Spectral and thermal sensing for nitrogen and water status in rainfed and irrigated wheat environments

Variable-rate technologies and site-specific crop nutrient management require real-time spatial information about the potential for response to in-season crop management interventions. Thermal and spectral properties of canopies can provide relevant information for non-destructive measurement of crop water and nitrogen stresses. In previous studies, foliage temperature was successfully estimated from canopy-scale (mixed foliage and soil) temperatures and the multispectral Canopy Chlorophyll Content Index (CCCI) was effective in measuring canopy-scale N status in rainfed wheat (Triticum aestivum L.) systems in Horsham, Victoria, Australia. In the present study, results showed that under irrigated wheat systems in Maricopa, Arizona, USA, the theoretical derivation of foliage temperature unmixing produced relationships similar to those in Horsham. Derivation of the CCCI led to an r2 relationship with chlorophyll a of 0.53 after Zadoks stage 43. This was later than the relationship (r2 = 0.68) developed for Horsham after Zadoks stage 33 but early enough to be used for potential mid-season N fertilizer recommendations. Additionally, ground-based hyperspectral data estimated plant N (g kg)1) in Horsham with an r2 = 0.86 but was confounded by water supply and N interactions. By combining canopy thermal and spectral properties, varying water and N status can potentially be identified eventually permitting targeted N applications to those parts of a field where N can be used most efficiently by the crop.

Yield of synthetic backcross-derived lines in rainfed environments of Australia

Wheat is one of the major food crops in the world. It is Australia's largest crop and most important agricultural commodity. In Australia the crop is grown under rainfed conditions with inherently important regional environmental differences; wheat growing areas are characterized by winter dominant rainfall in southern and western Australia and summer rainfall in northern Australia. Maximizing yield potential across these diverse regions is dependent upon managing, either genetically or agronomically, those factors in the environment that limit yield. The potential of synthetic backcross lines (SBLs) to increase yield in the diverse agroecological zones of Australia was investigated. Significant yield advantages were found for many of the SBLs across diverse environments. Depending on the environment, the yield of the SBLs ranged from 8% to 30% higher than the best local check in Australia. Apart from adaptation to semiarid water stressed conditions, some SBLs were also found to be significantly higher yielding under more optimal (irrigated) conditions. The four testing environments were classified into two groups, with the northern and southern environments being in separate groups. An elite group of SBLs was identified that exhibited broad adaptation across all diverse Australian environments included in this study. Other SBLs showed specific adaptation to either northern or southern Australia. This study showed that SBLs are likely to provide breeders with the opportunity to significantly improve wheat yield beyond what was previously possible in a number of diverse production environments.

CIMMYT-selected derived synthetic bread wheats for rainfed environments: Yield evaluation in Mexico and Australia.

Synthetic backcrossed-derived bread wheats (SBWs) from CIMMYT were grown in the Northwest of Mexico at Centro de Investigaciones Agrícolas del Noroeste (CIANO) and sites across Australia during three seasons. During three consecutive years Australia received “shipments” of different SBWs from CIMMYT for evaluation. A different set of lines was evaluated each season, as new materials became available from the CIMMYT crop enhancement program. These consisted of approximately 100 advanced lines (F7) per year. SBWs had been top and backcrossed to CIMMYT cultivars in the first two shipments and to Australian wheat cultivars in the third one. At CIANO, the SBWs were trialled under receding soil moisture conditions. We evaluated both the performance of each line across all environments and the genotype-by-environment interaction using an analysis that fits a multiplicative mixed model, adjusted for spatial field trends. Data were organised in three groups of multienvironment trials (MET) containing germplasm from shipment 1 (METShip1), 2 (METShip2), and 3 (METShip3), respectively. Large components of variance for the genotype × environment interaction were found for each MET analysis, due to the diversity of environments included and the limited replication over years (only in METShip2, lines were tested over 2 years). The average percentage of genetic variance explained by the factor analytic models with two factors was 50.3% for METShip1, 46.7% for METShip2, and 48.7% for METShip3. Yield comparison focused only on lines that were present in all locations within a METShip, or “core” SBWs. A number of core SBWs, crossed to both Australian and CIMMYT backgrounds, outperformed the local benchmark checks at sites from the northern end of the Australian wheat belt, with reduced success at more southern locations. In general, lines that succeeded in the north were different from those in the south. The moderate positive genetic correlation between CIANO and locations in the northern wheat growing region likely reflects similarities in average temperature during flowering, high evaporative demand, and a short flowering interval. We are currently studying attributes of this germplasm that may contribute to adaptation, with the aim of improving the selection process in both Mexico and Australia.

