Context Many wheat producers are increasing the biomass of cereal stubble retained after harvest through the adoption of stripper front harvesters, which result in taller standing stubble.Aims We investigated whether taller stubble affects the survival and dispersal of Fusarium pseudograminearum (Fp), the causative agent of Fusarium crown rot (FCR).Methods Field experiments at two sites in northern New South Wales were run for 3 years to investigate whether taller cereal stubble in Year 1 facilitated additional Fp colonisation, and subsequent effects on dispersal of Fp inoculum from chickpea harvest in Year 2 and FCR infection and expression in cereal crops in Year 3. Culturing and quantitative polymerase chain reaction (qPCR) methods assessed Fp colonisation and future disease risks.Key results In taller cereal stubble, Fp colonised an additional 91-92% of the stubble length in the 6 months post-harvest and persisted at higher levels for at least 1 year than did the shorter cereal stubble. Cutting cereal stubble short (in Year 1) therefore successfully restricted further colonisation by Fp. Significant displacement of Fp in the crown 6 months post-harvest resulted in significant decreases in Fp DNA overall; however, long-term survival of Fp was observed 10-20 cm above the crown.Conclusions Different residue management scenarios did not increase FCR risk for Year 3, likely owing to high inoculum levels across all treatments and unseasonably wet conditions in Years 2-3.Implications We provide important field-validation of Fp colonisation in standing cereal stubble and discuss implications for FCR management across regions and seasons.

Phytophthora root rot (PRR) of chickpea (Cicer arietinum) caused by Phytophthora medicaginis is an important disease. Partial resistance to PRR is sourced from Cicer echinospermum. In this study, we evaluated if lines with low levels of PRR foliage symptoms in two contrasting recombinant inbred line (RIL) populations parented by chickpea cultivars (Yorker and Rupali) and 04067-81-2-1-1 (C. echinospermum, interspecific breeding line) had a significant drag on yield parameters. For the Yorker × 04067-81-2-1-1 population with the highest level of PRR resistance, in the absence of PRR, low foliage symptom RIL had significantly later flowering and podding, lower grain yields, and lighter seed and shorter plant phenotypes than high foliage symptom RIL. A quantitative trait locus analysis identified significant QTL for flowering, height, 100-seed weight, and yield, and there was a significantly higher frequency of alleles for the negative agronomic traits (i.e., drag) from the 04067-81-2-1-1 parent in low foliage symptom RIL than in high foliage symptom RIL. For the Rupali × 04067-81-2-1-1 population with lower levels of PRR resistance, in the absence of PRR, low foliage symptom RIL had significantly lighter seed and shorter plants than high foliage symptom RIL. Significant QTL were detected, the majority were for the timing of flowering and podding (n = 18), others were for plant height, yield, and 100-seed weight. For this second population, the frequency of alleles for the negative agronomic traits from the 04067-81-2-1-1 parent did not differ between low and high foliage symptom RIL. The 100 seed weight of RIL under moderate PRR disease pressure showed some promise as a yield component trait to identify phenotypes with both high levels of PRR resistance and grain yield potential for further seed number evaluations. We identified that large population sizes are required to enable selection among chickpea × C. echinospermum crosses for high levels of PRR resistance without a significant drag on yield.

