Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance

Fifty-four different sugarcane resistance gene analogue (RGA) sequences were isolated, characterized, and used to identify molecular markers linked to major disease-resistance loci in sugarcane. Ten RGAs were identified from a sugarcane stem expressed sequence tag (EST) library; the remaining 44 were isolated from sugarcane stem, leaf, and root tissue using primers designed to conserved RGA motifs. The map location of 31 of the RGAs was determined in sugarcane and compared with the location of quantitative trait loci (QTL) for brown rust resistance. After 2 years of phenotyping, 3 RGAs were shown to generate markers that were significantly associated with resistance to this disease. To assist in the understanding of the complex genetic structure of sugarcane, 17 of the 31 RGAs were also mapped in sorghum. Comparative mapping between sugarcane and sorghum revealed syntenic localization of several RGA clusters. The 3 brown rust associated RGAs were shown to map to the same linkage group (LG) in sorghum with 2 mapping to one region and the third to a region previously shown to contain a major rust-resistance QTL in sorghum. These results illustrate the value of using RGAs for the identification of markers linked to disease resistance loci and the value of simultaneous mapping in sugarcane and sorghum.

Coordination and plasticity in leaf anatomical traits of invasive and native vine species

Premise of the study: Plant invasiveness can be promoted by higher values of adaptive traits (e.g., photosynthetic capacity, biomass accumulation), greater plasticity and coordination of these traits, and by higher and positive relative influence of these functionalities on fitness, such as increasing reproductive output. However, the data set for this premise rarely includes linkages between epidermal–stomatal traits, leaf internal anatomy, and physiological performance.• Methods: Three ecological pairs of invasive vs. noninvasive (native) woody vine species of South-East Queensland, Australia were investigated for trait differences in leaf morphology and anatomy under varying light intensity. The linkages of these traits with physiological performance (e.g., water-use efficiency, photosynthesis, and leaf construction cost) and plant adaptive traits of specific leaf area, biomass, and relative growth rates were also explored.• Key results: Except for stomatal size, mean leaf anatomical traits differed significantly between the two groups. Plasticity of traits and, to a very limited extent, their phenotypic integration were higher in the invasive relative to the native species. ANOVA, ordination, and analysis of similarity suggest that for leaf morphology and anatomy, the three functional strategies contribute to the differences between the two groups in the order phenotypic plasticity > trait means > phenotypic integration.• Conclusions: The linkages demonstrated in the study between stomatal complex/gross anatomy and physiology are scarce in the ecological literature of plant invasiveness, but the findings suggest that leaf anatomical traits need to be considered routinely as part of weed species assessment and in the worldwide leaf economic spectrum.

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.

Should I stay or should I go?: Rural and remote students in first year university stem courses

Research on the achievement of rural and remote students in science and mathematics is located within a context of falling levels of participation in physical science and mathematics courses in Australian schools, and underrepresentation of rural students in higher education. International studies such as the Programme of International Student Assessment (PISA), have reported lower levels of mathematical and scientific literacy in Australian students from rural and remote schools (Thomson et al, 2011). The SiMERR national survey of science, mathematics and ICT education in rural and regional Australia (Lyons et al, 2006) identified factors affecting student achievement in rural and remote schools. Many of the issues faced by rural and remote students in their schools are likely to have implications on their university enrolments in science, technology, engineering and mathematics (STEM) courses. For example, rural and remote students are less likely to attend university in general than their city counterparts and higher university attrition rates have been reported for remote students nationally. This paper examines the responses of a sample of rural/remote Australian first year STEM students at Australian universities to two questions. These related to their intentions to complete the course; and whether -and if so, why- they had ever considered withdrawing from their course. Results indicated that rural students who were still in their course by the end of first year were no more or less likely to consider withdrawing than were their peers from more populous centres. However, almost 20% of the rural cohort had considered withdrawing at some stage in their course, and their explanations provide insights into the reasoning of those who may not persist with their courses at university. These results, in the context of the greater attrition rate of remote students from university, point to the need to identify factors that positively impact on rural and remote students’ interest and achievement in science and mathematics. It also highlights a need for future research into the particular issues remote students may face in deciding whether or not to do science at the two key transition points of senior school and university/TAFE studies, and whether or not to persist in their tertiary studies. This paper is positioned at the intersection of two problems in Australian education. The first is a context of falling levels of participation in physical science and mathematics courses in Australian universities. The second is persistent inequitable access to, and retention in, tertiary education for students from rural and remote areas. Despite considerable research attention to both of these areas over recent years these problems have thus far proved to be intractable. This paper therefore aims to briefly review the relevant Australian literature pertaining to these issues; that is, declining STEM enrolments, and the underrepresentation and retention of rural/remote students in higher education. Given the related problems in these two overlapping domains, we then explore the views of first year rural students enrolled in courses, in relation to their intentions of withdrawing (or not) and the associated reasons for their views.

