Genetic diversity, aggressiveness and metalaxyl sensitivity of Pythium spinosum infecting cucumber in Oman

A total of 24 isolates of Pythium spinosum from cucumber obtained from five regions in Oman were characterized for genetic diversity using amplified fragment length polymorphism (AFLP) fingerprinting and three isolates from the Netherlands, South Africa and Japan were included for comparison. Isolates from Oman were also characterized for aggressiveness on cucumber seedlings and sensitivity to metalaxyl. Identity of all isolates was confirmed using sequences of the internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA), which showed more than 99% nucleotide similarity among all isolates. Using six primer-pair combinations, AFLP fingerprinting resolved 295 AFLP markers of which 193 were polymorphic among isolates from other countries and only six were polymorphic among isolates of P. spinosum from Oman. Seven different AFLP phenotypes of P. spinosum were recovered in Oman; two of them were found to contain over 79% of isolates and one was recovered from all regions in Oman. Phenotypes from Oman showed very high (?99%) levels of genetic similarity to each other compared to moderate (mean =53%) levels of genetic similarity with phenotypes from other countries. In addition, all isolates from Oman were found to be highly sensitive to metalaxyl and all were aggressive on cucumber seedlings at 25°C. The high genetic similarity among phenotypes of P. spinosum in Oman as well as recovering two major clones across regions may suggest that P. spinosum has been recently introduced in Oman via a common source.

Molecular discrimination of Perna (Mollusca: Bivalvia) species using the polymerase chain reaction and species-specific mitochondrial primers

This work was prompted by the need to be able to identify the invasive mussel species, Perna viridis, in tropical Australian seas using techniques that do not rely solely on morphology. DNA-based molecular methods utilizing a polymerase chain reaction (PCR) approach were developed to distinguish unambiguously between the three species in the genus Perna. Target regions were portions of two mitochondrial genes, cox1 and nad4, and the intergenic spacer between these that occurs in at least two Perna species. Based on interspecific sequence comparisons of the nad4 gene, a conserved primer has been designed that can act as a forward primer in PCRs for any Perna species. Four reverse primers have also been designed, based on nad4 and intergenic spacer sequences, which yield species-specific products of different lengths when paired with the conserved forward primer. A further pair of primers has been designed that will amplify part of the cox1 gene of any Perna species, and possibly other molluscs, as a positive control to demonstrate that the PCR is working.

Genetic control of wheat quality: interactions between chromosomal regions determining protein content and composition, dough rheology, and sponge and dough baking properties

While the genetic control of wheat processing characteristics such as dough rheology is well understood, limited information is available concerning the genetic control of baking parameters, particularly sponge and dough (S&D) baking. In this study, a quantitative trait loci (QTL) analysis was performed using a population of doubled haploid lines derived from a cross between Australian cultivars Kukri x Janz grown at sites across different Australian wheat production zones (Queensland in 2001 and 2002 and Southern and Northern New South Wales in 2003) in order to examine the genetic control of protein content, protein expression, dough rheology and sponge and dough baking performance. The study highlighted the inconsistent genetic control of protein content across the test sites, with only two loci (3A and 7A) showing QTL at three of the five sites. Dough rheology QTL were highly consistent across the 5 sites, with major effects associated with the Glu-B1 and Glu-D1 loci. The Glu-D1 5 + 10 allele had consistent effects on S&D properties across sites; however, there was no evidence for a positive effect of the high dough strength Glu-B1-al allele at Glu-B1. A second locus on 5D had positive effects on S&D baking at three of five sites. This study demonstrated that dough rheology measurements were poor predictors of S&D quality. In the absence of robust predictive tests, high heritability values for S&D demonstrate that direct selection is the current best option for achieving genetic gain in this product category.

Identification of genetic regions associated with black point in barley.

Black point (BP) can cause severe losses to the barley industry through downgrading and discounting of malting barley. The genetic improvement in BP resistance of barley is complex, requiring reliable screening tools, an understanding of genotype by environment interactions and an understanding of the biochemical mechanisms of melanisation involved in BP development. Thus the application of molecular markers for resistance to BP may be a useful tool for plant breeders. We have investigated the genetic regions associated with BP resistance in the barley F2 population, Valier/Binalong. Quantitative trait loci (QTLs) contributed by the resistant parent Valier, were detected on chromosomes 2HS, 2HC, 3HL, 4HL and a QTL contributed by the susceptible parent, Binalong was detected on 5HL. Three of the four QTLs were detected in two distinctly different environments. The differences observed in BP resistance between these two environments and the implications for accelerated screening are discussed. Identified SSR markers in these regions may be useful for selecting black point resistance in related breeding materials.

