ORCID Profile
0000-0002-9145-052X
Current Organisation
University of Adelaide
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Publisher: Wiley
Date: 15-02-2022
Publisher: Springer Science and Business Media LLC
Date: 26-07-2019
Publisher: Frontiers Media SA
Date: 29-03-2021
Abstract: Heat stress at booting stage causes significant losses to floret fertility (grain set) and hence yield in wheat ( Triticum aestivum L.) however, there is a lack of well-characterized sources of tolerance to this type of stress. Here, we describe the genetic analysis of booting stage heat tolerance in a cross between the Australian cultivars Drysdale (intolerant) and Waagan (tolerant), leading to the definition of a major-effect tolerance locus on the short arm of chromosome 2B, Wheat thermosensitive male sterile Drysdale/Waagan ( WtmsDW ). WtmsDW offsets between 44 and 65% of the losses in grain set due to heat, suggesting that it offers significant value for marker-assisted tolerance breeding. In lines lacking the WtmsDW tolerance allele, peaks in sensitivity were defined with reference to auricle distance, for various floret positions along the spike. Other (relatively minor) floret fertility response effects, including at the Rht-D1 dwarfing locus, were considered likely escape artifacts, due to their association with height and flowering time effects that might interfere with correct staging of stems for heat treatment. Heat stress increased grain set at distal floret positions in spikelets located at the top of the spike and increased the size of spikelets at the base of the spike, but these effects were offset by greater reductions in grain set at other floret positions. Potentially orthologous loci on chromosomes 1A and 1B were identified for heat response of flowering time. The potential significance of these findings for tolerance breeding and further tolerance screening is discussed.
Publisher: Oxford University Press (OUP)
Date: 13-06-2018
Abstract: The giant Australian cuttlefish, Sepia apama, forms a dense spawning aggregation at a single known location across its wide southern Australian distribution. After a rapid increase in fishing pressure on the aggregation in the late 1990s, a series of fishing closures were introduced before any biological information could be collected. We surveyed the habitats, timing, and spatial distribution of the spawning aggregation over 4 years, using underwater visual transects and passive tagging, to assess the suitability of the closures. We found that the annual aggregation was both temporally (April–August) and spatially (over 8 km of coastline) localized and predictable, with a consistent peak in abundances in late May–early June. Cuttlefish densities were generally highest over the shallow, broken bedrock habitat, which was more extensive in several sites left open to fishing. Although the original closure covered about 43% of the hard substrate, it accounted for only 23–37% of the total cuttlefish abundance. The extremely high densities recorded during this study verified that this is a massive spawning aggregation for cuttlefish species worldwide, and that it could be highly vulnerable to overexploitation in the absence of adequate protection, because it is so spatiotemporally predictable and localized.
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.
Publisher: Foundation for Open Access Statistic
Date: 2011
Publisher: Springer Science and Business Media LLC
Date: 12-2021
Publisher: Springer Science and Business Media LLC
Date: 14-09-2017
Publisher: Public Library of Science (PLoS)
Date: 03-06-2014
Publisher: Springer Science and Business Media LLC
Date: 22-04-2016
Publisher: CSIRO Publishing
Date: 2014
DOI: 10.1071/FP14060
Abstract: High temperatures during grain filling can reduce the yield of wheat and affect its grain protein concentration. The Gpc-B1 locus of wheat also affects grain protein concentration, but it is not known whether its effects interact with those of heat. The aim of this study was to investigate the effects of high temperature in lines with and without functional (high-protein) alleles at Gpc-B1. A highly replicated experiment was conducted in a glasshouse under control conditions (24/18°C, 14/10 h day/night), with half of the plants of each line or cultivar put into a heat chamber (37/27°C, 14/10 h day/night) at 15 days after anthesis for 3 days. Backcross derivatives with the Gpc-B1 introgression segment differed from their recurrent parents more than those without that segment. In some respects, the effects of the Gpc-B1 introgression were similar to those of the heat treatment: both could accelerate peduncle senescence, increase grain protein content and increase the percentage of unextractable polymeric protein. Unlike the heat treatment, Gpc-B1 did not reduce grain weight, indicating that factors that hasten senescence do not necessarily limit grain size. The presence of the Gpc-B1 segment did not exacerbate the effects of heat stress on any trait.