Cellular stages of root formation, root system quality and survival of Pinuselliottii var. elliottii x P. caribaea var. hondurensis cuttings in different temperature environments.

Time to first root in cuttings varies under different environmental conditions and understanding these differences is critical for optimizing propagation of commercial forestry species. Temperature environment (15, 25, 30 or 352C) had no effect on the cellular stages in root formation of the Slash * Caribbean Pine hybrid over 16 weeks as determined by histology. Initially callus cells formed in the cortex, then tracheids developed and formed primordia leading to external roots. However, speed of development followed a growth curve with the fastest development occurring at 25C and slowest at 15C with rooting percentages at week 12 of 80 and 0% respectively. Cutting survival was good in the three cooler temperature regimes (>80%) but reduced to 59% at 35C. Root formation appeared to be dependant on the initiation of tracheids because all un-rooted cuttings had callus tissue but no tracheids, irrespective of temperature treatment and clone.

Characterization of north-eastern Australian environments using APSIM for increasing rainfed maize production

Recurring water stresses are a major risk factor for rainfed maize cropping across the highly diverse agro-ecological environments of Queensland (Qld) and northern New South Wales (NNSW). Enhanced understanding of such agro-ecological diversity is necessary to more consistently sample target production environments for testing and targeting release of improved germplasm, and to improve the efficiency of the maize pre-breeding and breeding programs of Qld and New South Wales. Here, we used the Agricultural Production Systems Simulator (APSIM) – a well validated maize crop model to characterize the key distinctive water stress patterns and risk to production across the main maize growing regions of Qld and NNSW located between 15.8° and 31.5°S, and 144.5° and 151.8°E. APSIM was configured to simulate daily water supply demand ratios (SDRs) around anthesis as an indicator of the degree of water stress, and the final grain yield. Simulations were performed using daily climatic records during the period between 1890 and 2010 for 32 sites-soils in the target production regions. The runs were made assuming adequate nitrogen supply for mid-season maize hybrid Pioneer 3153. Hierarchical complete linkage analyses of the simulated yield resulted in five major clusters showing distinct probability distribution of the expected yields and geographic patterns. The drought stress patterns and their frequencies using SDRs were quantified using multivariate statistical methods. The identified stress patterns included no stress, mid-season (flowering) stress, and three terminal stresses differing in terms of severity. The combined frequency of flowering and terminal stresses was highest (82.9%), mainly in sites-soils combinations in the west of Qld and NNSW. Yield variability across the different sites-soils was significantly related to the variability in frequencies of water stresses. Frequencies of water stresses within each yield cluster tended to be similar, but different across clusters. Sites-soils falling within each yield cluster therefore could be treated as distinct maize production environments for testing and targeting newly developed maize cultivars and hybrids for adaptation to water stress patterns most common to those environments.

Physiological basis of yield variation in response to row spacing and plant density of mungbean grown in subtropical environments

In this study, we investigated the extent and physiological bases of yield variation due to row spacing and plant density configuration in the mungbean Vigna radiata (L.) Wilczek variety “Crystal” grown in different subtropical environments. Field trials were conducted in six production environments; one rain-fed and one irrigated trial each at Biloela and Emerald, and one rain-fed trial each at Hermitage and Kingaroy sites in Queensland, Australia. In each trial, six combinations of spatial arrangement of plants, achieved through two inter-row spacings of 1 m or 0.9 m (wide row), 0.5 m or 0.3 m (narrow row), with three plant densities, 20, 30 and 40 plants/m2, were compared. The narrow row spacing resulted in 22% higher shoot dry matter and 14% more yield compared to the wide rows. The yield advantage of narrow rows ranged from 10% to 36% in the two irrigated and three rain-fed trials. However, yield loss of up to 10% was also recorded from narrow rows at Emerald where the crop suffered severe drought. Neither the effects of plant density, nor the interaction between plant density and row spacing, however, were significant in any trial. The yield advantage of narrow rows was related to 22% more intercepted radiation. In addition, simulations by the Agricultural Production Systems Simulator model, using site-specific agronomy, soil and weather information, suggested that narrow rows had proportionately greater use of soil water through transpiration, compared to evaporation resulting in higher yield per mm of soil water. The long-term simulation of yield probabilities over 123 years for the two row configurations showed that the mungbean crop planted in narrow rows could produce up to 30% higher grain yield compared to wide rows in 95% of the seasons.