Scalloped Hammerhead microsatellite genotypes (eight loci) representing five regions on Australia's east coast and one location in central Indonesia.

Biodiversity of sharks in the tropical Indo-Pacific is high, but species-specific information to assist sustainable resource exploitation is scarce. The null hypothesis of population genetic homogeneity was tested for scalloped hammerhead shark (Sphyrna lewini, n=244) and the milkshark (Rhizoprionodon acutus, n=209) from northern and eastern Australia, using nuclear (S. lewini, eight microsatellite loci; R. acutus, six loci) and mitochondrial gene markers (873 base pairs of NADH dehydrogenase subunit 4). We were unable to reject genetic homogeneity for S. lewini, which was as expected based on previous studies of this species. Less expected were similar results for R. acutus, which is more benthic and less vagile than S. lewini. These features are probably driving the genetic break found between Australian and central Indonesian R. acutus (F-statistics; mtDNA, 0.751 to 0.903; microsatellite loci, 0.038 to 0.047). Our results support the spatially-homogeneous management plan for shark species in Queensland, but caution is advised for species yet to be studied.

Grey Mackerel (Scomberomorus semifasciatus) microsatellite genotypes (nine loci) representing twelve regions along Australia's northern coastline from the eastern coast of Queensland to the western coast of Western Australia.

Scomberomorus semifasciatus is an Australian endemic found in tropical, coastal waters from eastern to western Australia. Commercial and recreational exploitation is common and regulated by state-based authorities. This study used mitochondrial DNA sequence and microsatellite markers to elucidate the population structure of Scomberomorus semifasciatus collected from twelve, equidistant sampling locations. Samples (n=544) were genotyped with nine microsatellite loci, and 353 were sequenced for d-loop (384 bp) and ATP (800bp) mitochondrial DNA gene regions. Combined interpretation of microsatellite and mtDNA data identified four genetic stocks of S. semifasciatus: Western Australia, northwest coast of the Northern Territory, Gulf of Carpentaria and the east coast of Queensland. Connectivity among stocks across northern Australia from the Northern Territory to the east coast of Queensland was high, but in contrast, there was a clear genetic break between populations in Western Australia compared to the rest of northern Australia. This indicates a restriction to gene flow possibly associated with suboptimal habitat along the Kimberley coast (northwestern Australia). The appropriate scale of management for this species corresponds to the jurisdictions of the three Australian states, except that the Gulf of Carpentaria stock should be co-managed by authorities in Queensland and Northern Territory.

National Strawberry Varietal Improvement Program - Subtropical Regions

Industry development by providing competitive wonderful strawberry cutivars to subtropical industry and purchasers .

Making better fertiliser decisions for the cropping regions of Australia

Collating old fertilizer trial data for development of a national database on crop responses.

Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement.

A comprehensive analysis was conducted using 48 sorghum QTL studies published from 1995 to 2010 to make information from historical sorghum QTL experiments available in a form that could be more readily used by sorghum researchers and plant breeders. In total, 771 QTL relating to 161 unique traits from 44 studies were projected onto a sorghum consensus map. Confidence intervals (CI) of QTL were estimated so that valid comparisons could be made between studies. The method accounted for the number of lines used and the phenotypic variation explained by individual QTL from each study. In addition, estimated centimorgan (cM) locations were calculated for the predicted sorghum gene models identified in Phytozome (JGI GeneModels SBI v1.4) and compared with QTL distribution genome-wide, both on genetic linkage (cM) and physical (base-pair/bp) map scales. QTL and genes were distributed unevenly across the genome. Heterochromatic enrichment for QTL was observed, with approximately 22% of QTL either entirely or partially located in the heterochromatic regions. Heterochromatic gene enrichment was also observed based on their predicted cM locations on the sorghum consensus map, due to suppressed recombination in heterochromatic regions, in contrast to the euchromatic gene enrichment observed on the physical, sequence-based map. The finding of high gene density in recombination-poor regions, coupled with the association with increased QTL density, has implications for the development of more efficient breeding systems in sorghum to better exploit heterosis. The projected QTL information described, combined with the physical locations of sorghum sequence-based markers and predicted gene models, provides sorghum researchers with a useful resource for more detailed analysis of traits and development of efficient marker-assisted breeding strategies.

