the plant‐fungal association can lead to improvements in biomass and nutrient uptake. High‐throughput phenotyping allows us to non‐destructively interrogate the ‘hidden’ effects of AM fungi on sorghum growth and phenology. Eight genetically erse sorghum genotypes were grown in a soil amended with 2 or 20 mg P kg −1 and inoculated with an AM fungal culture of Rhizophagus irregularis . High‐throughput phenotyping uncovered the ‘hidden’ effects of AM fungi on growth and phenology, while grain biomass, nutrition, Zn and Fe bioavailability and root AM colonisation was determined after destructive harvest. Sorghum plants colonised by AM fungi generally performed better than non‐AM control plants, with greater yield, harvest indices, and grain P, Zn and Fe contents. During the early growth stages, AM colonisation led to temporary growth depressions. There were also AM fungal and P fertilisation effects on sorghum time‐of‐flowering. The sorghum genotype with the highest AM colonisation could barely produce grain when non‐inoculated. The two genotypes that failed to mature had very low AM colonisation. Generally, the genetically erse sorghum genotypes were highly responsive to AM colonisation and produced more grain of greater nutritive quality when colonised, without adverse consequences for micronutrient bioavailability.
Genome-wide association of barley plant growth under drought stress using a nested association mapping population
Publisher: Springer Science and Business Media LLC
Date: 11-04-2019
Applications of high-throughput plant phenotyping to study nutrient use efficiency
Publisher: Humana Press
Date: 10-2013
Resource allocation to growth or luxury consumption drives mycorrhizal responses
Publisher: Wiley
Date: 08-2019
DOI: 10.1111/ELE.13353
Abstract: Highly variable phenotypic responses in mycorrhizal plants challenge our functional understanding of plant-fungal mutualisms. Using non-invasive high-throughput phenotyping, we observed that arbuscular mycorrhizal (AM) fungi relieved phosphorus (P) limitation and enhanced growth of Brachypodium distachyon under P-limited conditions, while photosynthetic limitation under low nitrogen (N) was exacerbated by the fungus. However, these responses were strongly dependent on host genotype: only the faster growing genotype (Bd3-1) utilised P transferred from the fungus to achieve improved growth under P-limited conditions. Under low N, the slower growing genotype (Bd21) had a carbon and N surplus that was linked to a less negative growth response compared with the faster growing genotype. These responses were linked to the regulation of N : P stoichiometry, couples resource allocation to growth or luxury consumption in erse plant lineages. Our results attest strongly to a mechanism in plants by which plant genotype-specific resource economics drive phenotypic outcomes during AM symbioses.
Identification of salt tolerance QTL in a wheat RIL mapping population using destructive and non-destructive phenotyping (vol 48, pg 131, 2021)
Publisher: CSIRO Publishing
Date: 08-06-2022
DOI: 10.1071/FP20167_CO
Abstract: Bread wheat ( italic Triticum aestivum /italic L.) is one of the most important food crops, however it is only moderately tolerant to salinity stress. To improve wheat yield under saline conditions, breeding for improved salinity tolerance of wheat is needed. We have identified nine quantitative trail loci (QTL) for different salt tolerance sub-traits in a recombinant inbred line (RIL) population, derived from the bi-parental cross of Excalibur & #xd7 Kukri. This population was screened for salinity tolerance subtraits using a combination of both destructive and non-destructive phenotyping. Genotyping by sequencing (GBS) was used to construct a high-density genetic linkage map, consisting of 3236 markers, and utilised for mapping QTL. Of the nine mapped QTL, six were detected under salt stress, including QTL for maintenance of shoot growth under salinity ( italic QG /italic sub ( /sub italic sub -5 /sub /italic sub ) /sub italic .asl /italic - italic A /italic , italic QG /italic sub ( /sub italic sub -5 /sub /italic sub ) /sub italic .asl /italic - italic B /italic ) sodium accumulation ( italic QNa.asl /italic - italic A /italic ), chloride accumulation ( italic QCl.asl /italic - italic A /italic , italic QCl.asl /italic - italic A /italic ) and potassium& #x2009 :& #x2009 sodium ratio ( italic QK /italic : italic Na.asl /italic - italic DS2 /italic ). Potential candidate genes within these QTL intervals were shortlisted using bioinformatics tools. These findings are expected to facilitate the breeding of new salt tolerant wheat cultivars. /abstract abstract abstract-type="toc" Soil salinity causes major yield losses in bread wheat, which is moderately tolerant to salinity stress. Using high throughput genotyping and phenotyping techniques, we identified quantitative trail loci (QTL) for different salt tolerance sub-traits in bread wheat and shortlisted potential candidate genes. These QTL and candidate genes may prove useful in breeding for salt tolerant wheat cultivars.
