Australian Prawn Farming Manual: Health Management for profit

The Manual is an easy to read guide for running a low disease risk prawn farm in Australia. Using the combined knowledge of Australia's leading scientists, prawn farmers, extensionists and prawn health specialists, this manual captures what is known about the diseases that threaten the Australian prawn farming industry and how the of disease outbreak can be minimised. Funded by ACIAR and developed in collaboration with the Australian Prawn Farmers' Association, the Queensland Department of Primary Industries and Fisheries and the New South Wales Department of Primary Industries, the manual draws on five years of research conducted across the Australiasia region. The contents reflect the knowledge of a wide array of internationally recognised researchers and the wisdom and research gained through the efforts of the Australian prawn farming industry.

Hybridisation of Australian chickpea cultivars with wild Cicer spp. increases resistance to root-lesion nematodes (Pratylenchus thornei and P. neglectus).

Australian and international chickpea (Cicer arietinum) cultivars and germplasm accessions, and wild annual Cicer spp. in the primary and secondary gene pools, were assessed in glasshouse experiments for levels of resistance to the root-lesion nematodes Pratylenchus thornei and P. neglectus. Lines were grown in replicated experiments in pasteurised soil inoculated with a pure culture of either P. thornei or P. neglectus and the population density of the nematodes in the soil plus roots after 16 weeks growth was used as a measure of resistance. Combined statistical analyses of experiments (nine for P. thornei and four for P. neglectus) were conducted and genotypes were assessed using best linear unbiased predictions. Australian and international chickpea cultivars possessed a similar range of susceptibilities through to partial resistance. Wild relatives from both the primary (C. reticulatum and C. echinospermum) and secondary (C. bijugum) gene pools of chickpea were generally more resistant than commercial chickpea cultivars to either P. thornei or P. neglectus or both. Wild relatives of chickpea have probably evolved to have resistance to endemic root-lesion nematodes whereas modern chickpea cultivars constitute a narrower gene pool with respect to nematode resistance. Resistant accessions of C. reticulatum and C. echinospermum were crossed and topcrossed with desi chickpea cultivars and resistant F(4) lines were obtained. Development of commercial cultivars with the high levels of resistance to P. thornei and P. neglectus in these hybrids will be most valuable for areas of the Australian grain region and other parts of the world where alternating chickpea and wheat crops are the preferred rotation.

Post head-emergence frost resistance of barley genotypes in the northern grain region of Australia.

Post head-emergence frost causes substantial losses for Australian barley producers. Varieties with improved resistance would have a significant positive impact on Australian cropping enterprises. Five barley genotypes previously tested for reproductive frost resistance in southern Australia were tested, post head-emergence, in the northern grain region of Australia and compared with the typical northern control cultivars, Gilbert and Kaputar. All tested genotypes suffered severe damage to whole heads and stems at plant minimum temperatures less than -8degreesC. In 2003, 2004 and 2005, frost events reaching a plant minimum temperature of ~-6.5degreesC did not result in the complete loss of grain yield. Rather, partial seed set was observed. The control genotype, Gilbert, exhibited seed set that was greater than or equal to that of any genotype in each year, as did Kaputar when tested in 2005. Thus, Gilbert and Kaputar were at least as resistant as any tested genotype. This contrasts with trial results from the southern grain region where Gilbert was reported to be less resistant than Franklin, Amagi Nijo and Haruna Nijo. Hence, rankings for post head-emergence frost damage in the northern grain region differ from those previously reported. These results indicate that Franklin, Amagi Nijo and Haruna Nijo are not likely to provide useful sources of frost resistance or markers to develop improved varieties for the northern grain region of Australia.

A review of the biology, ecology, distribution and control of Mozambique tilapia, Oreochromis mossambicus (Peters 1852) (Pisces: Cichlidae) with particular emphasis on invasive Australian populations

Oreochromis mossambicus (Peters 1852) are native to the eastward flowing rivers of central and southern Africa but from the early 1930s they have been widely distributed around the world for aquaculture and for biological control of weeds and insects. While O. mossambicus are now not commonly used as an aquaculture species, the biological traits that made them a popular culture species including tolerance to wide ranging ecological conditions, generalist dietary requirements and rapid reproduction with maternal care have also made them a 'model' invader. Self-sustaining populations now exist in almost every region to which they have been imported. In Australia, since their introduction in the 1970s, O. mossambicus have become established in catchments along the east and west coasts and have the potential to colonise other adjacent drainages. It is thought that intentional translocations are likely to be the most significant factor in their spread in Australia. The ecological and physical tolerances and preferences, reproductive behaviour, hybridization and the high degree of plasticity in the life history traits of O. mossambicus are reviewed. Impacts of O. mossambicus on natural ecosystems including competitive displacement of native species, habitat alteration, predation and as a vector in the spread of diseases are discussed. Potential methods for eradicating or controlling invasive populations of O. mossambicus including physical removal, piscicides, screens, environmental management and genetic technologies are outlined.