Publisher: Foundation for Open Access Statistic
Date: 2017
Publisher: Wiley
Date: 22-02-2019
DOI: 10.1111/TPJ.14225
Publisher: Hindawi Limited
Date: 07-10-2016
DOI: 10.1111/AJGW.12163
Publisher: Frontiers Media SA
Date: 03-10-2022
Abstract: International production of chickpea is under constant threat from the fungal disease Ascochyta blight ( Ascochyta rabiei ). In Australia, there is limited cultivar resistance, and disease management is reliant on foliar applied fungicides. Several recently registered fungicides in Australia that combine active ingredients with different modes of actions, have been shown to have curative properties. In this study, in the presence of Ascochyta blight, disease severity, grain yield and quality were measured and the subsequent gross margin for growers calculated in seven field experiments conducted in Victoria (Australia) across three seasons. These experiments investigated the effects of: two cultivars with differing disease resistance (PBA Striker and Genesis 090), and several fungicide strategies for the control of Ascochyta blight. Fungicides that combine different modes of actions (Tebuconazole + Azoxystrobin, Bixafen + Prothioconazole and Fludioxonil + Pydiflumetofen) were applied before a rainfall event (preventative) or after the first signs of disease (post-infection). Older, single active fungicides compared included Captan, Chlorothalonil, and Propiconazole, all applied preventatively. Maximum disease severities ranged from 87% at Horsham and 94% at Curyo across three seasons with Nhill recording 87% during 2020. Demonstrating the benefit of cultivar resistance for Ascochyta blight management, grain yield losses were substantially lower in the partially resistant cultivar Genesis 090 (64%) compared to the susceptible cultivar PBA Striker (96%), at Curyo in 2020. The preventative fungicide strategies reduced grain yield losses from 96 and 64% to 51 and 15% for PBA Striker and Genesis 090, respectively, demonstrating the benefit of fungicides in Ascochyta blight management. Across seasons and environments, a comparison between fungicides applied preventatively or post-infection highlighted both were both profitable ($23–$1,095/ha), except when dry conditions limited grain yield to less than 0.6 t/ha. The post infection timing had greater yield losses in sites/seasons with higher rainfall, but with dual active ingredient fungicides and partially resistant cultivars this timing could allow a reduction in the number of fungicide applications, thus improving profitability. These experiments highlighted the importance of controlling Ascochyta blight through cultivar resistance and fungicides to improve grain yields, grain quality, and grower profitability.
Publisher: Wiley
Date: 12-2012
Publisher: Springer Science and Business Media LLC
Date: 22-05-2010
DOI: 10.1007/S00122-010-1352-3
Abstract: The genetic and phenotypic relationships among wheat quality predictors and sponge and dough bread making were evaluated in a population derived from a cross between an Australian cultivar 'Chara' and a Canadian cultivar 'Glenlea'. The genetic correlation across sites for sponge and dough loaf volume was high however, phenotypic correlations across sites for loaf volume were relatively low compared with rheological tests. The large difference between sites was most likely due to temperature differences during grain development reflected in a decrease in the percentage of unextractable polymeric protein and mixing time. Predictive tests (mixograph, extensograph, protein content and composition, micro-zeleny and flour viscosity) showed inconsistent and generally poor correlations with end-product performance (baking volume and slice area) at both sites, with no single parameter being effective as a predictor of end-product performance. The difference in the relationships between genetic and phenotypic correlations highlights the requirement to develop alternative methods of selection for breeders and bakers in order to maximise both genetic gain and predictive assessment of grain quality.
Publisher: SAGE Publications
Date: 07-2004
DOI: 10.1191/1471082X04ST068OA
Abstract: Joint modelling of location and scale parameters has generally been confined to exponential families. In this paper the location and scale parameters of the t distribution are allowed to depend on covariates. The closed form of the likelihood allows inference to proceed in a similar fashion to the Gaussian location and scale model and provides a framework for a simple scoring algorithm to estimate the parameters. The algorithm includes a procedure to estimate the degrees of freedom parameter of the t distribution. Homogeneity and asymptotic tests are discussed and a methodology is derived to detect heteroscedasticity when the response is t distributed. Simulations reveal considerable bias in the estimates of the degrees of freedom parameter and only minor bias in the estimated fixed effects associated with the scale parameter. In comparison, the estimated location effects are well behaved. To illustrate the joint modelling of location and scale parameters of the t distribution the methodology is applied to two data sets.
