The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes

Background Increased disease resistance is a key target of cereal breeding programs, with disease outbreaks continuing to threaten global food production, particularly in Africa. Of the disease resistance gene families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR) family is the most prevalent and ancient and is also one of the largest gene families known in plants. The sequence diversity in NBS-encoding genes was explored in sorghum, a critical food staple in Africa, with comparisons to rice and maize and with comparisons to fungal pathogen resistance QTL. Results In sorghum, NBS-encoding genes had significantly higher diversity in comparison to non NBS-encoding genes and were significantly enriched in regions of the genome under purifying and balancing selection, both through domestication and improvement. Ancestral genes, pre-dating species divergence, were more abundant in regions with signatures of selection than in regions not under selection. Sorghum NBS-encoding genes were also significantly enriched in the regions of the genome containing fungal pathogen disease resistance QTL; with the diversity of the NBS-encoding genes influenced by the type of co-locating biotic stress resistance QTL. Conclusions NBS-encoding genes are under strong selection pressure in sorghum, through the contrasting evolutionary processes of purifying and balancing selection. Such contrasting evolutionary processes have impacted ancestral genes more than species-specific genes. Fungal disease resistance hot-spots in the genome, with resistance against multiple pathogens, provides further insight into the mechanisms that cereals use in the “arms race” with rapidly evolving pathogens in addition to providing plant breeders with selection targets for fast-tracking the development of high performing varieties with more durable pathogen resistance.

Improved management of key northern region weeds: diverse problems, diverse solutions

The cropping region of northern Australia has a diverse range of cropping systems and weed flora. A fallow phase is commonly required between crops to enable the accumulation of stored soil water in these farming systems dominated by reduced tillage. During the fallow phase, weed control is important and is heavily reliant on herbicides. The most commonly used herbicide has been glyphosate. As a result of over-reliance on glyphosate, there are now seven confirmed glyphosate-resistant weeds and several glyphosate-tolerant species common in the region. As a result, the control of summer fallow weeds is become more complex. This paper outlines project work investigating improved weed control for summer fallows in the northern cropping region. Areas of research include weed ecology, chemical and non-chemical tactics, glyphosate resistance and resistance surveys. The project also has an economic and extension component. As a result of our research we have a better understanding of the ecology of major northern weeds and spread of glyphosate resistance in the region. We have identified and defined alternative herbicide and non-chemical approaches for the effective control of summer fallow weeds and have extended our research effectively to industry.

Harvest weed seed control: is there a role in northern region farming systems?

Harvest weed seed control (HWSC) is a new approach which targets weed seed removal and/or destruction during the crop harvest operation. The success of HWSC is dependant upon weed seed retention at harvest. To identify and define the potential value of HWSC in northern farming systems, we conducted a field survey. In total 1400 transects across 70 paddocks assessed weed distribution, density and seed production at harvest time in wheat, chickpea and sorghum crops. Seventy weed species were identified, of which many had large seed numbers retained at crop harvest. The most prevalent included common sowthistle, flaxleaf fleabane, awnless barnyard grass, wild oat, and African turnip weed. Our field survey has shown there is a role for HWSC in the northern farming system. Therefore the efficacy of specific HWSC systems on problematic weeds should be evaluated in the northern region.

Issues and solutions for researching weed eradication target species

Species biology drives the frequency, duration and extent of survey and control activities in weed eradication programs. Researching the key biological characters can be difficult when plants occur at limited locations and are controlled immediately by field crews who are dedicated to preventing reproduction. Within the National Four Tropical Weeds Eradication Program and the former National Siam Weed Eradication Program, key information needed by the eradication teams has been obtained through a combination of field, glasshouse and laboratory studies without jeopardising the eradication objective. Information gained on seed longevity, age to reproductive maturity, dispersal and control options has been used to direct survey and control activities. Planned and opportunistic data collections will continue to provide biological information to refine eradication activities.