Phytophthora root rot caused by Phytophthora medicaginis is an important disease of chickpeas (Cicer arietinum) in Australia with limited management options, increasing reliance on breeding for improved levels of genetic resistance. Resistance based on chickpea-Cicer echinospermum crosses is partial with a quantitative genetic basis provided by C. echinospermum and some disease tolerance traits originating from C. arietinum germplasm. Partial resistance is hypothesised to reduce pathogen proliferation, while tolerant germplasm may contribute some fitness traits, such as an ability to maintain yield despite pathogen proliferation. To test these hypotheses, we used P. medicaginis DNA concentrations in the soil as a parameter for pathogen proliferation and disease assessments on lines of two recombinant inbred populations of chickpea-C. echinospermum crosses to compare the reactions of selected recombinant inbred lines and parents. Our results showed reduced inoculum production in a C. echinospermum backcross parent relative to the C. arietinum variety Yorker. Recombinant inbred lines with consistently low levels of foliage symptoms had significantly lower levels of soil inoculum compared to lines with high levels of visible foliage symptoms. In a separate experiment, a set of superior recombinant inbred lines with consistently low levels of foliage symptoms was tested for soil inoculum reactions relative to control normalised yield loss. The in-crop P. medicaginis soil inoculum concentrations across genotypes were significantly and positively related to yield loss, indicating a partial resistance-tolerance spectrum. Disease incidence and the rankings for in-crop soil inoculum were correlated strongly to yield loss. These results indicate that soil inoculum reactions may be useful to identify genotypes with high levels of partial resistance.

In spite of its abundant presence in rice grains, auxin functions during grain development are not understood well. Absence of grain-specific auxin biosynthesis mutants in rice further limits our understanding in this respect. Here, we report a chemical biology approach to inhibit auxin biosynthesis specifically in early rice grains as well as its subsequent effects on final grain yield. Exogenous application of two auxin biosynthesis inhibitors, namely L-kynurenine (L-Kyn) and 4-phenoxyphenylboronic acid (PPBo), to spikelets daily from three to ten days after pollination (DAP) significantly reduced grain levels of indole-3-acetic acid (IAA), the predominant in planta auxin. The inhibitor-treated panicles showed extensive post-fertilisation seed abortion, leading to drastic reduction in total panicle weight at maturity. Locally synthesised auxin during early grain development may therefore play a crucial role in grain retention. This chemical biology approach can be an easy and cost-effective way to study auxin biosynthesis and signalling during grain development in rice and possibly other cereal crops. Highlight Auxin synthesised in early rice grains may play a crucial role in grain retention.

Stubble-borne cereal diseases are a major constraint to production in Australia, with associated costs rising as a result of increased adoption of conservation agriculture systems. The fungal pathogens that cause these diseases can saprotrophically colonise retained cereal residues, which may further increase inoculum levels post-harvest. Hence, saprotrophic colonisation by the stubble-borne fungal pathogens Fusarium pseudograminearum, Pyrenophora tritici-repentis and Bipolaris sorokiniana were compared under a range of moisture conditions for stubble of six cereal varieties (two bread wheat, two barley, one durum wheat and one oat). Sterile cereal stubble was inoculated separately with two isolates of each pathogen and placed, standing, under constant relative humidity conditions (90, 92.5, 95, 97.5 and 100%) for 7 days at 25 °C. Stubble was then cultured in increments of 1 cm to determine the percentage colonisation height of each tiller. Fusarium pseudograminearum colonised farther within tillers, leaving a greater proportion of the standing stubble colonised compared with B. sorokiniana and P. tritici-repentis, suggesting F. pseudograminearum has higher saprotrophic fitness. Saprotrophic colonisation also increased with increasing relative humidity for all pathogens and varied by cereal type. Disease management strategies, such as reduced cereal harvest height, may limit saprotrophic colonisation and improve stubble-borne disease management in conservation agriculture systems.

Cereal production in Australia is severely impacted by diseases such as Fusarium crown rot (caused predominantly by Fusarium pseudograminearum ) and common root rot (caused by Bipolaris sorokiniana ). These diseases are particularly difficult to manage because inoculum can survive at least three years within cereal stubble, or four years in soil in the case of B. sorokiniana . Microwave radiation may be able to reduce or eliminate inoculum within stubble and soil. Several cereal pathogens have been previously shown to be susceptible to microwave radiation, but the energy requirements to achieve a significant decrease in pathogen populations were not defined. Laboratory based microwave dose-response experiments on conidia of B. sorokiniana and macroconidia of F. pseudograminearum and F. cerealis revealed that all three pathogens are susceptible to microwave radiation, with lethal dose (LD) thresholds estimated for each pathogen. Bipolaris sorokiniana conidia required 103.8 Jg − 1 and 236.6 Jg − 1 of microwave radiation energy for LD50 and LD99, respectively, whilst F. pseudograminearum required 78.4 Jg − 1 and 300.8 Jg − 1 and F. cerealis required 95.3 Jg − 1 and 152.7 Jg − 1 for LD50 and LD99, respectively. These results were derived from experiments whereby samples were microwaved for up to 10 s using a domestic 1100 W microwave oven. These timing and energy requirements serve as a starting point to define requirements for further development of microwave radiation treatments under field conditions.

