Mapping quantitative trait loci for resistance to Pratylenchus thornei from synthetic hexaploid wheat in the International Triticeae Mapping Initiative (ITMI) population

Root-lesion nematode (Pratylenchus thornei) is a serious pathogen of wheat in many countries. The International Triticeae Mapping Initiative (ITMI) population of recombinant inbred lines (RILs) was assessed for resistance to P. thornei to determine the chromosome locations of the resistance genes. The ITMI population is derived from a cross between the resistant synthetic hexaploid wheat W-7984 and a susceptible bread wheat cultivar Opata 85. Two years of phenotypic data for resistance to P. thornei were obtained in replicated glasshouse trials. Quantitative trait locus (QTL) analysis was performed using available segregation and map data for 114 RILs. A QTL on chromosome 6DS showed consistent effects for reduced nematode numbers (partial resistance) across years and accounted for 11% and 23% of the phenotypic variation. A second QTL for P. thornei resistance on chromosome 2BS accounted for an additional 19% and 5%. Restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers associated with the QTLs are physically located in regions rich in major genes at the distal ends of the short chromosome arms of 6D and 2B. SSR markers with potential for marker-assisted selection of P. thornei resistance effective in different genetic backgrounds have been identified.

The accuracy of varietal selection using factor analytic models for multi-environment plant breeding trials

Modeling of cultivar x trial effects for multienvironment trials (METs) within a mixed model framework is now common practice in many plant breeding programs. The factor analytic (FA) model is a parsimonious form used to approximate the fully unstructured form of the genetic variance-covariance matrix in the model for MET data. In this study, we demonstrate that the FA model is generally the model of best fit across a range of data sets taken from early generation trials in a breeding program. In addition, we demonstrate the superiority of the FA model in achieving the most common aim of METs, namely the selection of superior genotypes. Selection is achieved using best linear unbiased predictions (BLUPs) of cultivar effects at each environment, considered either individually or as a weighted average across environments. In practice, empirical BLUPs (E-BLUPs) of cultivar effects must be used instead of BLUPs since variance parameters in the model must be estimated rather than assumed known. While the optimal properties of minimum mean squared error of prediction (MSEP) and maximum correlation between true and predicted effects possessed by BLUPs do not hold for E-BLUPs, a simulation study shows that E-BLUPs perform well in terms of MSEP.

Identification and host-plant associations of Australian Sericothripinae (Thysanoptera, Thripidae)

The Sericothripinae is a largely tropical group of about 140 species that are often strikingly bicoloured and have complex surface sculpture, but for which the biology is poorly known. Although 15 genera have been described in this subfamily, only three of these are currently recognised, with five new generic synonymies indicated here. In Australia, Sericothrips Haliday is introduced, with one European species deployed as a weed biological control agent. Hydatothrips Karny comprises 43 species worldwide, with six species found in Australia, of which two are shared with Southeast Asia, and four are associated with the native vine genus, Parsonsia. Neohydatothrips John comprises 96 species worldwide, with nine species in Australia, of which one is shared with Southeast Asia and two are presumably introduced from the Americas. Illustrated keys are provided to the three genera and 16 species from Australia, including six new species [Hydatothrips aliceae; H. bhattii; H. williamsi; Neohydatothrips barrowi, N. bellissi, N. katherinae]. One new specific synonym is recognised [Hydatothrips haschemi Girault (= H. palawanensis Kudo)], also four new generic synonyms [Neohydatothrips John (= Faureana Bhatti; Onihothrips Bhatti; Sariathrips Bhatti; Papiliothrips Bhatti); Sericothrips Haliday (= Sussericothrips Han)].