Publisher: Frontiers Media SA
Date: 22-10-2019
Publisher: Hindawi Limited
Date: 12-2012
DOI: 10.1017/S0016672312000493
Abstract: Mapping of quantitative trait loci (QTLs) underlying variation in quantitative traits continues to be a powerful tool in genetic study of plants and other organisms. Whole genome average interval mapping (WGAIM), a mixed model QTL mapping approach using all intervals or markers simultaneously, has been demonstrated to outperform composite interval mapping, a common approach for QTL analysis. However, the advent of high-throughput high-dimensional marker platforms provides a challenge. To overcome this, a dimension reduction technique is proposed for WGAIM for efficient analysis of a large number of markers. This approach results in reduced computing time as it is dependent on the number of genetic lines (or in iduals) rather than the number of intervals (or markers). The approach allows for the full set of potential QTL effects to be recovered. A proposed random effects version of WGAIM aims to reduce bias in the estimated size of QTL effects. Lastly, the two-stage outlier procedure used in WGAIM is replaced by a single stage approach to reduce possible bias in the selection of putative QTL in both WGAIM and the random effects version. Simulation is used to demonstrate the efficiency of the dimension reduction approach as well as demonstrate that while the approaches are very similar, the random WGAIM performs better than the original and modified fixed WGAIM by reducing bias and in terms of mean square error of prediction of estimated QTL effects. Finally, an analysis of a doubled haploid population is used to illustrate the three approaches.
Publisher: Wiley
Date: 22-01-2018
DOI: 10.1002/CCHE.10027
Publisher: Oxford University Press (OUP)
Date: 07-06-2019
DOI: 10.1093/AOB/MCZ094
Abstract: High exchangeable sodium percentage (ESP) and bulk density of sodic soils can reduce seedling emergence. This study examined variation in seedling coleoptile length and seminal root angle of wheat (Triticum aestivum. L) genotypes to determine whether these traits vary between genotypes that differ in their tolerance to sodic soils. Wheat genotypes were grown in three different experiments. First, four wheat genotypes were grown using soils of three ESPs (4, 10 and 17 %) and secondly in soils of three different bulk densities (1.2, 1.4 and 1.5 g cm–3) and ESP 10 %. Thirdly, seedling coleoptile length and seminal root angle were determined for 16 genotypes grown in a soil of ESP 10 % and bulk density 1.2 g cm–2. Seminal root angle and coleoptile length measurements from the current study were compared with seedling emergence rate and force measured previously. The seedling coleoptile length of all genotypes decreased with increasing soil ESP and bulk density, but with no significant differences between genotypes. In contrast, seminal root angles differed significantly between genotypes, but were not significantly affected by ESP or bulk density. There was an inverse relationship between the seminal root angle of the 16 genotypes and seedling emergence rate (R2 = 0.89) and also between seminal root angle and seedling emergence force (R2 = 0.61). Lack of significant variation in coleoptile length between genotypes suggests that this may not be a suitable characteristic to identify wheat tolerance to sodic conditions. However, a narrower seminal root angle was correlated with rate and force of seedling emergence, traits likely to improve establishment. The mechanism underlying this correlation is not yet clear. Genotypes with a narrow root angle had greater root depth. One possible mechanism might be that genotypes with narrow root angles were able to take up more soil moisture at depth, leading to a higher proportion of seedling emergence.
Publisher: Springer Science and Business Media LLC
Date: 31-08-2020
Publisher: Elsevier BV
Date: 04-2015
DOI: 10.1016/J.PLANTSCI.2015.01.008
Abstract: Mapping of quantitative trait loci associated with levels of in idual metabolites (mQTL) was combined with the mapping of agronomic traits to investigate the genetic basis of variation and co-variation in metabolites, agronomic traits, and plant phenology in a field-grown bread wheat population. Metabolome analysis was performed using liquid chromatography-mass spectrometry resulting in identification of mainly polar compounds, including secondary metabolites. A total of 558 metabolic features were obtained from the flag leaves of 179 doubled haploid lines, of which 197 features were putatively identified, mostly as alkaloids, flavonoids and phenylpropanoids. Coordinated genetic control was observed for several groups of metabolites, such as organic acids influenced by two loci on chromosome 7A. Five major phenology-related loci, which were introduced as cofactors in the analyses, differed in their impact upon metabolic and agronomic traits with QZad-aww-7A having more impact on the expression of both metabolite and agronomic QTL than Ppd-B1, Vrn-A1, Eps, and QZad-aww-7D. This QTL study validates the utility of combining agronomic and metabolomic traits as an approach to identify potential trait enhancement targets for breeding selection and reinforces previous results that demonstrate the importance of including plant phenology in the assessment of useful traits in this wheat mapping population.