Investigating glutamate receptor‐like gene co‐expression in Arabidopsis thaliana
Publisher: Wiley
Date: 05-03-2008
DOI: 10.1111/J.1365-3040.2008.01801.X
Abstract: There is increasing evidence of the important roles of glutamate receptors (GLRs) in plant development and in adaptation to stresses. However, the studies of these putative ion channels, both in planta and in Xenopus oocytes, may have been limited by our lack of knowledge of possible GLR heteromer formation in plants. We have developed a modification of the single-cell s ling technique to investigate GLR co-expression, and thus potential heteromer formation, in single cells of Arabidopsis thaliana leaves. Micro-EXpression lification (MEX) has allowed us to lify gene transcripts from a single cell, enabling expression of up to 100 gene transcripts to be assayed. We measured, on average, the transcripts of five to six different AtGLRs in a single cell. However, no consistent patterns of co-expression or cell-type-specific expression were detected, except that cells s led from the same plant showed similar expression profiles. The only discernible feature was the detection of AtGLR3.7 in every cell examined, an observation supported by GUS staining patterns in plants stably expressing promoter::uidA fusions. In addition, we found AtGLR3.7 expression in oocytes induces a Ba2+-, Ca2+- and Na+-permeable plasma membrane conductance.
High-throughput phenotyping reveals growth of Medicago truncatula is positively affected by arbuscular mycorrhizal fungi even at high soil phosphorus availability
Publisher: Wiley
Date: 03-04-2021
DOI: 10.1002/PPP3.10101
Abstract: Arbuscular mycorrhizal fungi (AMF) may contribute to enhanced yield and nutrition of host plants for the purpose of sustainable agriculture. However, the growth response of the host plant to mycorrhizal colonization is generally only measured at harvest, and thus management decisions regarding AMF are made using only a single time point. This study highlights that AMF can provide growth benefits to the host plant over its life. Greater knowledge of how plants respond to AMF over time will improve understanding of how the association functions and ultimately lead to improved management decisions regarding AMF in an agricultural context. Summary Colonization by arbuscular mycorrhizal fungi (AMF) can result in variable responses in the growth and mineral nutrition of host plants, and is highly dependent on soil nutrient condition limited studies have addressed the effects of AMF on plant growth over time. The aim of this study was to investigate the AMF effects on plant growth over the life of the plant, and interactions with soil phosphorus (P) and zinc (Zn) availability. We used a high‐throughput shoot phenotyping system to examine the temporal growth responses to AMF and soil P and Zn availabilities in the pasture legume Medicago truncatula . Plants were either inoculated with Rhizophagus irregularis or mock‐inoculated, and were examined under two soil P and five soil Zn availability treatments. Plants were then destructively harvested to obtain final biomass and shoot nutrition data. The growth of M. truncatula plants over time responded very differently to AMF depending on the soil P availability. At low P, projected shoot area and absolute growth rate (AGR) became increasingly greater in the mycorrhizal plants over the course of the experiment. At high P, there was a positive growth response to AMF until approximately 40 days after planting, after which the AGR of the non‐mycorrhizal plants increased and the response to AMF became neutral. Zinc availability was highly interactive with P availability, but not with AMF inoculation. This research demonstrates that growth responses to mycorrhizal fungi change over the plant's life, and are highly dependent on soil P availability.
High-Throughput Phenotyping to Detect Drought Tolerance QTL in Wild Barley Introgression Lines
Publisher: Public Library of Science (PLoS)
Date: 13-05-2014
Hyperspectral imaging and 3D technologies for plant phenotyping: From satellite to close-range sensing
Publisher: Elsevier BV
Date: 08-2020
High-throughput phenotyping of plant shoots
Publisher: Humana Press
Date: 2012
DOI: 10.1007/978-1-61779-995-2_2
Abstract: Advances in automated plant handling and image acquisition now make it possible to use digital imaging for the high-throughput phenotyping of plants. Various traits can be extracted from in idual images. However, the potential of this technology lies in the acquisition of time series. Since whole shoot imaging is nondestructive, plants can now be monitored throughout their lifecycle, and dynamic traits such as plant growth and development can be captured and quantified. The technique is applicable to a wide range of plants and research areas and makes high-throughput screens possible, reducing the time and labor needed for the phenotypic characterization of plants.