Cyanide poisoning in cattle from Dysphania glomulifera (red crumbweed): Using the internet for rapid plant identification and diagnostic advice: Case Report

A 300-strong Angus-Brahman cattle herd near Springsure, central Queensland, was being fed Acacia shirleyi (lancewood) browse during drought and crossed a 5-hectare, previously burnt area with an almost pure growth of Dysphania glomulifera subspecies glomulifera (red crumbweed) on their way to drinking water. Forty cows died of cyanide poisoning over 2 days before further access to the plant was prevented. A digital image of a plant specimen made on a flat-bed scanner and transmitted by email was used to identify D glomulifera. Specific advice on the plant's poisonous properties and management of the case was then provided by email within 2 hours of an initial telephone call by the field veterinarian to the laboratory some 600 km away. The conventional method using physical transport of a pressed dried plant specimen to confirm the identification took 5 days. D glomulifera was identified in the rumen of one of two cows necropsied. The cyanogenic potential of D glomulifera measured 4 days after collection from the site of cattle deaths was 18,600 mg HCN/kg in dry matter. The lethal dose of D glomulifera for a 420 kg cow was estimated as 150 to 190 g wet weight. The plant also contained 4.8% KNO3 equivalent in dry matter, but nitrate-nitrite poisoning was not involved in the deaths.

Testing insecticides against Phthorimaea operculella (Zeller) (Lepidoptera: Gelechiidae) using a tomato plant bioassay

A bioassay technique was developed to test the efficacy of insecticides against potato moth (Phthorimaea operculella (Zeller)) on tomatoes. The technique tested efficacy against both larvae in mines and neonate larvae that had not yet penetrated the leaf, and explained the failure of some insecticides to control P. operculella infestations in commercial tomato crops. Neonate larvae placed on leaves of potted plants several days before treatment provided larvae for testing of insecticides against larvae in mines; other neonates were placed on leaves after treatment to test efficacy against larvae yet to penetrate the leaf. The plants were sprayed with the candidate insecticides, held for 5-7 days, and larval mortality assessed. Chlorfenapyr (100, 200 g a.i. ha-1) and abamectin (8.1 g a.i. ha-1) were effective against neonate larvae and larvae in mines. Sulprofos (720 g a.i. ha -1), methomyl (450 g a.i. ha-1) and spinosad (96 g a.i. ha-1) were effective against neonate larvae but not against larvae in mines. Methamidophos (1102 g a.i. ha-1), endosulfan (700 g a.i. ha-1) and Bacillus thuringiensis kurstaki (1000 g ha-1) had some effect against exposed larvae but little against larvae in mines. Thiodicarb (525 g a.i. ha-1), azinphos-ethyl (440 g a.i. ha -1), imidacloprid (59.5 g a.i. ha-1), hexaflumuron (50 g a.i. ha-1), methoxyfenozide (300 g a.i. ha-1) and tebufenozide (200 g a.i. ha-1) were ineffective. A field trial using chlorfenapyr (25, 50, 100, 150 and 200 g a.i. ha-1) and methamidophos (1102 g a.i. ha-1) validated the bioassay technique, with chlorfenapyr effective in reducing the numbers of larvae in mines in leaves.

Plant hosts of the phytoplasmas and rickettsia-like-organisms associated with strawberry lethal yellows and green petal diseases

Candidatus Phytoplasma australiense (Ca. P. australiense) is associated with the plant diseases strawberry lethal yellows (SLY), strawberry green petal (SGP), papaya dieback (PDB), Australian grapevine yellows (AGY) and Phormium yellow leaf (PYL; New Zealand). Strawberry lethal yellows disease is also associated with a rickettsia-like-organism (RLO) or infrequently with the tomato big bud (TBB) phytoplasma, the latter being associated with a wide range of plant diseases throughout Australia. In contrast, the RLO has been identified only in association with SLY disease, and Ca. P. australiense has been detected only in a limited number of plant host species. The aim of this study was to identify plant hosts that are possible reservoirs of Ca. P. australiense and the SLY RLO. Thirty-one plant species from south-east Queensland were observed with disease between 2001 and 2003 and, of these, 18 species tested positive using phytoplasma-specific primers. The RLO was detected in diseased Jacksonia scoparia and Modiola caroliniana samples collected at Stanthorpe. The TBB phytoplasma was detected in 16 different plant species and Ca. P. australiense Australian grapevine yellows strain was detected in six species. The TBB phytoplasma was detected in plants collected at Nambour, Stanthorpe, Warwick and Brisbane. Ca. P. australiense was detected in plants collected at Nambour, Stanthorpe, Gatton and Allora. All four phytoplasmas were detected in diseased Gomphocarpus physocarpus plants collected at Toowoomba, Allora, Nambour and Gatton. These results indicated that the vector(s) of Ca. P. australiense are distributed throughout south-east Queensland and the diversity of phytoplasmas detected in G. physocarpus suggests it is a feeding source for phytoplasma insect vectors or it has a broad susceptibility to a range of phytoplasmas.