Publisher: Oxford University Press (OUP)
Date: 2022
DOI: 10.1093/GIGASCIENCE/GIAC038
Abstract: In diploid organisms, whole-genome haplotype assembly relies on the accurate identification and assignment of heterozygous single-nucleotide polymorphism alleles to the correct homologous chromosomes. This appropriate phasing of these alleles ensures that combinations of single-nucleotide polymorphisms on any chromosome, called haplotypes, can then be used in downstream genetic analysis approaches including determining their potential association with important phenotypic traits. A number of statistical algorithms and complementary computational software tools have been developed for whole-genome haplotype construction from genomic sequence data. However, many algorithms lack the ability to phase long haplotype blocks and simultaneously achieve a competitive accuracy. In this research we present HaploMaker, a novel reference-based haplotype assembly algorithm capable of accurately and efficiently phasing long haplotypes using paired-end short reads and longer Pacific Biosciences reads from diploid genomic sequences. To achieve this we frame the problem as a directed acyclic graph with edges weighted on read evidence and use efficient path traversal and minimization techniques to optimally phase haplotypes. We compared the HaploMaker algorithm with 3 other common reference-based haplotype assembly tools using public haplotype data of human in iduals from the Platinum Genome project. With short-read sequences, the HaploMaker algorithm maintained a competitively low switch error rate across all haplotype lengths and was superior in phasing longer genomic regions. For longer Pacific Biosciences reads, the phasing accuracy of HaploMaker remained competitive for all block lengths and generated substantially longer block lengths than the competing algorithms. HaploMaker provides an improved haplotype assembly algorithm for diploid genomic sequences by accurately phasing longer haplotypes. The computationally efficient and portable nature of the Java implementation of the algorithm will ensure that it has maximal impact in reference-sequence–based haplotype assembly applications.
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/AN15172
Abstract: Beef cattle reproductive rate in northern Australia is low and substantial effort is underway to make improvements. Collection of calf birth date to inform female reproductive rate data is often not practical. Therefore, there is a need to find alternative methods for collecting birth date data. The aim of the project was to trial an automated animal weighing technology (walk over weigh) to estimate calving date for cows in a northern breeding herd grazing in an extensive pasture system. Two-hundred and thirty-two Wagyu cows from a herd of 1195 with confirmed pregnancy tests were stocked in a paddock with a walk over weigh unit at the entry point of the water yard. Each calf born in the paddock was weighed, ear-tagged and a DNA s le collected. After processing, cleaning and smoothing the data, weight profiles of the 232 cows over a 119-day period were analysed. From the weight profiles and confirmed DNA parentage, 96 out of a possible 162 (59%) cows that calved had a correct calving date prediction. It is proposed that improvements in calving date prediction could be increased through engineering changes designed to slow cow movement over the walk over weigh unit. The trial demonstrated with the proposed changes that walk over weigh could be used to estimate calving date in extensive beef herds, with the expectation that this information could be used in genetic evaluation to improve reproductive rate in northern Australia.