White shark (Carcharodon carcharias) microsatellite genotypes (six loci) from regions along Australia's southern and eastern coastline.

Despite international protection of white sharks (Carcharodon carcharias), important conservation parameters such as abundance, population structure and genetic diversity are largely unknown. The tissue of 97 predominately juvenile white sharks sampled from spatially distant eastern and southwestern Australian coastlines was sequenced for the mitochondrial DNA (mtDNA) control region and genotyped with six nuclear-encoded microsatellite loci. MtDNA population structure was found between the eastern and southwestern coasts (FST = 0.142, p < 0.001), implying female natal philopatry. This concords with recent satellite and acoustic tracking findings which suggest the sustained presence of discrete east coast nursery areas. Furthermore, population subdivision was found between the same regions with biparentally inherited microsatellite markers (FST = 0.009, p <0.05), suggesting that males may also exhibit some degree of reproductive philopatry. Five sharks captured along the east coast had mtDNA haplotypes that resembled western Indian Ocean sharks more closely than Australian/New Zealand sharks, suggesting that transoceanic dispersal or migration resulting in breeding may occur sporadically. Our most robust estimate of contemporary genetic effective population size was low and below the threshold at which adaptive potential may be lost. For a variety of reasons, these contemporary estimates were at least one, possibly two orders of magnitude below our historical effective size estimates. Further population decline could expose these genetically isolated populations to detrimental genetic effects. Regional Australian white shark conservation management units should be implemented until genetic population structure, size and diversity can be investigated in more detail. Reference: Blower, D. C., Pandolfi, J. M., Gomez-Cabrera, M. del C., Bruce, B. D. & Ovenden, J. R. (In press - April 2012). Population genetics of Australian white sharks reveals fine-scale spatial structure, transoceanic dispersal events and low effective population sizes. Marine Ecology Progress Series.

Estimating winter crop area across seasons and regions using time-sequential MODIS imagery.

The wheat grain industry is Australia's second largest agricultural export commodity. There is an increasing demand for accurate, objective and near real-time crop production information by industry. The advent of the Moderate Resolution Imaging Spectroradiometer (MODIS) satellite platform has augmented the capability of satellite-based applications to capture reflectance over large areas at acceptable pixel scale, cost and accuracy. The use of multi-temporal MODIS-enhanced vegetation index (EVI) imagery to determine crop area was investigated in this article. Here the rigour of the harmonic analysis of time-series (HANTS) and early-season metric approaches was assessed when extrapolating over the entire Queensland (QLD) cropping region for the 2005 and 2006 seasons. Early-season crop area estimates, at least 4 months before harvest, produced high accuracy at pixel and regional scales with percent errors of -8.6% and -26% for the 2005 and 2006 seasons, respectively. In discriminating among crops at pixel and regional scale, the HANTS approach showed high accuracy. The errors for specific area estimates for wheat, barley and chickpea were 9.9%, -5.2% and 10.9% (for 2005) and -2.8%, -78% and 64% (for 2006), respectively. Area estimates of total winter crop, wheat, barley and chickpea resulted in coefficient of determination (R(2)) values of 0.92, 0.89, 0.82 and 0.52, when contrasted against the actual shire-scale data. A significantly high coefficient of determination (0.87) was achieved for total winter crop area estimates in August across all shires for the 2006 season. Furthermore, the HANTS approach showed high accuracy in discriminating cropping area from non-cropping area and highlighted the need for accurate and up-to-date land use maps. The extrapolability of these approaches to determine total and specific winter crop area estimates, well before flowering, showed good utility across larger areas and seasons. Hence, it is envisaged that this technology might be transferable to different regions across Australia.