Simple sequence repeat markers associated with three quantitative trait loci for black point resistance can be used to enrich selection populations in bread wheat

Black point in wheat has the potential to cost the Australian industry $A30.4 million a year. It is difficult and expensive to screen for resistance, so the aim of this study was to validate 3 previously identified quantitative trait loci (QTLs) for black point resistance on chromosomes 2B, 4A, and 3D of the wheat variety Sunco. Black point resistance data and simple sequence repeat (SSR) markers, linked to the resistance QTLs and suited to high-throughput assay, were analysed in the doubled haploid population, Batavia (susceptible) × Pelsart (resistant). Sunco and Pelsart both have Cook in their pedigree and both have the Triticum timopheevii translocation on 2B. SSR markers identified for the 3 genetic regions were gwm319 (2B, T. timopheevii translocation), wmc048 (4AS), and gwm341 (3DS). Gwm319 and wmc048 were associated with black point resistance in the validation population. Gwm341 may have an epistatic influence on the trait because when resistance alleles were present at both gwm319 and wmc048, the Batavia-derived allele at gwm341 was associated with a higher proportion of resistant lines. Data are presented showing the level of enrichment achieved for black point resistance, using 1, 2, or 3 of these molecular markers, and the number of associated discarded resistant lines. The level of population enrichment was found to be 1.83-fold with 6 of 17 resistant lines discarded when gwm319 and wmc048 were both used for selection. Interactions among the 3 QTLs appear complex and other genetic and epigenetic factors influence susceptibility to black point. Polymorphism was assessed for these markers within potential breeding material. This indicated that alternative markers to wmc048 may be required for some parental combinations. Based on these results, marker-assisted selection for the major black point resistance QTLs can increase the rate of genetic gain by improving the selection efficiency and may facilitate stacking of black point resistances from different sources.

Simulating the effects of saline and sodic subsoils on wheat crops growing on Vertosols

Soils with high levels of chloride and/or sodium in their subsurface layers are often referred to as having subsoil constraints (SSCs). There is growing evidence that SSCs affect wheat yields by increasing the lower limit of a crop's available soil water (CLL) and thus reducing the soil's plant-available water capacity (PAWC). This proposal was tested by simulation of 33 farmers' paddocks in south-western Queensland and north-western New South Wales. The simulated results accounted for 79% of observed variation in grain yield, with a root mean squared deviation (RMSD) of 0.50 t/ha. This result was as close as any achieved from sites without SSCs, thus providing strong support for the proposed mechanism that SSCs affect wheat yields by increasing the CLL and thus reducing the soil's PAWC. In order to reduce the need to measure CLL of every paddock or management zone, two additional approaches to simulating the effects of SSCs were tested. In the first approach the CLL of soils was predicted from the 0.3-0.5 m soil layer, which was taken as the reference CLL of a soil regardless of its level of SSCs, while the CLL values of soil layers below 0.5 m depth were calculated as a function of these soils' 0.3-0.5 m CLL values as well as of soil depth plus one of the SSC indices EC, Cl, ESP, or Na. The best estimates of subsoil CLL values were obtained when the effects of SSCs were described by an ESP-dependent function. In the second approach, depth-dependent CLL values were also derived from the CLL values of the 0.3-0.5 m soil layer. However, instead of using SSC indices to further modify CLL, the default values of the water-extraction coefficient (kl) of each depth layer were modified as a function of the SSC indices. The strength of this approach was evaluated on the basis of correlation of observed and simulated grain yields. In this approach the best estimates were obtained when the default kl values were multiplied by a Cl-determined function. The kl approach was also evaluated with respect to simulated soil moisture at anthesis and at grain maturity. Results using this approach were highly correlated with soil moisture results obtained from simulations based on the measured CLL values. This research provides strong evidence that the effects of SSCs on wheat yields are accounted for by the effects of these constraints on wheat CLL values. The study also produced two satisfactory methods for simulating the effects of SSCs on CLL and on grain yield. While Cl and ESP proved to be effective indices of SSCs, EC was not effective due to the confounding effect of the presence of gypsum in some of these soils. This study provides the tools necessary for investigating the effects of SSCs on wheat crop yields and natural resource management (NRM) issues such as runoff, recharge, and nutrient loss through simulation studies. It also facilitates investigation of suggested agronomic adaptations to SSCs.