Publisher: Unpublished
Date: 2019
Publisher: Springer Science and Business Media LLC
Date: 08-09-2017
Publisher: Springer Science and Business Media LLC
Date: 07-12-2020
DOI: 10.1007/S00122-019-03495-X
Abstract: Resistance QTL to root lesion nematode (Pratylenchus thornei) in wheat (Triticum aestivum), QRlnt.sk-6D and QRlnt.sk-2B, were mapped to intervals of 3.5 cM/1.77 Mbp on chromosome 6D and 1.4 cM/2.19 Mbp on chromosome 2B, respectively. Candidate resistance genes were identified in the QTL regions and molecular markers developed for marker-assisted breeding. Two previously known resistance QTL for root lesion nematode (Pratylenchus thornei) in bread wheat (Triticum aestivum), QRlnt.sk-6D and QRlnt.sk-2B, were fine-mapped using a Sokoll (moderately resistant) by Krichauff (susceptible) doubled haploid (DH) population and six newly developed recombinant inbred line populations. Bulked segregation analysis with the 90K wheat SNP array identified linked SNPs which were subsequently converted to KASP assays for mapping in the DH and RIL populations. On chromosome 6D, 60 KASP and five SSR markers spanned a total genetic distance of 23.7 cM. QRlnt.sk-6D was delimited to a 3.5 cM interval, representing 1.77 Mbp in the bread wheat cv. Chinese Spring reference genome sequence and 2.29 Mbp in the Aegilops tauschii genome sequence. These intervals contained 42 and 43 gene models in the respective annotated genome sequences. On chromosome 2B, 41 KASP and 5 SSR markers produced a map spanning 19.9 cM. QRlnt.sk-2B was delimited to 1.4 cM, corresponding 3.14 Mbp in the durum wheat cv. Svevo reference sequence and 2.19 Mbp in Chinese Spring. The interval in Chinese Spring contained 56 high-confidence gene models. Intervals for both QTL contained genes with similarity to those previously reported to be involved in disease resistance, namely genes for phenylpropanoid biosynthetic pathway-related enzymes, NBS-LRR proteins and protein kinases. The potential roles of these candidate genes in P. thornei resistance are discussed. The KASP markers reported in this study could potentially be used for marker-assisted breeding of P. thornei-resistant wheat cultivars.
Publisher: Springer Science and Business Media LLC
Date: 20-04-2014
DOI: 10.1007/S00122-014-2308-9
Abstract: A whole genome average interval mapping approach identified eight QTL associated with P. thornei resistance in a DH population from a cross between the synthetic-derived wheat Sokoll and cultivar Krichauff. Pratylenchus thornei are migratory nematodes that feed and reproduce within the wheat root cortex, causing cell death (lesions) resulting in severe yield reductions globally. Genotypic selection using molecular markers closely linked to Pratylenchus resistance genes will accelerate the development of new resistant cultivars by reducing the need for laborious and expensive resistance phenotyping. A doubled haploid wheat population (150 lines) from a cross between the synthetic-derived cultivar Sokoll (P. thornei resistant) and cultivar Krichauff (P. thornei moderately susceptible) was used to identify quantitative trait loci (QTL) associated with P. thornei resistance. The resistance identified in the glasshouse was validated in a field trial. A genetic map was constructed using Diversity Array Technology and the QTL regions identified were further targeted with simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers. Six significant and two suggestive P. thornei resistance QTL were detected using a whole genome average interval mapping approach. Three QTL were identified on chromosome 2B, two on chromosome 6D, and a single QTL on each of chromosomes 2A, 2D and 5D. The QTL on chromosomes 2BS and 6DS mapped to locations previously identified to be associated with Pratylenchus resistance. Together, the QTL on 2B (QRlnt.sk-2B.1-2B.3) and 6D (QRlnt.sk-6D.1 and 6D.2) explained 30 and 48 % of the genotypic variation, respectively. Flanking PCR-based markers based on SSRs and SNPs were developed for the major QTL on 2B and 6D and provide a cost-effective high-throughput tool for marker-assisted breeding of wheat with improved P. thornei resistance.
Publisher: CSIRO Publishing
Date: 2018
DOI: 10.1071/CP17406
Abstract: Genetic improvement in phosphorus (P) use efficiency (i.e. the ratio of biomass or yield at nil P to that at a given rate of application) is an important goal to improve P recovery and P efficiency of farming systems. Experiments were conducted at three sites in South Australia between 2009 and 2011 to characterise genetic variation in yield with no applied P and in the response to P fertiliser among a erse range of barley (Hordeum vulgare L.) genotypes. In each experiment, 39–54 genotypes were grown at 0 or 30 kg P/ha. Responses to P were measured near the beginning of stem elongation by using normalised difference vegetation index (NDVI) and by harvesting the grain. Rhizosheath size was also measured on seedlings. Consistent differences in growth and yield at 0 kg P/ha were measured among the genotypes. By contrast, there were large environmental effects on responses to P, but some genotypes showed consistent responses. Measurements of growth, yield and P uptake on a subset of genotypes showed that most of the variation in biomass and yield could be attributed to variation in P-uptake efficiency (net total P uptake per unit available P) rather than to P-utilisation efficiency (biomass or yield per unit total P uptake). The size of the rhizosheath made a small contribution to variation in NDVI but not grain yield, suggesting that rhizosheath size may be of some benefit to early growth but that this does not persist through to yield. Genetic correlations between NDVI and yield were often weak but were generally positive at 0 kg P/ha. Correlations between responses in NDVI and responses in grain yield were low and often negative. The study identified several barley genotypes that showed consistent differences in yield at low P and responses to P however, selection for P efficiency based solely on responses in vegetative growth may not be appropriate. Variation in P uptake appeared to be more important than P-utilisation efficiency for P efficiency in barley.