Phytophthora medicaginis causing Phytophthora root rot of chickpea (Cicer arietinum) is an important disease, with genetic resistance using C. arietinum x Cicer echinospermum crosses as the main disease management strategy. We evaluated pathogenic variation in P. medicaginis populations with the aim of improving phenotyping methods for disease resistance. We addressed the question of individual isolate aggressiveness across four different seedling-based phenotyping methods conducted in glasshouses and one field-based phenotyping method. Our results revealed that a seedling media surface inoculation method used on a susceptible C. arietinum variety and a moderately resistant C. arietinum x C. echinospermum backcross detected the greatest variability in aggressiveness among 37 P. medicaginis isolates. Evaluations of different components of resistance, using our different phenotyping methods, revealed that differential pathogen-isolate reactions occur with some phenotyping methods. We found support for our hypotheses that the level of aggressiveness of P. medicaginis isolates depends on the phenotyping method, and that phenotyping methods interact with both isolate and host genotype reactions. Our cup-based root inoculation method showed promise as a non-field-based phenotyping method, as it provided significant correlations with genotype-isolate rankings in the field experiment for a number of disease parameters.

Endosperm of rice and other cereals accumulates high concentrations of the predominant in planta auxin, indole-3-acetic acid (IAA) during early grain development. However, IAA signalling and function during endosperm development are poorly understood. Here, we report that OsYUC12 (an auxin biosynthesis gene) and OsIAA29 (encoding a non-canonical AUX/IAA) are both expressed exclusively in grains, reaching a maximum 5 to 6 days after pollination. OsYUC12 expression is localized in the aleurone, sub-aleurone and embryo, whereas OsIAA29 expression is restricted to a narrow strip in the dorsal aleurone, directly under the vascular bundle. Although rice has been reported to lack endosperm transfer cells (ETCs), this region of the aleurone is enriched with sugar transporters and is likely to play a key role in apoplastic nutrient transfer, analogous to ETCs in other cereals. OsIAA29 has orthologues only in grass species; expression of which is also specific to early grain development. OsYUC12 and OsIAA29 are temporally co-expressed with two genes (AL1 and OsPR602) previously linked to the development of dorsal aleurone or ETCs. Also up regulated at the same time are a cluster of MYB-related genes (designated OsMRPLs) homologous to ZmMRP-1, which regulates maize ETC development. Wheat homologues of ZmMRP-1 are also expressed in ETCs. Although previous work has suggested that other cereals do not have orthologues of ZmMRP-1, our work suggests OsIAA29 and OsMRPLs and their homologues in other grasses are part of an auxin-regulated, conserved signalling network involved in the differentiation of cells with ETC-like function in developing cereal grains. Main Conclusion Non-canonical AUX/IAA protein, OsIAA29, and ZmMPR-1 homologues, OsMRPLs, are part of an auxin-related signalling cascade operating in the dorsal aleurone during early rice grain development.