Comparative analysis of Tritrichomonas foetus (Riedmuller, 1928) cat genotype, T. foetus (Riedmuller, 1928) cattle genotype and Tritrichomonas suis (Davaine, 1875) at 10 DNA loci

The parasitic protists in the genus Tritrichomonas cause significant disease in domestic cattle and cats. To assess the genetic diversity of feline and bovine isolates of Tritrichomonas foetus (Riedmuller, 1928) Wenrich and Emmerson, 1933, we used 10 different genetic regions, namely the protein coding genes of cysteine proteases 1,2 and 4-9 (CP1, 2, 4-9) involved in the pathogenesis of the disease caused by the parasite. The cytosolic malate dehydrogenase 1 (MDH1) and internal transcribed spacer region 2 of the rDNA unit (ITS2) were included as additional markers. The gene sequences were compared with those of Tritrichomonas suis (Davaine. 1875) Morgan and Hawkins, 1948 and Tritrichomonas mobilensis Culberson et al., 1986. The study revealed 100% identity for all 10 genes among all feline isolates (=T. foetus cat genotype), 100% identity among all bovine isolates (=T. foetus cattle genotype) and a genetic distinctness of 1% between the cat and cattle genotypes of T. foetus. The cattle genotype of T. foetus was 100% identical to T. suis at nine loci (CP1, 2,4-8, ITS2, MDH1). At CP9, three out of four T. suis isolates were identical to the T. foetus cattle genotype, while the T. suis isolate SUI-H3B sequence contained a single unique nucleotide substitution. Tritrichomonas mobilensis was 0.4% and 0.7% distinct from the cat and cattle genotypes of T. foetus, respectively. The genetic differences resulted in amino acid changes in the CP genes, most pronouncedly in CP2, potentially providing a platform for elucidation of genotype-specific host-pathogen interactions of T. foetus. On the basis of this data we judge T. suis and T. foetus to be subjective synonyms. For the first time, on objective nomenclatural grounds, the authority of T. suis is given to Davaine, 1875, rather than the commonly cited Gruby and Delafond, 1843. To maintain prevailing usage of T. foetus, we are suppressing the senior synomym T. suis Davaine, 1875 according to Article 23.9, because it has never been used as a valid name after 1899 and T. foetus is widely discussed as the cause of bovine trichomonosis. Thus bovine, feline and porcine isolates should all be given the name T. foetus. This promotes the stability of T. foetus for the veterinary and economically significant venereal parasite causing bovine trichomonosis. (C) 2012 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Molecular phylogenetic analysis reveals six new species of Diaporthe from Australia

Six new species of Diaporthe, D. beilharziae on Indigofera australis, D. fraxini-angustifoliae on Fraxinus angustifolia subsp. oxycarpa, D. litchicola on Litchi chinensis, D. nothofagi on Nothofagus cunninghamii, D. pascoei on Persea americana and D. salicicola on Salix purpurea from Australia are described and illustrated based on morphological characteristics and molecular analyses. Three of the new species no longer produced sporulating structures in culture and two of these were morphologically described from voucher specimens. Phylogenetic relationships of the new species with other Diaporthe species are revealed by DNA sequence analyses based on the internal transcribed spacer (ITS) region, and partial regions of the β-tubulin (BT) and translation elongation factor 1-alpha (TEF). © 2013 Mushroom Research Foundation.

Analysis of Crude Protein and Allergen Abundance in Peanuts (Arachis hypogaea cv. Walter) from Three Growing Regions in Australia

The effects of plant growth conditions on concentrations of proteins, including allergens, in peanut (Arachis hypogaea L.) kernels are largely unknown. Peanuts (cv. Walter) were grown at five sites (Taabinga, Redvale, Childers, Bundaberg, and Kairi) covering three commercial growing regions in Queensland, Australia. Differences in temperature, rainfall, and solar radiation during the growing season were evaluated. Kernel yield varied from 2.3 t/ha (Kairi) to 3.9 t/ha (Childers), probably due to differences in solar radiation. Crude protein appeared to vary only between Kairi and Childers, whereas Ara h 1 and 2 concentrations were similar in all locations. 2D-DIGE revealed significant differences in spot volumes for only two minor protein spots from peanuts grown in the five locations. Western blotting using peanut-allergic serum revealed no qualitative differences in recognition of antigens. It was concluded that peanuts grown in different growing regions in Queensland, Australia, had similar protein compositions and therefore were unlikely to show differences in allergenicity.