Publisher: Oxford University Press (OUP)
Date: 09-2018
Abstract: Genomic selection applied to plant breeding enables earlier estimates of a line’s performance and significant reductions in generation interval. Several factors affecting prediction accuracy should be well understood if breeders are to harness genomic selection to its full potential. We used a panel of 10,375 bread wheat (Triticum aestivum) lines genotyped with 18,101 SNP markers to investigate the effect and interaction of training set size, population structure and marker density on genomic prediction accuracy. Through assessing the effect of training set size we showed the rate at which prediction accuracy increases is slower beyond approximately 2,000 lines. The structure of the panel was assessed via principal component analysis and K-means clustering, and its effect on prediction accuracy was examined through a novel cross-validation analysis according to the K-means clusters and breeding cohorts. Here we showed that accuracy can be improved by increasing the ersity within the training set, particularly when relatedness between training and validation sets is low. The breeding cohort analysis revealed that traits with higher selection pressure (lower allelic ersity) can be more accurately predicted by including several previous cohorts in the training set. The effect of marker density and its interaction with population structure was assessed for marker subsets containing between 100 and 17,181 markers. This analysis showed that response to increased marker density is largest when using a erse training set to predict between poorly related material. These findings represent a significant resource for plant breeders and contribute to the collective knowledge on the optimal structure of calibration panels for genomic prediction.
Publisher: Frontiers Media SA
Date: 28-04-2021
Abstract: A better understanding of the genetics of salinity tolerance in chickpea would enable breeding of salt tolerant varieties, offering potential to expand chickpea production to marginal, salinity-affected areas. A Recombinant Inbred Line population was developed using accelerated-Single Seed Descent of progeny from a cross between two chickpea varieties, Rupali (salt-sensitive) and Genesis836 (salt-tolerant). The population was screened for salinity tolerance using high-throughput image-based phenotyping in the glasshouse, in hydroponics, and across 2 years of field trials at Merredin, Western Australia. A genetic map was constructed from 628 unique in-silico DArT and SNP markers, spanning 963.5 cM. Markers linked to two flowering loci identified on linkage groups CaLG03 and CaLG05 were used as cofactors during genetic analysis to remove the confounding effects of flowering on salinity response. Forty-two QTL were linked to growth rate, yield, and yield component traits under both control and saline conditions, and leaf tissue ion accumulation under salt stress. Residuals from regressions fitting best linear unbiased predictions from saline conditions onto best linear unbiased predictions from control conditions provided a measure of salinity tolerance per se , independent of yield potential. Six QTL on CaLG04, CaLG05, and CaLG06 were associated with tolerance per se . In total, 21 QTL mapped to two distinct regions on CaLG04. The first distinct region controlled the number of filled pods, leaf necrosis, seed number, and seed yield specifically under salinity, and co-located with four QTL linked to salt tolerance per se . The second distinct region controlled 100-seed weight and growth-related traits, independent of salinity treatment. Positional cloning of the salinity tolerance-specific loci on CaLG04, CaLG05, and CaLG06 will improve our understanding of the key determinants of salinity tolerance in chickpea.
