Genetic variability of Tomato spotted wilt virus in Australia and validation of real time RT-PCR for its detection in single and bulked leaf samples

The potential for large-scale use of a sensitive real time reverse transcription polymerase chain reaction (RT-PCR) assay was evaluated for the detection of Tomato spotted wilt virus (TSWV) in single and bulked leaf samples by comparing its sensitivity with that of DAS-ELISA. Using total RNA extracted with RNeasy® or leaf soak methods, real time RT-PCR detected TSWV in all infected samples collected from 16 horticultural crop species (including flowers, herbs and vegetables), two arable crop species, and four weed species by both assays. In samples in which DAS-ELISA had previously detected TSWV, real time RT-PCR was effective at detecting it in leaf tissues of all 22 plant species tested at a wide range of concentrations. Bulk samples required more robust and extensive extraction methods with real time RT-PCR, but it generally detected one infected sample in 1000 uninfected ones. By contrast, ELISA was less sensitive when used to test bulked samples, once detecting up to 1 infected in 800 samples with pepper but never detecting more than 1 infected in 200 samples in tomato and lettuce. It was also less reliable than real time RT-PCR when used to test samples from parts of the leaf where the virus concentration was low. The genetic variability among Australian isolates of TSWV was small. Direct sequencing of a 587 bp region of the nucleoprotein gene (S RNA) of 29 isolates from diverse crops and geographical locations yielded a maximum of only 4.3% nucleotide sequence difference. Phylogenetic analysis revealed no obvious groupings of isolates according to geographic origin or host species. TSWV isolates, that break TSWV resistance genes in tomato or pepper did not differ significantly in the N gene region studied, indicating that a different region of the virus genome is responsible for this trait.

New microsatellite loci for Carcharhinid sharks (Carcharhinus tilstoni and C. sorrah) and their cross-amplification in other shark species

Twelve microsatellite DNA markers were isolated in the spot-tail shark (Carcharhinus sorrah) and nine were isolated in Australian black-tip shark (Carcharhinus tilstoni). These loci plus 18 others developed for sharks from the genera Negaprion, Ginglymostoma, Carcharodon and Isurus were tested for amplification success on four species of Carcharhinus (including C. sorrah and C. tilstoni) and four other species representing three diverse families. Cross-amplification was most common within families. Five loci were subsequently tested for polymorphism on 50 C. sorrah and 60 C. tilstoni. The number of alleles per locus was two to 24 and the average heterozygosity was 0.54 (range 0.16-0.87) for C. sorrah and 0.64 (range 0.44-0.78) for C. tilstoni. These loci may be useful tools for genetic analyses of the Carcharhinidae.

The introduction and release of Chiasmia inconspicua and C. assimilis (Lepidoptera: Geometridae) for the biological control of Acacia nilotica in Australia

Two geometrid moths Chiasmia inconspicua and Chiasmia assimilis, identified as potential biological control agents for prickly acacia Acacia nilotica subsp. indica, were collected in Kenya and imported into quarantine facilities in Australia where laboratory cultures were established. Aspects of the biologies of both insects were studied and CLIMEX® models indicating the climatically favourable areas of Australia were developed. Host range tests were conducted using an approved test list of 74 plant species and no-choice tests of neonate larvae placed on both cut foliage and potted plants. C. inconspicua developed through to adult on prickly acacia and, in small numbers, Acacia pulchella. C. assimilis developed through to adult on prickly acacia and also in very small numbers on A. pulchella, A. deanei, A. decurrens, and A. mearnsii. In all experiments, the response on prickly acacia could be clearly differentiated from the responses on the non-target species. Both insects were approved for release in Australia. Over a three-year period releases were made at multiple sites in north Queensland, almost all in inland areas. There was no evidence of either insect's establishment and both colonies were terminated. A new colony of C. assimilis was subsequently established from insects collected in South Africa and releases of C. assimilis from this new colony were made into coastal and inland infestations of prickly acacia. Establishment was rapid at one coastal site and the insect quickly spread to other infestations. Establishment at one inland area was also confirmed in early 2006. The establishment in coastal areas supported a CLIMEX model that indicated that the climate of coastal areas was more suitable than inland areas.