bHLH05 Is an Interaction Partner of MYB51 and a Novel Regulator of Glucosinolate Biosynthesis in Arabidopsis
Publisher: Oxford University Press (OUP)
Date: 21-07-2014
A simplified method for the analysis of transcription factor–promoter interactions that allows high‐throughput data generation
Publisher: Wiley
Date: 08-04-2007
Germanium as a tool to dissect boron toxicity effects in barley and wheat
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/FP12329
Abstract: Tolerance to boron (B) toxicity in barley (Hordeum vulgare L.) is partially attributable to HvNIP2 , an aquaporin with permeability to B, as well as to silicon, arsenic and germanium (Ge). In this study, we mapped leaf symptoms of Ge toxicity in a doubled-haploid barley population (Clipper × Sahara 3771). Two quantitative trait loci (QTL) associated with Ge toxicity symptoms were identified, located on Chromosomes 6H and 2H. These QTL co-located with two of four B toxicity tolerance loci previously mapped in the same population. The B toxicity tolerance gene underlying the 6H locus encodes HvNIP2 , whereas the gene(s) and mechanisms underlying the 2H locus are as yet unknown. We provide ex les of the application of Ge in studying specific aspects of B toxicity tolerance in plants, including screening of wheat (Triticum aestivum L.) and barley populations for altered function of HvNIP2 and related proteins. In particular, Ge may facilitate elucidation of the mechanism and gene(s) underlying the barley Chromosome 2H B tolerance locus.
Mapping of novel salt tolerance QTL in an Excalibur × Kukri doubled haploid wheat population
Publisher: Springer Science and Business Media LLC
Date: 30-07-2018
DOI: 10.1007/S00122-018-3146-Y
Abstract: Novel QTL for salinity tolerance traits have been detected using non-destructive and destructive phenotyping in bread wheat and were shown to be linked to improvements in yield in saline fields. Soil salinity is a major limitation to cereal production. Breeding new salt-tolerant cultivars has the potential to improve cereal crop yields. In this study, a doubled haploid bread wheat mapping population, derived from the bi-parental cross of Excalibur × Kukri, was grown in a glasshouse under control and salinity treatments and evaluated using high-throughput non-destructive imaging technology. Quantitative trait locus (QTL) analysis of this population detected multiple QTL under salt and control treatments. Of these, six QTL were detected in the salt treatment including one for maintenance of shoot growth under salinity ( QG (1 – 5) .asl - 7A ), one for leaf Na + exclusion ( QNa.asl - 7A ) and four for leaf K + accumulation ( QK.asl - 2B.1 , QK.asl - 2B.2 , QK.asl - 5A and QK:Na.asl - 6A ). The beneficial allele for QG (1 – 5) .asl - 7A (the maintenance of shoot growth under salinity) was present in six out of 44 mainly Australian bread and durum wheat cultivars. The effect of each QTL allele on grain yield was tested in a range of salinity concentrations at three field sites across 2 years. In six out of nine field trials with different levels of salinity stress, lines with alleles for Na + exclusion and/or K + maintenance at three QTL ( QNa.asl - 7A , QK.asl - 2B.2 and QK:Na.asl - 6A ) excluded more Na + or accumulated more K + compared to lines without these alleles. Importantly, the QK.asl - 2B.2 allele for higher K + accumulation was found to be associated with higher grain yield at all field sites. Several alleles at other QTL were associated with higher grain yields at selected field sites.
A single nucleotide substitution in TaHKT1;5-D controls shoot Na+ accumulation in bread wheat
Publisher: Cold Spring Harbor Laboratory
Date: 24-01-2020
DOI: 10.1101/2020.01.21.909887
Abstract: Improving salinity tolerance in the most widely cultivated cereal, bread wheat ( Triticum aestivum L.), is essential to increase grain yields on saline agricultural lands. A Portuguese landrace, Mocho de Espiga Branca accumulates up to 6 folds greater leaf and sheath sodium (Na + ) than two Australian cultivars, Gladius and Scout, under salt stress. Despite high leaf and sheath Na + concentrations, Mocho de Espiga Branca maintained similar salinity tolerance compared to Gladius and Scout. A naturally occurring single nucleotide substitution was identified in the gene encoding a major Na + transporter TaHKT1 -D in Mocho de Espiga Branca, which resulted in a L190P amino acid residue variation. This variant prevents Mocho de Espiga Branca from retrieving Na + from the root xylem leading to a high shoot Na + concentration. The identification of the tissue tolerant Mocho de Espiga Branca will accelerate the development of more elite salt tolerant bread wheat cultivars.
Integrating Ecological Stoichiometry to Understand Nutrient Limitation and Potential for Competition in Mixed Pasture Assemblages
Publisher: Springer Science and Business Media LLC
Date: 29-06-2021
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Linkage Infrastructure, Equipment And Facilities - Grant ID: LE230100107
Start Date: 2023
End Date: 06-2024
Amount: $1,042,177.00
Funder: Australian Research Council
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