Remote sensing of leaf area index: enhanced retrieval from close-range and remotely sensed optical observations

A wide range of models used in agriculture, ecology, carbon cycling, climate and other related studies require information on the amount of leaf material present in a given environment to correctly represent radiation, heat, momentum, water, and various gas exchanges with the overlying atmosphere or the underlying soil. Leaf area index (LAI) thus often features as a critical land surface variable in parameterisations of global and regional climate models, e.g., radiation uptake, precipitation interception, energy conversion, gas exchange and momentum, as all areas are substantially determined by the vegetation surface. Optical wavelengths of remote sensing are the common electromagnetic regions used for LAI estimations and generally for vegetation studies. The main purpose of this dissertation was to enhance the determination of LAI using close-range remote sensing (hemispherical photography), airborne remote sensing (high resolution colour and colour infrared imagery), and satellite remote sensing (high resolution SPOT 5 HRG imagery) optical observations. The commonly used light extinction models are applied at all levels of optical observations. For the sake of comparative analysis, LAI was further determined using statistical relationships between spectral vegetation index (SVI) and ground based LAI. The study areas of this dissertation focus on two regions, one located in Taita Hills, South-East Kenya characterised by tropical cloud forest and exotic plantations, and the other in Gatineau Park, Southern Quebec, Canada dominated by temperate hardwood forest. The sampling procedure of sky map of gap fraction and size from hemispherical photographs was proven to be one of the most crucial steps in the accurate determination of LAI. LAI and clumping index estimates were significantly affected by the variation of the size of sky segments for given zenith angle ranges. On sloping ground, gap fraction and size distributions present strong upslope/downslope asymmetry of foliage elements, and thus the correction and the sensitivity analysis for both LAI and clumping index computations were demonstrated. Several SVIs can be used for LAI mapping using empirical regression analysis provided that the sensitivities of SVIs at varying ranges of LAI are large enough. Large scale LAI inversion algorithms were demonstrated and were proven to be a considerably efficient alternative approach for LAI mapping. LAI can be estimated nonparametrically from the information contained solely in the remotely sensed dataset given that the upper-end (saturated SVI) value is accurately determined. However, further study is still required to devise a methodology as well as instrumentation to retrieve on-ground green leaf area index . Subsequently, the large scale LAI inversion algorithms presented in this work can be precisely validated. Finally, based on literature review and this dissertation, potential future research prospects and directions were recommended.

Velocity ratio in the analysis of linear dynamical systems

The transfer matrix method is known to be well suited for a complete analysis of a lumped as well as distributed element, one-dimensional, linear dynamical system with a marked chain topology. However, general subroutines of the type available for classical matrix methods are not available in the current literature on transfer matrix methods. In the present article, general expressions for various aspects of analysis-viz., natural frequency equation, modal vectors, forced response and filter performance—have been evaluated in terms of a single parameter, referred to as velocity ratio. Subprograms have been developed for use with the transfer matrix method for the evaluation of velocity ratio and related parameters. It is shown that a given system, branched or straight-through, can be completely analysed in terms of these basic subprograms, on a stored program digital computer. It is observed that the transfer matrix method with the velocity ratio approach has certain advantages over the existing general matrix methods in the analysis of one-dimensional systems.

Effects of age, length, and pattern of burial on survival of Mikania micrantha stem sections

For many landholders in the South Pacific, weed control of Mikania micrantha Kunth is conducted by manual or mechanical means, leaving fragments on or below the ground to reshoot and grow. Effects of age, length (number of nodes), and pattern of burial on the survival of stem sections of M. micrantha were examined in the field in Viti Levu, Fiji. The experiment was arranged in a randomized factorial design, with number of nodes, age of stem sections, and pattern (depth and orientation) of stem burial as factors. Stem sections with two or three nodes had significantly greater survival (30% and 25%, respectively) than those with one node (12%). Mature stem sections had a significantly greater survival rate (31%) than young stem sections (13%) when buried in either the horizontal or the vertical position. Vertical plantings had significantly greater survival (43%) than horizontal plantings (10%), and for both orientations survival decreased with depth of burial. Only 8% of stem sections survived when cut into smaller (3 to 5 cm) sections and buried at a depth of 10 cm. This study revealed that cutting the M. micrantha stems into smaller sections (<3 cm) and burying them at depths of 10 cm or greater would improve the overall management of M. micrantha in crop and noncrop systems.