Mapping of adult plant resistance to net form of net blotch in three Australian barley populations

Net form of net blotch (NFNB), caused by Pyrenophora teres Drechs. f. teres Smedeg., is a serious disease problem for the barley industry in Australia and other parts of the world. Three doubled haploid barley populations, Alexis/Sloop, WI2875-1/Alexis, and Arapiles/Franklin, were used to identify genes conferring adult plant resistance to NFNB in field trials. Quantitative trait loci (QTLs) identified were specific for adult plant resistance because seedlings of the parental lines were susceptible to the NFNB isolates used in this study. QTLs were identified on chromosomes 2H, 3H, 4H, and 7H in both the Alexis/Sloop and WI2875-1/Alexis populations and on chromosomes 1H, 2H, and 7H in the Arapiles/Franklin population. Using QTLNetwork, epistatic interactions were identified between loci on chromosomes 3H and 6H in the Alexis/Sloop population, between 2H and 4H in the WI2875-1/Alexis population, and between 5H and 7H in the Arapiles/Franklin population. Comparisons with earlier studies of NFNB resistance indicate the pathotype-dependent nature of many resistance QTLs and the importance of establishing an international system of pathotype nomenclature and differential testing.

Coolamon subterranean clover (Trifolium subterraneum L. var. subterraneum)

Coolamon is a mid-season to late-season flowering F4-derived crossbred subterranean clover of var. subterraneum, developed by the collaborating organisations of the National Annual Pasture Legume Improvement Program. It is a replacement for Junee and has been selected for release on the basis of its greater herbage production and persistence, and its resistance to both known races of clover scorch. Coolamon is recommended for sowing in Western Australia, New South Wales, Victoria, South Australia and Queensland. It is best suited to well-drained, moderately acidic soils in areas with a growing season of 6.5-8 months that extends into November. Coolamon is best suited to phase farming and permanent pasture systems. It can also be used in cropping rotations, but at least 2 years of pasture are required between crops. Coolamon has been granted Plant Breeders Rights in Australia.

Fate of potassium fertilisers applied to clay soils under rainfed grain cropping in south-east Queensland, Australia