The effect of auxin on wheat (Triticum aestivum L.) grain size is contentious. Additionally, the contributions to the IAA pool from de novo synthesis versus hydrolysis of IAA-glucose are unclear. Here, we describe the first comprehensive study of tryptophan aminotransferase and indole-3-pyruvate mono-oxygenase expression from 5 to 20 days after anthesis. A comparison of expression data with measurements of endogenous IAA via combined liquid chromatography-tandem mass spectrometry using heavy isotope labelled internal standards indicates that TaTAR2-B3, TaYUC9-A1, TaYUC9-B, TaYUC9-D1, TaYUC10-A and TaYUC10-D are primarily responsible for IAA production in developing grains. Furthermore, these genes are expressed specifically in developing grains, like those found in rice (Oryza sativa L.) and maize (Zea mays L.). Our results cast doubt on the proposed role of THOUSAND-GRAIN WEIGHT gene, TaTGW6, in promoting larger grain size via negative effects on grain IAA content. Work on this gene overlooked the contribution of IAA biosynthesis from tryptophan. Although IAA synthesis occurs primarily in the endosperm, we show the TaYUC9-1 group is also strongly expressed in the embryo. Within the endosperm, TaYUC9-1 expression is highest in aleurone and transfer cells, suggesting that IAA has a key role in differentiation of these tissues as has been proposed for other cereals.

A large and persistent soil seed bank characterises many important grass weeds, including Nassella trichotoma (Nees) Hack. ex Arechav. (serrated tussock), a major weed in Australia and other countries. In the present study we examined the effects of constant and alternating temperatures in regulating primary and secondary dormancy and the creation and maintenance of its soil seed bank in northern NSW, Australia. One-month-old seeds were stored at 4, 25°C, 40/10°C and 40°C, in a laboratory, and germination tests were conducted every two weeks. Few seeds germinated following storage at 4°C, compared with seeds stored at 25°C, 40/10°C and 40°C. Nylon bags containing freshly harvested seeds were buried among N. trichotoma stands in early summer, and germination tests conducted following exhumation after each season over the next 12 months. Seeds buried over summer and summer plus autumn had higher germination than seeds buried over summer plus autumn plus winter, but germination increased again in the subsequent spring. Seeds stored for zero, three, six and 12 months at laboratory temperatures were placed on a thermogradient plate with 81 temperature combinations, followed by incubation at constant 25°C of un-germinated seeds. Constant high or low temperatures prolonged primary dormancy or induced secondary dormancy whereas alternating temperatures tended to break dormancy. Few temperature combinations resulted in more than 80% germination.

The role of auxin in developing grains of wheat ( Triticum aestivum ) is contentious with contradictory reports indicating either positive or negative effects of IAA (indole-3-acetic acid) on grain size. In addition, the contributions to the IAA pool from de novo synthesis via tryptophan, and from hydrolysis of IAA-glucose are unclear. Here we describe the first comprehensive study of tryptophan aminotransferase and indole-3-pyruvate mono-oxygenase expression during wheat grain development from 5 to 20 days after anthesis. A comparison of expression data with measurements of endogenous IAA via combined liquid chromatography-tandem mass spectrometry with heavy isotope labelled internal standards indicates that TaTAR2.3-1B, TaYUC9-A1, TaYUC9-B, TaYUC9-D1, TaYUC10-A and TaYUC10-D are primarily responsible for IAA production in developing grains. Furthermore, we show that IAA synthesis is controlled by genes expressed specifically in developing wheat grains as has already been reported in rice ( Oryza sativa ) and maize ( Zea mays ). Our results cast doubt on the proposed role of THOUSAND-GRAIN WEIGHT gene, TaTGW6 , in promoting larger grain size via negative effects on grain IAA content. The work on TaTGW6 has overlooked the contribution of the dominant IAA biosynthesis pathway. Although IAA synthesis occurs primarily in the endosperm of wheat grains, we show that the TaYUC9-1 group is also strongly expressed in the embryo. Within the endosperm, TaYUC9-1 expression is highest in aleurone and transfer cells, supporting data from other cereals suggesting that IAA has a key role in differentiation of these tissues.### Competing Interest StatementThe authors have declared no competing interest.