Anthelmintic resistance in ovine gastrointestinal nematodes in inland southern Queensland

Objective To establish the prevalence of anthelmintic resistance in ovine gastrointestinal nematodes in southern Queensland. Design An observational parasitological study using the faecal egg count reduction test. Methods Sheep farms (n = 20) enrolled in this study met the twin criteria of using worm testing for drench decisions and having concerns about anthelmintic efficacy. On each farm, 105 sheep were randomly allocated to one of six treatment groups or an untreated control group. Faecal samples were collected on day 0 and days 10–14 for worm egg counts and larval differentiation. Single- and multi-combination anthelmintics, persistent and non-persistent, oral liquid or capsule, pour-on and injectable formulations were tested. Monepantel was not tested. Farmers also responded to a questionnaire on drenching practices. Results Haemonchus contortus was the predominant species. Efficacy <95% was recorded on 85% of farms for one or more anthelmintics and on 10% of farms for six anthelmintics. No resistance was identified on three farms. The 4-way combination product was efficacious (n = 4 farms). Napthalophos resistance was detected on one farm only. Resistance to levamisole (42% of farms), moxidectin injection (50% of farms) and the closantel/abamectin combination (67% of farms) was identified. Moxidectin oral was efficacious against Trichostrongylus colubriformis, which was predominant on only one farm. Of the farms tested, 55% ran meat breeds, 60% dosed more than the recommended dose rate and 70% always, mostly or when possible practised a ‘drench and move’ strategy. Conclusion This level of anthelmintic resistance in southern Queensland will severely compromise worm control and force increased use of monepantel.

Biological management of the invasive Vachellia nilotica ssp. indica (Benth.) Kyal. & Boatwr. (Fabales: Mimosoideae) in tropical Australia: stress-inducing potential of Anomalococcus indicus Ramakrishna (Insecta: Hemiptera: Coccoidea: Lecanodiaspididae), an agent of promise

Vachellia nilotica ssp. indica (hereafter, V. n. indica) is an important tree weed in Australia. Its dense populations induce undesirable changes in the vast areas of northern Australia. Because chemical and mechanical management options appear unviable for various reasons, biological management of this tree is considered a better option. Among the many trialled arthropods in Australian context, Anomalococcus indicus, a lecanodiaspid native to India, has been identified as a potent-candidate, since in India, its native terrain, it is the most widespread and occurs throughout the year. Severe infestations of A. indicus cause defoliation, wilting and death of branches, and occasionally the tree. Populations of A. indicus have been brought into Australia and are being tested for its host specificity under quarantine conditions. This article reports the physiological damage and stress it inflicts in the shoots of V. n. indica. Younger-nymphal instars of A. indicus feed on cortical-parenchyma cells of young stems, whereas the older instars and adults feed from the phloem of old stems. Two conspicuous responses of V. n. indica arising in response to the feeding action of A. indicus are changes in the cell-wall dynamics and irregular cell divisions. The feeding action of A. indicus elicits a sequence of reactions in the stem tissues of V. n. indica such as differentiation of thick-walled elements in the outer cortical parenchyma, differential thickening of cells with supernumerary layers of either suberin or lignin, proliferations of parenchyma and phloem, wall thickening and obliteration of inner lumen of phloem cells, and the sieve plates plugged with callosic deposits. The responses are the culminations of interaction between the virulence factor (one or more of the salivary proteins?) from A. indicus and the resistance factor in V. n. indica. We have analysed structural changes in the context of their functions, by comparing the feeding action of A. indicus with that of other hemipteroids. From the level of stress it induces, this study confirms that A. indicus has the potential to be an effective biological management of V. n. indica in Australia. © 2014 © 2014 Taylor & Francis and Aboricultural Association.

Increased virulence of rabbit haemorrhagic disease virus associated with genetic resistance in wild Australian rabbits (Oryctolagus cuniculus)

The release of myxoma virus (MYXV) and Rabbit Haemorrhagic Disease Virus (RHDV) in Australia with the aim of controlling overabundant rabbits has provided a unique opportunity to study the initial spread and establishment of emerging pathogens, as well as their co-evolution with their mammalian hosts. In contrast to MYXV, which attenuated shortly after its introduction, rapid attenuation of RHDV has not been observed. By studying the change in virulence of recent field isolates at a single field site we show, for the first time, that RHDV virulence has increased through time, likely because of selection to overcome developing genetic resistance in Australian wild rabbits. High virulence also appears to be favoured as rabbit carcasses, rather than diseased animals, are the likely source of mechanical insect transmission. These findings not only help elucidate the co-evolutionary interaction between rabbits and RHDV, but reveal some of the key factors shaping virulence evolution.