Negative potassium (K) balances in all broadacre grain cropping systems in northern Australia are resulting in a decline in the plant-available reserves of K and necessitating a closer examination of strategies to detect and respond to developing K deficiency in clay soils. Grain growers on the Red Ferrosol soils have increasingly encountered K deficiency over the last 10 years due to lower available K reserves in these soils in their native condition. However, the problem is now increasingly evident on the medium-heavy clay soils (Black and Grey Vertosols) and is made more complicated by the widespread adoption of direct drill cropping systems and the resulting strong strati. cation of available K reserves in the top 0.05-0.1 m of the soil pro. le. This paper reports glasshouse studies examining the fate of applied K fertiliser in key cropping soils of the inland Burnett region of south-east Queensland, and uses the resultant understanding of K dynamics to interpret results of field trials assessing the effectiveness of K application strategies in terms of K availability to crop plants. At similar concentrations of exchangeable K (K-exch), soil solution K concentrations and activity of K in the soil solution (AR(K)) varied by 6-7-fold between soil types. When K-exch arising from different rates of fertiliser application was expressed as a percentage of the effective cation exchange capacity (i.e. K saturation), there was evidence of greater selective adsorption of K on the exchange complex of Red Ferrosols than Black and Grey Vertosols or Brown Dermosols. Both soil solution K and AR(K) were much less responsive to increasing K-exch in the Black Vertosols; this is indicative of these soils having a high K buffer capacity (KBC). These contrasting properties have implications for the rate of diffusive supply of K to plant roots and the likely impact of K application strategies (banding v. broadcast and incorporation) on plant K uptake. Field studies investigating K application strategies (banding v. broadcasting) and the interaction with the degree of soil disturbance/mixing of different soil types are discussed in relation to K dynamics derived from glasshouse studies. Greater propensity to accumulate luxury K in crop biomass was observed in a Brown Ferrosol with a KBC lower than that of a Black Vertosol, consistent with more efficient diffusive supply to plant roots in the Ferrosol. This luxury K uptake, when combined with crops exhibiting low proportional removal of K in the harvested product (i.e. low K harvest index coarse grains and winter cereals) and residue retention, can lead to rapid re-development of stratified K profiles. There was clear evidence that some incorporation of K fertiliser into soil was required to facilitate root access and crop uptake, although there was no evidence of a need to incorporate K fertiliser any deeper than achieved by conventional disc tillage (i.e. 0.1-0.15 m). Recovery of fertiliser K applied in deep (0.25-0.3 m) bands in combination with N and P to facilitate root proliferation was quite poor in Red Ferrosols and Grey or Black Vertosols with moderate effective cation exchange capacity (ECEC, 25-35 cmol(+)/kg), was reasonable but not enough to overcome K deficiency in a Brown Dermosol (ECEC 11 cmol(+)/kg), but was quite good on a Black Vertosol (ECEC 50-60 cmol(+)/kg). Collectively, results suggest that frequent small applications of K fertiliser, preferably with some soil mixing, is an effective fertiliser application strategy on lighter clay soils with low KBC and an effective diffusive supply mechanism. Alternately, concentrated K bands and enhanced root proliferation around them may be a more effective strategy in Vertosol soils with high KBC and limited diffusive supply. Further studies to assess this hypothesis are needed.

Review: Near infrared spectroscopy of faeces to evaluate the nutrition and physiology of herbivores

Near infrared (NIR) spectroscopy, usually in reflectance mode, has been applied to the analysis of faeces to measure the concentrations of constituents such as total N, fibre, tannins and delta C-13. In addition, an unusual and exciting application of faecal NIR [F.NIR] analyses is to directly predict attributes of the diet of herbivores such as crude protein and fibre contents, proportions of plant species and morphological components, diet digestibility and voluntary DM intake. This is an unusual application of NIR spectroscopy insofar as the spectral measurements are made, not on the material of interest [i.e. the diet), but on a derived material (i.e. faeces). Predictions of diet attributes from faecal spectra clearly depend on there being sufficient NIR spectral information in the diet residues present in faeces to describe the diet, although endogenous components of faeces such as undigested debris of micro-organisms from the rumen and Large intestine and secretions into the gastrointestinal tract wilt also contribute spectral information. Spectra of forage and of faeces derived from the forage are generally similar and the observed differences are principally in the spectral regions associated with constituents of forages known to be of low, or of high, digestibility. Some diet components (for example, ureal which are likely to be entirely digested apparently cannot be predicted from faecal NIR spectra because they cannot contribute to faecal spectra except through modifying the microbial and endogenous components. The errors and robustness of F.NIR calibrations to predict the crude protein concentration and digestibility of the diet of herbivores are generally comparable with those to directly predict the same attributes in forage from NIR spectra of the forage. Some attributes of the animal, such as species, gender, pregnancy status and parasite burden have been successfully discriminated into classes based on their faecal NIR spectra. Such discrimination was likely associated with differences in the diet selected and/or differences in the metabolites excreted in the faeces. NIR spectroscopy of faeces has usually involved scanning dried and ground samples in monochromators in the 400-2500nm or 1100-2500nm ranges. Results satisfactory for the purpose have also been reported for dried and ground faeces scanned using a diode array instrument in the 800-1700nm range and for wet faeces and slurries of excreta scanned with monochromators. Chemometric analysis of faecal spectra has generally used the approaches established for forage analysis. The capacity to predict many attributes of the diet, and some aspects of animal physiology, from NIR spectra of faeces is particularly useful to study the quality and quantity of the diet selected by both domestic and feral grazing herbivores and to enhance production and management of both herbivores and their grazing environment.