Soil nematode populations have the potential to indicate ecosystem disturbances. In response to questions about nematode interactions with soilborne diseases and whether genetically modified cotton altered nematode populations, several fields in the Namoi cotton growing area of Australia were sampled between 2005 and 2007. No significant interactions were observed, but nematodes numbers were low and postulated to be due to the use of the nematicide aldicarb. Aldicarb was removed from the system in 2011 and in 2015 funding allowed some fields to be resampled to determine if there had been a change in the nematode numbers following aldicarb removal. No significant changes in the total nematode numbers were observed, implying that the removal of aldicarb had little impact on the total nematode population size. However, an increase in plant parasitic nematodes was observed in both fields, but the species identified and the levels of change were not considered a threat to cotton production nor driven solely by altered pesticide chemistry. Additionally, greater numbers of higher order coloniser-persisters in the 2015 samples suggests that the current cotton production system is less disruptive to the soil ecosystem than that of a decade ago.

There is no conclusive evidence that Helicoverpa spp. (Lepidoptera: Noctuidae) in Australia have evolved significant levels of resistance to Bollgard II ® cotton (which expresses two Bt toxin genes, cry1Ac and cry2Ab ). However, there is evidence of surviving larvae on Bollgard II cotton in the field. The distribution and survival of early‐instar Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) larvae were examined on whole Bollgard II and non‐Bt cotton plants in greenhouse bioassays. The expression of Cry toxins in various parts of Bollgard II plants was compared to the survival of larvae in those locations. Only 1% of larvae survived after 6 days on greenhouse‐grown Bollgard II plants compared to 31% on non‐Bt cotton plants. Overall, and across all time intervals, more larvae survived on reproductive parts (squares, flowers, and bolls) than on vegetative parts (leaves, stems, and petioles) on Bollgard II plants. The concentration of Cry1Ac toxin did not differ between plant structures, whereas Cry2Ab toxin differed significantly, but there was no relationship between the level of expression and the location of larvae. This study provides no evidence that lower expression of Cry toxins in the reproductive parts of plants explains the survival of H. armigera larvae on Bollgard II cotton.

Soil sodicity degrades land and more than half of the world's sodic soils are in Australia. Farmers in Australia produce and export cotton grown in sodic soils. Undesirable physicochemical constraints (e.g. high pH, high bulk density, low porosity and reduced oxygen content) are associated with sodic soils and may adversely affect microbial interactions in the rhizosphere, including mycorrhizal associations. This viewpoint focusses on facts and gaps in our knowledge about mycorrhizal associations in sodic soils, with special attention to cotton systems. We highlight the difference between saline and sodic soil conditions and the impacts they may have on host plant-mycorrhizae symbiosis. This viewpoint identifies the need for more research on the potential impact of sodicity on mycorrhizal species diversity, functionality and benefits to crop growth. Changes in agronomic management strategies to maximize mycorrhizal symbiosis benefits are suggested, especially for those plant species, like cotton, that are highly reliant on mycorrhizal symbiosis for optimal growth and nutrient uptake.

A pot experiment investigated the effects of root diseases (Pythium and Rhizoctonia) under drought conditions at either tillering or anthesis stages on the water-use efficiency (WUE), water relations, and yield components of wheat cultivars Janz and Mulgara. The pathogens reduced transpiration in Janz during drought at tillering and in both cultivars during the period of recovery after drought at anthesis. However, the pathogens did not affect WUE. WUE did not differ between well-watered plants and those droughted at tillering but it was reduced by 80% by drought at anthesis. Un-infected plants of cultivar Janz subjected to drought at tillering had a higher total water potential (psi(w)) and osmotic potential (psi(s)) than diseased plants. However, psi(s) of un-inoculated plants that were droughted at anthesis was lower than diseased plants in the period following anthesis. Yield components were significantly higher in well-watered than droughted plants and higher in cv. Mulgara than cv. Janz. The pathogens affected transpiration during tillering, but not at later stages, when roots developed beyond the inoculation point. Although the pathogens caused damage to the roots, the effects on water relations parameters were minor. This suggests that wheat can tolerate moderate levels of these root diseases under drought.