Interference and management of parthenium: The world's most important invasive weed

Parthenium (Parthenium hysterophorus L.) is one of the most aggressive herbaceous weeds of the Asteraceae family. It is widely distributed, almost across the world and has become the most important invasive weed. Comprehensive information on interference and control of this devastating species is required to facilitate better management decisions. A broad review on the interference and management of this weed is presented here. Inspite of its non-tropical origin, parthenium grows quite successfully under a wide range of environmental conditions. It is spreading rapidly in Australia, Western Africa, Asia, and Caribbean countries, and has become a serious weed of pastures, wastelands, roadsides, railwaysides, water courses, and agricultural crops. The infestations of parthenium have been reported to reduce grain and forage yields by 40–90%. The spread of parthenium has been attributed to its allelopathic activity, strong competitiveness for soil moisture and nutrients, and its capability to exploit natural biodiversity. Allelochemicals released from parthenium has been reported to decrease germination and growth of agronomic crops, vegetables, trees, and many other weed species. Growth promoting effects of parthenium extracts at low concentrations have also been reported in certain crops. Many pre- and post-emergence herbicides have been evaluated for the control of parthenium in cropped and non-cropped areas. The most effective herbicides are clomazone, metribuzin, atrazine, glyphosate, metsulfuron methyl, butachlor, bentazone, dicamba, and metsulfuron methyl. Extracts, residues, and essential oils of many allelopathic herbs (Cassia, Amaranthus, and Xanthium species), grasses (Imperata and Desmostachya species), and trees (Eucalyptus, Azadirachta, Mangifera species, etc.) have demonstrated inhibitory activities on seed germination and seedling growth of parthenium. Metabolites of several fungi, e.g., Fusarium oxysporun and Fusarium monilifonne, exhibit bioherbicidal activity against seeds and seedlings of this weed. Intercropping, displacement by competitive plant species like Cassia species, bisset bluegrass, florgen blugress, buffelgrass, along with the use of biological control agents like Mexican beetle, seed-feeding and stem-boring weevils, stem-galling and leaf-mining moth, and sap-feeding plant hopper, have been reported as possible strategies for the management of parthenium. An appropriate integration of these approaches could help minimize spread of parthenium and provide sustainable weed management with reduced environmental concerns.

The critical period for weed control in dry-seeded rice

The critical crop-weed competition period in a dry-seeded rice system is an important consideration in formulating weed management strategies. Field experiments were conducted in the summer seasons of 2012 and 2013 at the Punjab Agricultural University, Ludhiana, India, to determine the extent of yield loss in two different rice cultivars (PR 114 and PR 115) with different periods of weed interference. Twelve weed control timings were used to identify critical periods of weed competition in dry-seeded rice. PR 114, a long-duration rice cultivar (145 d) having slower initial growth than PR 115 (125 d), was more prone to yield losses. In both years, 100% yield loss was observed where weeds were not controlled throughout the season. In weed-free plots, the grain yield of PR 114 was 6.39-6.80 t ha-1, for PR 115, it was 6.49-6.87 t ha-1. Gompertz and logistic equations fitted to yield data in response to increasing periods of weed control and weed interference showed that, PR 114 had longer critical periods than PR 115. Critical weed-free periods to achieve 95% of weed-free yield for PR 114 was longer than for PR 115 by 31 days in 2012 and 26 days in 2013. Weed infestation also influenced the duration of critical periods. Higher weed pressure in 2012 than in 2013 increased the duration of the critical period of crop-weed competition in that year. The identification of critical crop-weed competition periods for different cultivars will facilitate improved decision-making regarding the timing of weed control and the adoption of cultivars having high weed-suppressing abilities. This will also contribute to the development of integrated weed management in dry-seeded rice systems.