Soil sorption-desorption of phosphorus from piggery effluent compared with inorganic sources

The leaching of phosphorus (P) within soils can be a limiting consideration for the sustainable operation of intensive livestock enterprises. Sorption curves are widely used to assist estimation of P retention, though the effect of effluent constituents on their accuracy is not well understood. We conducted a series of P-sorption-desorption batch experiments with an Oxic Haplustalf (soil 1), Haplusterts (soils 2 and 3), and a Natrustalf (soil 4). Phosphorus sources included effluent, orthophosphate-P in a matrix replicating the effluent's salt constituents (the reference solution), and an orthophosphate-P solution. Treated soils were incubated for up to 193 days before sequential desorption extraction. Effluent constituents, probably the organic or particulate components, temporarily increased the vulnerability of sorbed-P to desorption. The increase in vulnerability was removed by 2-113 days of incubation (25 degrees C). Despite vigorous extraction for 20 consecutive days, some P sorbed as part of the treatments of soils 1 and 2 was not desorbed. The increased vulnerability due to effluent constituents lasted a maximum of about one cropping season and, for all other treatments, adsorption curves overestimated vulnerability to desorption. Therefore, adsorption curves provide a conservative estimate of vulnerability to desorption where effluent is used in continued crop production in these soils.

Concordant molecular and phenotypic data delineate new taxonomy and conservation priorities for the endangered mountain yellow-legged frog

The mountain yellow-legged frog Rana muscosa sensu lato, once abundant in the Sierra Nevada of California and Nevada, and the disjunct Transverse Ranges of southern California, has declined precipitously throughout its range, even though most of its habitat is protected. The species is now extinct in Nevada and reduced to tiny remnants in southern California, where as a distinct population segment, it is classified as Endangered. Introduced predators (trout), air pollution and an infectious disease (chytridiomycosis) threaten remaining populations. A Bayesian analysis of 1901 base pairs of mitochondrial DNA confirms the presence of two deeply divergent clades that come into near contact in the Sierra Nevada. Morphological studies of museum specimens and analysis of acoustic data show that the two major mtDNA clades are readily differentiated phenotypically. Accordingly, we recognize two species, Rana sierrae, in the northern and central Sierra Nevada, and R. muscosa, in the southern Sierra Nevada and southern California. Existing data indicate no range overlap. These results have important implications for the conservation of these two species as they illuminate a profound mismatch between the current delineation of the distinct population segments (southern California vs. Sierra Nevada) and actual species boundaries. For example, our study finds that remnant populations of R. muscosa exist in both the southern Sierra Nevada and the mountains of southern California, which may broaden options for management. In addition, despite the fact that only the southern California populations are listed as Endangered, surveys conducted since 1995 at 225 historic (1899-1994) localities from museum collections show that 93.3% (n=146) of R. sierrae populations and 95.2% (n=79) of R. muscosa populations are extinct. Evidence presented here underscores the need for revision of protected population status to include both species throughout their ranges.

In vitro propagation of Corymbia torelliana x C. citriodora (Myrtaceae) via cytokinin-free node culture

Hybrids between Corymbia torelliana (F.Muell.) K.D.Hill & L.A.S.Johnson and C. citriodora subsp. variegata (F.Muell.) A.R.Bean & M.W.McDonald are used extensively to establish forestry plantations in subtropical Australia. Methods were developed for in vitro seed germination, shoot multiplication and plantlet formation that could be used to establish in vitro and ex vitro clone banks of juvenile Corymbia hybrids. Effects of sodium hypochlorite concentration and exposure time on seed contamination and germination, and effects of cytokinin and auxin concentrations on shoot multiplication and subsequent rooting, were assessed. A two-step surface sterilisation procedure, involving 70% ethanol followed by 1% sodium hypochlorite, provided almost no contamination and at least 88% germination. A novel method of cytokinin-free node culture proved most effective for in vitro propagation. Lateral bud break of primary shoots was difficult to induce by using cytokinin, but primary shoots rooted prolifically, elongated rapidly and produced multiple nodes in the absence of exogenous cytokinin. Further multiplication was obtained either by elongating lateral shoots of nodal explants in cytokinin-free medium or by inducing organogenic callus and axillary shoot proliferation with 2.2 µm benzyladenine. Plantlets were produced using an in vitro soil-less method that provided extensive rooting in sterile propagation mixture. These methods provide a means for simultaneous laboratory storage and field-testing of clones before selection and multiplication of desired genotypes.