Approaches to selecting native plant replacements for fleshy-fruited invasive species

Invasive plants are a serious threat to biodiversity. Yet, in some cases, they may play an important ecological role in heavily modified landscapes, such as where fleshy-fruited invasive plants support populations of native frugivores. How can such conservation conflicts be managed? We advocate an approach in which native fleshy-fruited plants are ranked on their ability to provide the fruit food resources for native frugivores currently being provided by invasive plants. If these native taxa are preferentially used, where ecologically appropriate, in plantings for restoration and in park and garden settings, they could help support native frugivore populations in the event of extensive invasive plant control. We develop and critically examine six approaches to selecting candidate native plant taxa: a multivariate approach based on the frugivore assemblage, a scoring model, and several multivariate approaches (including trait combinations having the greatest correlation with the diet of the native frugivore assemblage) based on the functional traits of fruit morphology, phenology, conspicuousness, and accessibility. To illustrate these approaches, we use a case study with Bitou bush (Chrysanthemoides monilifera subsp. rotundata) (Asteraceae), an Australian Weed of National Significance. The model using a dissimilarity value generated from all available traits identified a set of species used by the frugivores of C. monilifera more than null models. A replacement approach using species ranked by either all traits available or the frugivore community appears best suited to guide selection of plants in restoration practice.

Predicting dispersal and recruitment of Miconia calvescens (Melastomataceae) in Australian tropical rainforests

Miconia calvescens (Melastomataceae) is a serious invader in the tropical Pacific, including the Hawaiian and Tahitian Islands, and currently poses a major threat to native biodiversity in the Wet Tropics of Australia. The species is fleshy-fruited, small-seeded and shade tolerant, and thus has the potential to be dispersed widely and recruit in relatively intact rainforest habitats, displacing native species. Understanding and predicting the rate of spread is critical for the design and implementation of effective management actions. We used an individual-based model incorporating a dispersal function derived from dispersal curves for similar berry-fruited native species, and life-history parameters of fecundity and mortality to predict the spatial structure of a Miconia population after a 30 year time period. We compared the modelled population spatial structure to that of an actual infestation in the rainforests of north Queensland. Our goal was to assess how well the model predicts actual dispersion and to identify potential barriers and conduits to seed movement and seedling establishment. The model overpredicts overall population size and the spatial extent of the actual infestation, predicting individuals to occur at a maximum 1,750 m from the source compared with the maximum distance of any detected individual in the actual infestation of 1,191 m. We identify several characteristic features of managed invasive populations that make comparisons between modelled outcomes and actual infestations difficult. Our results suggest that the model’s ability to predict both spatial structure and spread of the population will be improved by incorporating a spatially explicit element, with dispersal and recruitment probabilities that reflect the relative suitability of different parts of the landscape for these processes.

Worldwide phylogeography of the globally invasive plant: Jatropha gossypiifolia

Dhileepan, Raghu and colleagues recently published their paper 'Worldwide phylogeography of the globally invasive plant: Jatropha gossypiifolia' in Proceedings of the 16th Australian Weeds Conference. They used chloroplast microsatellites to establish patterns of phylogeographic structure in the native and introduced range of Jatropha gossypiifolia, and to determine the origin(s) of introductions and the level of genetic diversity present in native and introduced populations. J. gossypiifolia exhibited limited phylogeographic structure in its native range which was best explained by contemporary movement associated with the ornamental plant trade. Multiple introductions from diverse source locations and no reduction in genetic diversity was found in the introduced range which includes Australia, Africa and Asia. These results have implications for our current biocontrol project.