Markers for seedling and adult plant crown rot resistance in four partially resistant bread wheat sources

Key message: QTLidentified for seedling and adult plant crown rot resistance in four partially resistant hexaploid wheat sources. PCR-based markers identified for use in marker-assisted selection. Abstract: Crown rot, caused by Fusarium pseudograminearum, is an important disease of wheat in many wheat-growing regions globally. Complete resistance to infection by F. pseudograminearum has not been observed in a wheat host, but germplasm with partial resistance to this pathogen has been identified. The partially resistant wheat hexaploid germplasm sources 2-49, Sunco, IRN497 and CPI133817 were investigated in both seedling and adult plant field trials to identify markers associated with the resistance which could be used in marker-assisted selection programs. Thirteen different quantitative trait loci (QTL) conditioning crown rot resistance were identified in the four different sources. Some QTL were only observed in seedling trials whereas others appeared to be adult plant specific. For example while the QTL on chromosomes 1AS, 1BS, and 4BS contributed by 2-49 and on 2BS contributed by Sunco were detected in both seedling and field trials, the QTL on 1DL present in 2-49 and the QTL on 3BL in IRN497 were only detected in seedling trials. Genetic correlations between field trials of the same population were strong, as were correlations between seedling trials of the same population. Low to moderate correlations were observed between seedling and field trials. Flanking markers, most of which are less than 10 cM apart, have now been identified for each of the regions associated with crown rot resistance.

Association mapping of resistance to Puccinia hordei in Australian barley breeding germplasm

Key message “To find stable resistance using association mapping tools, QTL with major and minor effects on leaf rust reactions were identified in barley breeding lines by assessing seedlings and adult plants.” Abstract Three hundred and sixty (360) elite barley (Hordeum vulgare L.) breeding lines from the Northern Region Barley Breeding Program in Australia were genotyped with 3,244 polymorphic diversity arrays technology markers and the results used to map quantitative trait loci (QTL) conferring a reaction to leaf rust (Puccinia hordei Otth). The F3:5 (Stage 2) lines were derived or sourced from different geographic origins or hubs of international barley breeding ventures representing two breeding cycles (2009 and 2011 trials) and were evaluated across eight environments for infection type at both seedling and adult plant stages. Association mapping was performed using mean scores for disease reaction, accounting for family effects using the eigenvalues from a matrix of genotype correlations. In this study, 15 QTL were detected; 5 QTL co-located with catalogued leaf rust resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. The adult plant resistance gene Rph20 was identified across the majority of environments and pathotypes. The QTL detected in this study offer opportunities for breeding for more durable resistance to leaf rust through pyramiding multiple genomic regions via marker-assisted selection.

Overcoming barriers to the successful implementation of a classical biological control strategy for the exotic invasive weed Mikania micrantha in the Asia-Pacific region

Mikania micrantha (Asteraceae) commonly known as mikania, is a major invasive alien plant (IAP) in the tropical humid agricultural and forest zones of the Asia-Pacific region. This fast-growing Neotropical vine is able to smother plants in agricultural ecosystems, agroforestry and natural habitats, reducing productivity and biodiversity. Fungal pathogens were first investigated for the classical biological control of this weed in 1996. This resulted in the selection and screening of the highly host-specific and damaging rust pathogen, Puccinia spegazzinii (Pucciniales). It was first released in India and China in 2005/6, although it is not believed to have established. Since then, it has been released successfully in Taiwan, Papua New Guinea (PNG), Fiji and most recently Vanuatu. The rust has established and is spreading rapidly after applying lessons learned from the first releases on the best rust pathotype and release strategy. In PNG, direct monitoring of vegetation change has demonstrated that the rust is having a significant impact on M. micrantha, with no unpredicted non-target impacts. Despite this, the authorities in many countries where mikania is a problem remain cautious about releasing the rust. In Western Samoa, introduction of the rust was not pursued because of a conflict of interest, and the perception that mikania suppresses even worse weeds. For some, ‘pathophobia’ is still a major obstacle. In Indonesia, where insects for weed CBC have been introduced, pathogens will currently not be considered. In other countries such as Bhutan and Myanmar, there are no baseline data on the presence and impact of IAPs and, with no history of CBC, no institutional framework for implementing this approach. Malaysia has a well-developed framework, but capacity needs to be built in the country. Overall, it remains critical to have champions at decision making levels. Hence, even with an effective ‘off-the-shelf’ agent available, implementation of mikania CBC still requires significant inputs tailored to the countries’ specific needs.