Salinity tolerance of twelve hybrid Bermudagrass (Cynodon Dactylon (L.) Pers. x C. Transvaalensis Burtt Davy) genotypes

Salinity is an increasingly important issue in both rural and urban areas throughout much of Australia. The use of recycled/reclaimed water and other sources of poorer quality water to irrigate turf is also increasing. Hybrid Bermudagrass (Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt Davey), together with the parent species C. dactylon, are amongst the most widely used warm-season turf grass groups. Twelve hybrid Bermudagrass genotypes and one accession each of Bermudagrass (C. dactylon), African Bermudagrass (C. transvaalensis) and seashore paspalum (Paspalum vaginatum Sw.) were grown in a glasshouse experiment with six different salinity treatments applied hydroponically through the irrigation water (ECW = <0.1, 6, 12, 18, 24 or 30 dSm-1) in a flood-and-drain system. Each pot was clipped progressively at 2-weekly intervals over the 12-week experimental period to determine dry matter production; leaf firing was rated visually on 3 occasions during the last 6 weeks of salinity treatment. At the end of the experiment, dry weights of roots and crowns below clipping height were also determined. Clipping yields declined sharply after about the first 6 weeks of salinity treatment, but then remained stable at substantially lower levels of dry matter production from weeks 8 to 12. Growth data over this final 4-week experimental period is therefore a more accurate guide to the relative salinity tolerance of the 15 entries than data from the preceding 8 weeks. Based on these data, the 12 hybrid Bermudagrass genotypes showed moderate salinity tolerance, with FloraDwarfM, 'Champion Dwarf', NovotekM and 'TifEagle' ranking as the most salt tolerant and 'Patriot', 'Santa Ana', 'Tifgreen' and TifSport M the least tolerant within the hybrid group. Nevertheless, Santa Ana, for example, maintained relatively strong root growth as salinity increased, and so may show better salt tolerance in practice than predicted from the growth data alone. The 12 hybrid Bermudagrasses and the single African Bermudagrass genotype were all ranked above FloraTeXM Bermudagrass in terms of salt tolerance. However, seashore paspalum, which is widely acknowledged as a halophytic species showing high salt tolerance, ranked well above all 14 Cynodon genotypes in terms of salinity tolerance.

Factors contributing to wear tolerance of Bermudagrass (Cynodon dactylon (L.) Pers., C. dactylon x C. transvaalensis Burtt-Davey) on a sand-based profile under simulated sports field conditions

Wear resistance and recovery of 8 Bermudagrass (Cynodon dactylon (L.) Pers.) and hybrid Bermudagrass (C. Dactylon x C. transvaalensis Burtt-Davey) cultivars grown on a sandbased soil profile near Brisbane, Australia, were assessed in 4 wear trials conducted over a two year period. Wear was applied on a 7-day or a 14-day schedule by a modified Brinkman Traffic Simulator for 6-14 weeks at a time, either during winter-early spring or during summer-early autumn. The more frequent wear under the 7-day treatment was more damaging to the turf than the 14-day wear treatment, particularly during winter when its capacity for recovery from wear was severely restricted. There were substantial differences in wear tolerance among the 8 cultivars investigated, and the wear tolerance rankings of some cultivars changed between years. Wear tolerance was associated with high shoot density, a dense stolon mat strongly rooted to the ground surface, high cell wall strength as indicated by high total cell wall content, and high levels of lignin and neutral detergent fiber. Wear tolerance was also affected by turf age, planting sod quality, and wet weather. Resistance to wear and recovery from wear are both important components of wear tolerance, but the relative importance of their contributions to overall wear tolerance varies seasonally with turf growth rate.