Fate of key food-borne pathogens associated with intensive pig and poultry farming environments

Intensive pig and poultry farming in Australia can be a source of pathogens with implications for food-safety and/or human illness. Seven studies were undertaken with the following objectives: · Assess the types of zoonotic pathogens in waste · Assess the transfer of pathogens during re-use both within the shed and externally in the environment · The potential for movement of pathogens via aerosols In the first and second studies the extent of zoonotic pathogens was evaluated in both piggery effluent and chicken litter and Salmonella and Campylobacter were detected in both wastes. In the third study the dynamics of Salmonella during litter re-use was examined and results showed a trend for lower Salmonella levels and serovar diversity in re-used litter compared to new litter. Thus, re-use within the poultry farming system posed no increased risk. The fourth study addressed the direct risks of pathogens to farm workers due to reuse of piggery effluent within the pig shed. Based on air-borne Escherichia coli (E. coli) levels, re-using effluent did not pose a risk. In the fifth study high levels of Arcobacter spp. were detected in effluent ponds and freshly irrigated soils with potential food-safety risks during the irrigation of food-crops and pasture. The sixth and seventh studies addressed the risks from aerosols from mechanically ventilated sheds. Staphylococci were shown to have potential as markers, with airborne levels gradually dropping and reaching background levels at 400 m distance. Salmonella was detected (at low levels) both inside and outside the shed (at 10 m). Campylobacter was detected only once inside the shed during the 3-year period (at low levels). Results showed there was minimal risk to humans living adjacent to poultry farms This is the first comprehensive analysis studying key food-safety pathogens and potential public health risks associated with intensively farmed pigs and poultry in Australia.

Integrating Rapid Phenotyping and Speed Breeding to Improve Stay-Green and Root Adaptation of Wheat in Changing, Water-Limited, Australian Environments

Temperatures have increased and in-crop rainfall decreased over recent decades in many parts of the Australian wheat cropping region. With these trends set to continue or intensify, improving crop adaptation in the face of climate change is particularly urgent in this, already drought-prone, cropping region. Importantly, improved performance under water-limitation must be achieved while retaining yield potential during more favourable seasons. A multi-trait-based approach to improve wheat yield and yield stability in the face of water-limitation and heat has been instigated in northern Australia using novel phenotyping techniques and a nested association mapping (NAM) approach. An innovative laboratory technique allows rapid root trait screening of hundreds of lines. Using soil grown seedlings, the method offers significant advantages over many other lab-based techniques. Another recently developed method allows novel stay-green traits to be quantified objectively for hundreds of genotypes in standard field trial plots. Field trials in multiple locations and seasons allow evaluation of targeted trait values and identification of superior germplasm. Traits, including yield and yield components are measured for hundreds of NAM lines in rain fed environments under various levels of water-limitation. To rapidly generate lines of interest, the University of Queensland “speed breeding” method is being employed, allowing up to 7 plant generations per annum. A NAM population of over 1000 wheat recombinant inbred lines has been progressed to the F5 generation within 18 months. Genotyping the NAM lines with the genome-wide DArTseq molecular marker system provides up to 40,000 markers. They are now being used for association mapping to validate QTL previously identified in bi-parental populations and to identify novel QTL for stay-green and root traits. We believe that combining the latest techniques in physiology, phenotyping, genetics and breeding will increase genetic progress toward improved adaptation to water-limited environments.

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function.

Simulating crop-parasitic weed interactions using APSIM: Model evaluation and application

The parasitic weed Orobanche crenata inflicts major damage on faba bean, lentil, pea and other crops in Mediterranean environments. The development of methods to control O. crenata is to a large extent hampered by the complexity of host-parasite systems. Using a model of host-parasite interactions can help to explain and understand this intricacy. This paper reports on the evaluation and application of a model simulating host-parasite competition as affected by environment and management that was implemented in the framework of the Agricultural Production Systems Simulator (APSIM). Model-predicted faba bean and O. crenata growth and development were evaluated against independent data. The APSIM-Fababean and -Parasite modules displayed a good capability to reproduce effects of pedoclimatic conditions, faba bean sowing date and O. crenata infestation on host-parasite competition. The r(2) values throughout exceeded 0.84 (RMSD: 5.36 days) for phenological, 0.85 (RMSD: 223.00 g m(-2)) for host growth and 0.78 (RMSD: 99.82 g m(-2)) for parasite growth parameters. Inaccuracies of simulated faba bean root growth that caused some bias of predicted parasite number and host yield loss may be dealt with by more flexibly simulating vertical root distribution. The model was applied in simulation experiments to determine optimum sowing windows for infected and non-infected faba bean in Mediterranean environments. Simulation results proved realistic and testified to the capability of APSIM to contribute to the development of tactical approaches in parasitic weed control.