Publisher: Springer Science and Business Media LLC
Date: 15-06-2021
DOI: 10.1038/S41598-021-91424-8
Abstract: Interactions between plants and herbivores are key drivers of evolution and ecosystem complexity. We investigated the role of plant labile carbohydrates and nitrogen on wheat-aphid relations in a 2 2 factorial combining [CO 2 ] and nitrogen supply. We measured life history traits (assay 1) and feeding behaviour (assay 2) of bird-cherry oat aphid ( Rhopalosiphum padi L.) and English grain aphid ( Sitobion avenae F.) forced to feed on single leaf laminae, and reproduction of R. padi in a setting where insects moved freely along the plant (assay 3). Experimental setting impacted aphid traits. Where aphids were constrained to single leaf, high nitrogen reduced their fitness and discouraged phloem feeding. Where aphids could move throughout the plant, high nitrogen enhanced their reproduction. Aphid responses to the interaction between nitrogen and [CO 2 ] varied with experimental setting. The number of R. padi adults varied tenfold with plant growing conditions and correlated negatively with molar concentration of sugars in stem (assay 3). This finding has two implications. First, the common interpretation that high nitrogen favours insect fitness because protein-rich animal bodies have to build from nitrogen-poor plant food needs expanding to account for the conspicuous association between low nitrogen and high concentration of labile carbohydrates in plant, which can cause osmotic stress in aphids. Second, the function of labile carbohydrates buffering grain growth needs expanding to account for the osmotic role of carbohydrates in plant resistance to aphids.
Publisher: Springer Science and Business Media LLC
Date: 20-12-2013
DOI: 10.1007/S00122-012-2015-3
Abstract: Improved mapping, multi-environment quantitative trait loci (QTL) analysis and dissection of allelic effects were used to define a QTL associated with grain yield, thousand grain weight and early vigour on chromosome 3BL of bread wheat (Triticum aestivum L.) under abiotic stresses. The QTL had pleiotropic effects and showed QTL x environment interactions across 21 erse environments in Australia and Mexico. The occurrence and the severity of water deficit combined with high temperatures during the growing season affected the responsiveness of this QTL, resulting in a reversal in the direction of allelic effects. The influence of this QTL can be substantial, with the allele from one parent (RAC875) increasing grain yield by up to 12.5 % (particularly in environments where both heat and drought stress occurred) and the allele from the other parent (Kukri) increasing grain yield by up to 9 % in favourable environments. With the application of additional markers and the genotyping of additional recombinant inbred lines, the genetic map in the QTL region was refined to provide a basis for future positional cloning.
Publisher: Frontiers Media SA
Date: 13-08-2015
Publisher: Hapres
Date: 2020
Publisher: Springer Science and Business Media LLC
Date: 03-2023
DOI: 10.1007/S00122-023-04332-Y
Abstract: Novel sources of genetic resistance to tan spot in Australia have been discovered using one-step GWAS and genomic prediction models that accounts for additive and non-additive genetic variation. Tan spot is a foliar disease in wheat caused by the fungal pathogen Pyrenophora tritici-repentis (Ptr) and has been reported to generate up to 50% yield losses under favourable disease conditions. Although farming management practices are available to reduce disease, the most economically sustainable approach is establishing genetic resistance through plant breeding. To further understand the genetic basis for disease resistance, we conducted a phenotypic and genetic analysis study using an international ersity panel of 192 wheat lines from the Maize and Wheat Improvement Centre (CIMMYT), the International Centre for Agriculture in the Dry Areas (ICARDA) and Australian (AUS) wheat research programmes. The panel was evaluated using Australian Ptr isolates in 12 experiments conducted in three Australian locations over two years, with assessment for tan spot symptoms at various plant development stages. Phenotypic modelling indicated high heritability for nearly all tan spot traits with ICARDA lines displaying the greatest average resistance. We then conducted a one-step whole-genome analysis of each trait using a high-density SNP array, revealing a large number of highly significant QTL exhibiting a distinct lack of repeatability across the traits. To better summarise the genetic resistance of the lines, a one-step genomic prediction of each tan spot trait was conducted by combining the additive and non-additive predicted genetic effects of the lines. This revealed multiple CIMMYT lines with broad genetic resistance across the developmental stages of the plant which can be utilised in Australian wheat breeding programmes to improve tan spot disease resistance.