Morphological and developmental comparisons of seven greens quality hybrid bermudagrass (Cynodon dactylon (L.)Pers.x C transvaalensis Burtt-Davy

Fine-textured hybrid bermudagrass [Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] cultivars have been widely used for golf putting greens and lawn bowls greens in warm-climate areas for more than 40 years. During the past decade, the choice of cultivar for professional turfgrass managers has been expanded by a range of secondgeneration hybrid bermudagrasses, which differ from the first-generation cultivars ‘Tifgreen’ and ‘Tifdwarf ’ in their management requirements. In this paper, we present comparative morphological and developmental data for seven cultivars (Champion Dwarf, FloraDwarf, MS-Supreme, Novotek, Tifdwarf, TifEagle, Tifgreen) grown in spaced plant and sward experiments at Cleveland, Australia (27º32’S lat, 153º15’E long, 25 masl). The four ‘ultradwarf ’ cultivars (Champion Dwarf, MS-Supreme, FloraDwarf, TifEagle) showed slower vertical extension and produced fewer inflorescences than Tifdwarf, Tifgreen, and Novotek. However, in terms of the length of stolon internodes and their overall rate of lateral spread, Champion Dwarf, FloraDwarf, and TifEagle were comparable to Tifdwarf; MS-Supreme (with longer internodes) spread faster laterally, though slower than Tifgreen (which had the longest stolon internodes). In unmown swards, the four ultradwarfs produced shorter leaves than Tifgreen, Tifdwarf, and Novotek, but only Champion Dwarf produced significantly narrower leaves than Tifgreen, Tifdwarf, and Novotek, with TifEagle leaves also significantly narrower than those of Tifgreen and Novotek. Minimum threshold temperatures for growth were approximately 9° to 10°C (air temperature) and 15° to 16°C at 10 cm soil depth.

Relationships between Indole-3-butyric Acid, Photoinhibition and Adventitious rooting of Corymbia torelliana, C. citriodora and F1 Hybrid Cuttings

Rooted cutting propagation is widely used for maximising tree yield, quality and uniformity in conjunction with clonal selection. Some eucalypt species are deployed as rooted cuttings but many are considered to difficult to root. This study examined IBA effects on photoinhibition, root formation, mortality and root and shoot development in cuttings of Corymbia torelliana, C. citriodora and their hybrids. IBA had little or no effect on photoinhibition but it had strong, dose-dependent effects on root formation and mortality. IBA frequently increases primary root number of rooted cutting but it did not increase total root weight, length, surface area or volume, possibly because the highest doe (8g IBA/kg IBA/kg powder) caused leaf abscission and sometimes reduced leaf area (by 55-79%)or shoot dry weight (by 40-58%). An intermediate dose (3g IBA/kg powder) most consistnely improved root formation with little or no effect on mortality or shoot development. Across the F1 hybrid families this treatment increased the number of rooted cuttings by 72-121% and more than ddoubled the number of primary roots per rooted cutting (from 1.1-1.7 roots to 3.5-4.1 roots). This simple treatment will facilitate commercial multiplication of superior individuals or selected families of C. torelliana x C. citriodora through a vegetative propagation system.

Towards better management of Australia’s shark fishery: genetic analyses reveal unexpected ratios of cryptic blacktip species Carcharhinus tilstoni and C. limbatus

The common blacktip shark (Carcharhinus limbatus) and the Australian blacktip shark (C. tilstoni) are morphologically similar species that co-occur in subtropical and tropical Australia. In striking contrast to what has been previously reported, we demonstrate that the common blacktip shark is not rare in northern Australia but occurs in approximately equal frequencies with the Australian blacktip shark. Management of shark resources in northern Australia needs to take account of this new information. Species identification was performed using nucleotide sequences of the control, NADH dehydrogenase subunit 4 (ND4) and cytochrome oxidase I (COI) regions in the mitochondrial genome. The proportion of overall genetic variation (FST) between the two species was small (0.042, P < 0.01) based on allele frequencies at five microsatellite loci. We confirm that a third blacktip species (C. amblyrhynchoides, graceful shark) is closely related to C. tilstoni and C. limbatus and can be distinguished from them on the basis of mtDNA sequences from two gene regions. The Australian blacktip shark (C. tilstoni) was not encountered among 20 samples from central Indonesia that were later confirmed to be common blacktip and graceful sharks. Fisheries regulators urgently need new information on life history, population structure and morphological characters for species identification of blacktip shark species in Australia.

Soil C stocks in grains and sugar farming systems

Quantify soil C stocks in grains and sugarcane cropping systems of Queensland, including impacts of management practices.

Evaluation of wood characteristics of tropical post-mid rotation plantation Eucalyptus cloeziana and E. pellita: Part (c) Wood quality and structural properties.