Little is known about how the adverse physical and chemical environment in sodic soils affects plantmycorrhizal relationships. We investigated mycorrhizal colonisation and plant nutrient uptake of cotton plants under highly stressed (Exchangeable Na percentage (ESP) 21) and less stressed (ESP 7) conditions with two rates of applied P. The relative hyphal contribution to P uptake was quantified using dual isotope labelling techniques (P-32 and P-33). Root colonisation and P uptake of mycorrhizal cotton plants reduced by 16% and 20%, respectively, in highly sodic soil as compared to plants in low sodic soil, however, the relative proportion of P delivered via hyphal pathways (P-32 from root-free hyphal compartment) was similar. Under high P conditions, the relative increase in the proportion of P-33 (root + hyphae compartment) taken up by inoculated plants was greater in the low sodic soil relative to the high sodic soil. Mycorrhization improved early seedling vigour, and nutrient uptake. Reduced colonisation and hyphal exploration of the soil, possibly due to the physical and chemical constraints imposed by highly-sodic soil, rather than poorer mycorrhizal function, may be responsible for limited early P uptake of cotton in highly-sodic soil. (C) 2016 Elsevier Ltd. All rights reserved.

Despite the reported importance of mycorrhizal symbioses for early growth and nutrient acquisition of cotton, little is known about how sodicity affects this relationship. Changes in mycorrhizal colonisation and nutrient uptake of cotton in a range of naturally non-sodic (exchangeable sodium percentages (ESP) <6) and low-sodic soils (ESP 6-10), from cotton production areas in southern Queensland and northern New South Wales, with different ESP (ranged between 1.4 and 9.8) was investigated in a glasshouse experiment. The experiment was a complete factorial design with 11 recently-collected soils and two mycorrhizae treatments (either inoculated with fresh "live" mycorrhizal inoculum or without inoculum). Linear mixed model analysis showed minimal effects of sodicity, when ESP was less than 10, on mycorrhizal colonisation, associated plant growth and nutrient uptake. Principle component and regression analysis showed that other sources of variation including soil pH and soil P content, rather than sodicity, might drive cotton colonisation in Vertosols with low to moderate ESP. The colonisation percentage was positively linearly correlated with P. Mg, and Zn uptake of cotton plants. Further investigation into mycorrhizal spore density and species diversity under sodic soil conditions is warranted. (C) 2017 Elsevier GmbH. All rights reserved.

Diabetic retinopathy (DR) is a common retinal complication associated with diabetes. It is a major cause of blindness in middle as well as older age groups. Therefore early detection through regular screening and timely intervention will be highly beneficial in effectively controlling the progress of the disease. Since the ratio of people afflicted with the disease to the number of eye specialist who can screen these patients is very high, there is a need of automated diagnostic system for diabetic retinopathy changes in the eye so that only diseased persons can be referred to the specialist for further intervention and treatment.

The majority of terrestrial plants form some type of mycorrhizal symbiosis. This established symbiosis therefore exists in most commercially important crops, which includes cotton. Arbuscular mycorrhizal fungus (AMF) can colonise 50%–90% of cotton root length under field and controlled conditions. Mycorrhization improves growth and nutrient uptake (especially phosphorus) of cotton, particularly at the early growth stages. Mycorrhizal symbioses help plants to counter the stresses imposed by physical and chemical soil constraints; however, adverse environmental conditions may restrict the mycorrhizal associations and consequently may reduce nutrient uptake and impair plant growth. In Australia, cotton is mainly grown on sodic soils that contain more than 6% of the total cations as exchangeable sodium. High levels of sodium in the soil create adverse physical and chemical soil conditions that may negatively affect mycorrhizal symbioses of cotton. This review discusses the cotton mycorrhizal colonisation, plant growth, and disease protection effects, potential negative effects of physical and chemical properties of sodic soils, and influences of some agronomic management practices. In addition, the research gaps were identified and some practical applications of the research outcomes were suggested.