Publisher: CSIRO Publishing
Date: 2012
DOI: 10.1071/CP12244
Abstract: Many of the soils in the Australian cereal belt have subsoils with chemical and physical properties that restrict root growth, which limits water use and yield. On alkaline sodic soils salinity, high pH, high available boron (B), deficiencies of zinc (Zn) and manganese (Mn) and high soil strength occur commonly and aluminium (Al) toxicity restricts root growth on acid soils. While the effects of in idual subsoil constraints have been studied there is some debate about the relative importance to yield of the different soil stresses across the region. To address this issue yield variation among a set of 52 varieties of bread wheat was analysed using yield data from 233 trials conducted over 12 years. The trials were conducted in all mainland States but the majority were in South Australia and Western Australia. Each variety was characterised for its response to high B, high pH, Al toxicity, salinity, deficiencies in Zn and Mn and resistance to root lesion nematode (Pratylenchus neglectus), root growth through strong soil, seminal root angle, carbon isotope discrimination (CID) and maturity. This data was then used to examine the contribution of each trait to the genetic variation in yield at each of the 233 trials. The contribution of a specific trait to the genetic variation in yield at each site was used to infer the importance of a particular constraint to yield at that site. Of the traits linked to soil constraints, salinity tolerance, (measured by Na+ exclusion) was most often associated with genetic variation in grain yield (34% of all experiments), followed by tolerance to high Al (26%) and B tolerance (21%). Tolerance to low Zn and Mn were not consistently associated with yield variation. However, maturity was the trait that was most frequently associated with yield variation (51% of experiments), although the relative importance of early and late flowering varied among the States. Yield variation was largely associated with early flowering in Western Australia and the relative importance of late flowering increased as trials moved eastward into South Australia, Victoria and New South Wales. Narrow, rather than wide, seminal root angle was more commonly associated with high yield (25% of sites) and there was little evidence of any regional pattern in the importance of root angle. CID was important in 18% of trials with a low CID being most commonly associated with high yields. The yield advantage at sites where a trait contributed significantly to yield variation ranged from ~15% for Na+ exclusion and B tolerance to 4% for tolerance to high pH. The analysis has provided an assessment of the relative importance of a range of traits associated with adaptation to environments where subsoil constraints are likely to affect yield and has indicated patterns in the importance and effects of these traits that may be linked to regional variation in rainfall and soils.
Publisher: Oxford University Press (OUP)
Date: 20-03-2016
DOI: 10.1093/JXB/ERW125
Publisher: Oxford University Press (OUP)
Date: 09-05-2013
Publisher: Public Library of Science (PLoS)
Date: 20-07-2016
Publisher: Wiley
Date: 26-11-2015
DOI: 10.1111/NPH.13757
Abstract: The separation of toxic effects of sodium (Na + ) and chloride (Cl − ) by the current methods of mixed salts and subsequent determination of their relevance to breeding has been problematic. We report a novel method (Na + humate) to study the ionic effects of Na + toxicity without interference from Cl − , and ionic and osmotic effects when combined with salinity (NaCl). Three cereal species ( Hordeum vulgare , Triticum aestivum and Triticum turgidum ssp. durum with and without the Na + exclusion gene Nax2 ) differing in Na + exclusion were grown in a potting mix under sodicity (Na + humate) and salinity (NaCl), and water use, leaf nutrient profiles and yield were determined. Under sodicity, Na + ‐excluding bread wheat and durum wheat with the Nax2 gene had higher yield than Na + ‐accumulating barley and durum wheat without the Nax2 gene. However, under salinity, despite a 100‐fold difference in leaf Na + , all species yielded similarly, indicating that osmotic stress negated the benefits of Na + exclusion. In conclusion, Na + exclusion can be an effective mechanism for sodicity tolerance, while osmoregulation and tissue tolerance to Na + and/or Cl − should be the main foci for further improvement of salinity tolerance in cereals. This represents a paradigm shift for breeding cereals with salinity tolerance.
Publisher: Springer Science and Business Media LLC
Date: 07-12-2018
DOI: 10.1007/S00122-018-3256-6
Abstract: Major QTL for Phytophthora root rot resistance have been identified in three mapping populations with independent sources of resistance contributed by C. echinospermum and C. arietinum. Phytophthora root rot (PRR) caused by the oomycete Phytophthora medicaginis is a major soil-borne disease of chickpea in Australia. With no economic in-crop control of PRR, a genetic approach to improve resistance is the most practical management option. Moderate field resistance has been incorporated in the cultivated C. arietinum variety, Yorker, and a higher level of resistance has been identified in a derivative of wild chickpea (C. echinospermum, interspecific breeding line 04067-81-2-1-1). These genotypes and two other released varieties were used to develop one intra-specific and two interspecific F
Publisher: Public Library of Science (PLoS)
Date: 26-07-2016
No related grants have been discovered for Julian Taylor.