The leaf-feeding geometrid Isturgia disputaria (Guenee)-A potential biological control agent for prickly acacia, Vachellia nilotica subsp. indica (Benth.) Kyal. & Boatwr. (Mimosaceae) in Australia

Prickly acacia (Vachellia nilotica subsp. indica), a native multipurpose tree in India, is a weed of National significance, and a target for biological control in Australia. Based on plant genetic and climatic similarities, native range surveys for identifying potential biological control agents for prickly acacia were conducted in India during 2008-2011. In the survey leaf-feeding geometrid, Isturgia disputaria Guenee (syn. Tephrina pulinda), widespread in Tamil Nadu and Karnataka States, was prioritized as a potential biological control agent based on field host range, damage potential and no choice test on non target plant species. Though the field host range study exhibited that V. nilotica ssp. indica and V. nilotica ssp. tomentosa were the primary hosts for successful development of the insect, I. disputaria, replicated no - choice larval feeding and development tests conducted on cut foliage and live plants of nine non-target acacia test plant species in India revealed the larval feeding and development on three of the nine non-target acacia species, V. tortilis, V. planiferons and V. leucophloea in addition to the V. nilotica ssp. indica and V. nilotica ssp. tomentosa. However, the proportion of larvae developing into adults was higher on V. nilotica subsp. indica and V. nilotica subsp. tomentosa, with 90% and 80% of the larvae completing development, respectively. In contrast, the larval mortality was higher on V. tortilis (70%), V. leucophloea (90%) and V. planiferons (70%). The no-choice test results support the earlier host specificity test results of I. disputaria from Pakistan, Kenya and under quarantine in Australia. Contrasting results between field host range and host use pattern under no-choice conditions are discussed.

Growth analysis and biomass partitioning of Cyperus iria in response to rice planting density and nitrogen rate

Cyperus iria is a weed of rice with widespread occurrence throughout the world. Because of concerns about excessive and injudicious use of herbicides, cultural weed management approaches that are safe and economical are needed. Developing such approaches will require a better understanding of weed biology and ecology, as well as of weed response to increases in crop density and nutrition. Knowledge of the effects of nitrogen (N) fertilizer on crop-weed competitive interactions could also help in the development of integrated weed management strategies. The present study was conducted in a screenhouse to determine the effects of rice planting density (0, 5, 10, and 20 plants pot−1) and N rate (0, 50, 100, and 150 kg ha−1) on the growth of C. iria. Tiller number per plant decreased by 73–88%, leaf number by 85–94%, leaf area by 85–98%, leaf biomass by 92–99%, and inflorescence biomass by 96–99% when weed plants were grown at 20 rice plants pot−1 (i.e., 400 plants m−2) compared with weed plants grown alone. All of these parameters increased when N rates were increased. On average, weed biomass increased by 118–389% and rice biomass by 121–275% with application of 50–150 kg N ha−1, compared to control. Addition of N favored weed biomass production relative to rice biomass. Increased N rates reduced the root-to-shoot weight ratio of C. iria. Rice interference reduced weed growth and biomass and completely suppressed C. iria when no N was applied at high planting densities (i.e., 20 plants pot−1). The weed showed phenotypic plasticity in response to N application, and the addition of N increased the competitive ability of the weed over rice at densities of 5 and 10 rice plants pot−1 compared with 20 plants pot−1. The results of the present study suggest that high rice density (i.e., 400 plants m−2) can help suppress C. iria growth even at high N rates (150 kg ha−1).