ScreeningCorymbiapopulations for resistance toPuccinia psidii

Disease screening to determine the threat Puccinia psidii poses to plantation and native eucalypts in Australia was undertaken in half-sib families of two contrasting eucalypt species, Eucalyptus cloeziana and E. argophloia. Artificial inoculation with a single-lesion isolate of P. psidii was used to screen these species for resistance to the biotype of P. psidii established in Australia. The objective was to characterize resistance to P. psidii within these two distinct species: E. argophloia, a vulnerable species with a narrow distribution, and E. cloeziana, a species with a broad and extensive distribution in Queensland. Results for E. cloeziana indicate that inland provenances are more resistant to P. psidii infection than provenances from coastal regions. Heritability estimates for the two assessment systems used (resistance on a 1-to-5 ordinal scale verses resistance on a 0-to-1 binomial scale) were low to high (0.24 to 0.63) for E. argophloia and moderate to high (0.4 to 0.91) for E. cloeziana, indicating a significant level of additive genetic variance for rust resistance within the populations. This study demonstrates the potential to select resistant families within the tested populations and indicates that P. psidii could detrimentally affect these species in native forests, nurseries, and plantations.

Screening Eucalyptus cloeziana and E. argophloia populations for resistance to Puccinia psidii

Disease screening to determine the threat Puccinia psidii poses to plantation and native eucalypts in Australia was undertaken in half-sib families of two contrasting eucalypt species, Eucalyptus cloeziana and E. argophloia. Artificial inoculation with a single-lesion isolate of P. psidii was used to screen these species for resistance to the biotype of P. psidii established in Australia. The objective was to characterize resistance to P. psidii within these two distinct species: E. argophloia, a vulnerable species with a narrow distribution, and E. cloeziana, a species with a broad and extensive distribution in Queensland. Results for E. cloeziana indicate that inland provenances are more resistant to P. psidii infection than provenances from coastal regions. Heritability estimates for the two assessment systems used (resistance on a 1-to-5 ordinal scale verses resistance on a 0-to-1 binomial scale) were low to high (0.24 to 0.63) for E. argophloia and moderate to high (0.4 to 0.91) for E. cloeziana, indicating a significant level of additive genetic variance for rust resistance within the populations. This study demonstrates the potential to select resistant families within the tested populations and indicates that P. psidii could detrimentally affect these species in native forests, nurseries, and plantations. Disease screening to determine the threat Puccinia psidii poses to plantation and native eucalypts in Australia was undertaken in half-sib families of two contrasting eucalypt species, Eucalyptus cloeziana and E. argophloia. Artificial inoculation with a single-lesion isolate of P. psidii was used to screen these species for resistance to the biotype of P. psidii established in Australia. The objective was to characterize resistance to P. psidii within these two distinct species: E. argophloia, a vulnerable species with a narrow distribution, and E. cloeziana, a species with a broad and extensive distribution in Queensland. Results for E. cloeziana indicate that inland provenances are more resistant to P. psidii infection than provenances from coastal regions. Heritability estimates for the two assessment systems used (resistance on a 1-to-5 ordinal scale verses resistance on a 0-to-1 binomial scale) were low to high (0.24 to 0.63) for E. argophloia and moderate to high (0.4 to 0.91) for E. cloeziana, indicating a significant level of additive genetic variance for rust resistance within the populations. This study demonstrates the potential to select resistant families within the tested populations and indicates that P. psidii could detrimentally affect these species in native forests, nurseries, and plantations.

A boat hitchhiker's guide to survival: Cabomba caroliniana desiccation resistance and survival ability

Cabomba caroliniana is a submersed macrophyte that has become a serious invader. Cabomba predominantly spreads by stem fragments, in particular through unintentional transport on boat trailers ('hitch hiking'). Desiccation resistance affects the potential dispersal radius. Therefore, knowledge of maximum survival times allows predicting future dispersal. Experiments were conducted to assess desiccation resistance and survival ability of cabomba fragments under various environmental scenarios. Cabomba fragments were highly tolerant of desiccation. However, even relatively low wind speeds resulted in rapid mass loss, indicating a low survival rate of fragments exposed to air currents, such as fragments transported on a boat trailer. The experiments indicated that cabomba could survive at least 3 h of overland transport if exposed to wind. However, even small clumps of cabomba could potentially survive up to 42 h. Thus, targeting the transport of clumps of macrophytes should receive high priority in management. The high resilience of cabomba to desiccation demonstrates the risk of continuing spread. Because of the high probability of fragment viability on arrival, preventing fragment uptake on boat trailers is paramount to reduce the risk of further spread. These findings will assist improving models that predict the spread of aquatic invasive macrophytes.