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

Background: Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. Results: The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion: Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.

Crop and environmental attributes underpinning genotype by environment interaction in synthetic-derived bread wheat evaluated in Mexico and Australia

Synthetic backcrossed-derived bread wheats (SBWs) from CIMMYT were grown in the north-west of Mexico (CIANO) and sites across Australia during 3 seasons. A different set of lines was evaluated each season, as new materials became available from the CIMMYT crop enhancement program. Previously, we have evaluated both the performance of genotypes across environments and the genotype x environment interaction (G x E). The objective of this study was to interpret the G x E for yield in terms of crop attributes measured at individual sites and to identify the potential environmental drivers of this interaction. Groups of SBWs with consistent yield performance were identified, often comprising closely related lines. However, contrasting performance was also relatively common among sister lines or between a recurrent parent and its SBWs. Early flowering was a common feature among lines with broad adaptation and/or high yield in the northern Australian wheatbelt, while yields in the southern region did not show any association with the maturity type. Lines with high yields in the southern and northern regions had cooler canopies during flowering and early grain filling. Among the SBWs with Australian genetic backgrounds, lines best adapted to CIANO were tall (>100 cm), with a slightly higher ground cover. These lines also displayed a higher concentration of water-soluble carbohydrates in the stem at flowering, which was negatively correlated with stem number per unit area when evaluated in southern Australia (Horsham). Possible reasons for these patterns are discussed. Selection for yield at CIANO did not specifically identify the lines best adapted to northern Australia, although they were not the most poorly adapted either. In addition, groups of lines with specific adaptation to the south would not have been selected by choosing the highest yielding lines at CIANO. These findings suggest that selection at CIMMYT for Australian environments may be improved by either trait based selection or yield data combined with trait information. Flowering date, canopy temperature around flowering, tiller density, and water-soluble carbohydrate concentration in the stem at flowering seem likely candidates.

Simulating pasture growth rates in Australian and New Zealand grazing systems

DairyMod, EcoMod, and the SGS Pasture Model are mechanistic biophysical models developed to explore scenarios in grazing systems. The aim of this manuscript was to test the ability of the models to simulate net herbage accumulation rates of ryegrass-based pastures across a range of environments and pasture management systems in Australia and New Zealand. Measured monthly net herbage accumulation rate and accumulated yield data were collated from ten grazing system experiments at eight sites ranging from cool temperate to subtropical environments. The local climate, soil, pasture species, and management (N fertiliser, irrigation, and grazing or cutting pattern) were described in the model for each site, and net herbage accumulation rates modelled. The model adequately simulated the monthly net herbage accumulation rates across the range of environments, based on the summary statistics and observed patterns of seasonal growth, particularly when the variability in measured herbage accumulation rates was taken into account. Agreement between modelled and observed growth rates was more accurate and precise in temperate than in subtropical environments, and in winter and summer than in autumn and spring. Similarly, agreement between predicted and observed accumulated yields was more accurate than monthly net herbage accumulation. Different temperature parameters were used to describe the growth of perennial ryegrass cultivars and annual ryegrass; these differences were in line with observed growth patterns and breeding objectives. Results are discussed in the context of the difficulties in measuring pasture growth rates and model limitations.

Developmental and physiological traits associated with high yield and stay-green phenotype in wheat

Water availability is a key limiting factor in wheat production in the northern grain belt of Australia. Varieties with improved adaptation to such conditions are actively sought. The CIMMYT wheat line SeriM82 has shown a significant yield advantage in multi-environment screening trials in this region. The objective of this study was to identify the physiological basis of the adaptive traits underpinning this advantage. Six detailed experiments were conducted to compare the growth, development, and yield of SeriM82 with that of the adapted cultivar, Hartog. The experiments were undertaken in field environments that represented the range of moisture availability conditions commonly encountered by winter crops grown on the deep Vertosol soils of this region. The yield of SeriM82 was 6-28% greater than that of Hartog, and SeriM82 exhibited a stay-green phenotype by maintaining green leaf area longer during the grain-filling period in all environments where yield was significantly greater than Hartog. However, where the availability of deep soil moisture was limited, SeriM82 failed to exhibit significantly greater yield or to express the stay-green phenotype. Thus, the stay-green phenotype was closely associated with the yield advantage of SeriM82. SeriM82 also exhibited higher mean grain mass than Hartog in all environments. It is suggested that small differences in water use before anthesis, or greater water extraction from depth after anthesis, could underlie the stay-green phenotype. The inability of SeriM82 to exhibit stay-green and higher yield where deep soil moisture was depleted indicates that extraction of deep soil moisture is important.