Fungal Planet description sheets: 371-399

Novel species of fungi described in the present study include the following from Australia: Neoseptorioides eucalypti gen. & sp. nov. from Eucalyptus radiata leaves, Phytophthora gondwanensis from soil, Diaporthe tulliensis from rotted stem ends of Theobroma cacao fruit, Diaporthe vawdreyi from fruit rot of Psidium guajava, Magnaporthiopsis agrostidis from rotted roots of Agrostis stolonifera and Semifissispora natalis from Eucalyptus leaf litter. Furthermore, Neopestalotiopsis egyptiaca is described from Mangifera indica leaves (Egypt), Roussoella mexicana from Coffea arabica leaves (Mexico), Calonectria monticola from soil (Thailand), Hygrocybe jackmanii from littoral sand dunes (Canada), Lindgomyces madisonensis from submerged decorticated wood (USA), Neofabraea brasiliensis from Malus domestica (Brazil), Geastrum diosiae from litter (Argentina), Ganoderma wiiroense on angiosperms (Ghana), Arthrinium gutiae from the gut of a grasshopper (India), Pyrenochaeta telephoni from the screen of a mobile phone (India) and Xenoleptographium phialoconidium gen. & sp. nov. on exposed xylem tissues of Gmelina arborea (Indonesia). Several novelties are introduced from Spain, namely Psathyrella complutensis on loamy soil, Chlorophyllum lusitanicum on nitrified grasslands (incl. Chlorophyllum arizonicum comb. nov.), Aspergillus citocrescens from cave sediment and Lotinia verna gen. & sp. nov. from muddy soil. Novel foliicolous taxa from South Africa include Phyllosticta carissicola from Carissa macrocarpa, Pseudopyricularia hagahagae from Cyperaceae and Zeloasperisporium searsiae from Searsia chirindensis. Furthermore, Neophaeococcomyces is introduced as a novel genus, with two new combinations, N. aloes and N. catenatus. Several foliicolous novelties are recorded from La Réunion, France, namely Ochroconis pandanicola from Pandanus utilis, Neosulcatispora agaves gen. & sp. nov. from Agave vera-cruz, Pilidium eucalyptorum from Eucalyptus robusta, Strelitziana syzygii from Syzygium jambos (incl. Strelitzianaceae fam. nov.) and Pseudobeltrania ocoteae from Ocotea obtusata (Beltraniaceae emend.). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

Genome-wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus

Brassica napus is one of the most important oil crops in the world, and stem rot caused by the fungus Sclerotinia sclerotiorum results in major losses in yield and quality. To elucidate resistance genes and pathogenesis-related genes, genome-wide association analysis of 347 accessions was performed using the Illumina 60K Brassica SNP (single nucleotide polymorphism) array. In addition, the detached stem inoculation assay was used to select five highly resistant (R) and susceptible (S) B. napus lines, 48 h postinoculation with S. sclerotiorum for transcriptome sequencing. We identified 17 significant associations for stem resistance on chromosomes A8 and C6, five of which were on A8 and 12 on C6. The SNPs identified on A8 were located in a 409-kb haplotype block, and those on C6 were consistent with previous QTL mapping efforts. Transcriptome analysis suggested that S. sclerotiorum infection activates the immune system, sulphur metabolism, especially glutathione (GSH) and glucosinolates in both R and S genotypes. Genes found to be specific to the R genotype related to the jasmonic acid pathway, lignin biosynthesis, defence response, signal transduction and encoding transcription factors. Twenty-four genes were identified in both the SNP-trait association and transcriptome sequencing analyses, including a tau class glutathione S-transferase (GSTU) gene cluster. This study provides useful insight into the molecular mechanisms underlying the plant's response to S. sclerotiorum.

Ratio of Diffusion Coefficient to Mobility for Electrons in SF6-Air and Freon-Nitrogen Mixtures

The ratio of diffusion coefficient to mobility (D/¿) for electrons has been measured in SF6-air and freon-nitrogen mixtures for various concentrations of SF6 and freon in the mixtures over the range 140¿ E/p¿ 220 V.cm-1 - torr-1. In SF6-air mixtures, the values of D/¿ were always observed to lie intermediate between the values for the pure gases. However, in freon-nitrogen mixtures, with a small concentration (10 percent) of freon in the mixture, the values of D/¿ are found to lie above the boundaries determined by the pure gases. In this mixture, over the lower E/p range (140 to 190) the electrons appear to lose a large fraction of their energy by the excitation of the complex freon molecules, while at higher E/p values (200 to 240), the excitation and consequent deexcitation of nitrogen molecules and its metastables seem to cause an increased rate of ionization of freon molecules.