This study provides information about wood quality, structural properties, processing characterists and product suitability of wood harvested from fast-grown hardwood plantations. Wood quality attributes tested included density, extractive content, unit shrinkage, heartwood proportion and sapwood width. Structural properties tested included small clear and full section strength and stiffness, hardness, joint group, visual grade assessment and natural vibration-based grade assessment. The variation between the inner, intermediate and outer heartwood zones and the variation between provenances was also tested. Overall, the wood qualtiy attributes measured for 19 year-old E. cloeziana and 15 year-old E. pellita plantation material fall between those expected from the wood of mature, native forest trees and those found in younger plantation material of the same species.

Finding genes for economically important traits: Brahman cattle puberty.

Age at puberty is an important component of reproductive performance in beef cattle production systems. Brahman cattle are typically late-pubertal relative to Bos taurus cattle and so it is of economic relevance to select for early age at puberty. To assist selection and elucidate the genes underlying puberty, we performed a genome-wide association study (GWAS) using the BovineSNP50 chip (similar to 54 000 polymorphisms) in Brahman bulls (n = 1105) and heifers (n = 843) and where the heifers were previously analysed in a different study. In a new attempt to generate unbiased estimates of single-nucleotide polymorphism (SNP) effects and proportion of variance explained by each SNP, the available data were halved on the basis of year and month of birth into a calibration and validation set. The traits that defined age at puberty were, in heifers, the age at which the first corpus luteum was detected (AGECL, h(2) = 0.56 +/- 0.11) and in bulls, the age at a scrotal circumference of 26 cm (AGE26, h(2) = 0.78 +/- 0.10). At puberty, heifers were on average older (751 +/- 142 days) than bulls (555 +/- 101 days), but AGECL and AGE26 were genetically correlated (r = 0.20 +/- 0.10). There were 134 SNPs associated with AGECL and 146 SNPs associated with AGE26 (P < 0.0001). From these SNPs, 32 (similar to 22%) were associated (P < 0.0001) with both traits. These top 32 SNPs were all located on Chromosome BTA 14, between 21.95 Mb and 28.4 Mb. These results suggest that the genes located in that region of BTA 14 play a role in pubertal development in Brahman cattle. There are many annotated genes underlying this region of BTA 14 and these are the subject of current research. Further, we identified a region on Chromosome X where markers were associated (P < 1.00E-8) with AGE26, but not with AGECL. Information about specific genes and markers add value to our understanding of puberty and potentially contribute to genomic selection. Therefore, identifying these genes contributing to genetic variation in AGECL and AGE26 can assist with the selection for early onset of puberty.

Fungal Planet description sheets: 128-153

Novel species of microfungi described in the present study include the following from Australia: Catenulostroma corymbiae from Corymbia, Devriesia stirlingiae from Stirlingia, Penidiella carpentariae from Carpentaria, Phaeococcomyces eucalypti from Eucalyptus, Phialophora livistonae from Livistona, Phyllosticta aristolochiicola from Aristolochia, Clitopilus austroprunulus on sclerophyll forest litter of Eucalyptus regnans and Toxicocladosporium posoqueriae from Posoqueria. Several species are also described from South Africa, namely: Ceramothyrium podocarpi from Podocarpus, Cercospora chrysanthemoides from Chrysanthemoides, Devriesia shakazului from Aloe, Penidiella drakensbergensis from Protea, Strelitziana cliviae from Clivia and Zasmidium syzygii from Syzygium. Other species include Bipolaris microstegii from Microstegium and Synchaetomella acerina from Acer (USA), Brunneiapiospora austropalmicola from Rhopalostylis (New Zealand), Calonectria pentaseptata from Eucalyptus and Macadamia (Vietnam), Ceramothyrium melastoma from Melastoma (Indonesia), Collembolispora aristata from stream foam (Czech Republic), Devriesia imbrexigena from glazed decorative tiles (Portugal), Microcyclospora rhoicola from Rhus (Canada), Seiridium phylicae from Phylica (Tristan de Cunha, Inaccessible Island), Passalora lobeliaefistulosis from Lobelia (Brazil) and Zymoseptoria verkleyi from Poa (The Netherlands). Valsalnicola represents a new ascomycete genus from Alnus (Austria) and Parapenidiella a new hyphomycete genus from Eucalyptus (Australia). Morphological and culture characteristics along with ITS DNA barcodes are also provided. © 2012 Nationaal Herbarium Nederland & Centraalbureau voor Schimmelcultures.