Mapping Quantitative Trait Loci for Partial Resistance to Powdery Mildew in an Australian Barley Population

Genomic regions influencing resistance to powdery mildew [Blumeria graminis (DC.) E.O. Speer f. sp. hordei Em. Marchal] were detected in a doubled haploid (DH) barley (Hordeum vulgare L.) population derived from a cross between the breeding line ND24260 and cultivar Flagship when evaluated across four field environments in Australia and Uruguay. Significant quantitative trait loci (OIL) for resistance to B. graminis were detected on six of the seven chromosomes (1H, 2H, 3H, 4H, 5H, and 7H). A QTL with large effect donated by ND24260 mapped to the short arm of chromosome 1H (1 HS) conferring near immunity to B. graminis in Australia but was ineffective in Uruguay. Three OIL donated by Flagship contributed partial resistance to B. graminis and were detected in at least two environments. These OIL were mapped to chromosomes 3H, 4H, and 5H (5HS) accounting for up to 18.6, 3.4, and 8.8% phenotypic variation, respectively. The 5HS QTL contributed partial resistance to B. graminis in all field environments in both Australia and Uruguay and aligned with the genomic region of Rph20, a gene conferring adult plant resistance (APR) to leaf rust (Puccinia hordei Otth), which is found in some cultivars having Vada' or 'Emir' in their parentage. Selection for favorable marker haplotypes within the 3H, 4H, and 5H QTL regions can be performed even in the presence of single (major) gene resistance. Pyramiding such QTL may provide an effective and potentially durable form of resistance to B. graminis.

Population Expansion and Genetic Structure in Carcharhinus brevipinna in the Southern Indo-Pacific

Background:Quantifying genetic diversity and metapopulation structure provides insights into the evolutionary history of a species and helps develop appropriate management strategies. We provide the first assessment of genetic structure in spinner sharks (Carcharhinus brevipinna), a large cosmopolitan carcharhinid, sampled from eastern and northern Australia and South Africa. Methods and Findings:Sequencing of the mitochondrial DNA NADH dehydrogenase subunit 4 gene for 430 individuals revealed 37 haplotypes and moderately high haplotype diversity (h = 0.6770 ±0.025). While two metrics of genetic divergence (ΦST and FST) revealed somewhat different results, subdivision was detected between South Africa and all Australian locations (pairwise ΦST, range 0.02717–0.03508, p values ≤ 0.0013; pairwise FST South Africa vs New South Wales = 0.04056, p = 0.0008). Evidence for fine-scale genetic structuring was also detected along Australia’s east coast (pairwise ΦST = 0.01328, p < 0.015), and between south-eastern and northern locations (pairwise ΦST = 0.00669, p < 0.04).Conclusions: The Indian Ocean represents a robust barrier to contemporary gene flow in C. brevipinna between Australia and South Africa. Gene flow also appears restricted along a continuous continental margin in this species, with data tentatively suggesting the delineation of two management units within Australian waters. Further sampling, however, is required for a more robust evaluation of the latter finding. Evidence indicates that all sampled populations were shaped by a substantial demographic expansion event, with the resultant high genetic diversity being cause for optimism when considering conservation of this commercially-targeted species in the southern Indo-Pacific.

Large-scale characterization of drought pattern: a continent-wide modelling approach applied to the Australian wheatbelt – spatial and temporal trends

* Plant response to drought is complex, so that traits adapted to a specific drought type can confer disadvantage in another drought type. Understanding which type(s) of drought to target is of prime importance for crop improvement. * Modelling was used to quantify seasonal drought patterns for a check variety across the Australian wheatbelt, using 123 yr of weather data for representative locations and managements. Two other genotypes were used to simulate the impact of maturity on drought pattern. * Four major environment types summarized the variability in drought pattern over time and space. Severe stress beginning before flowering was common (44% of occurrences), with (24%) or without (20%) relief during grain filling. High variability occurred from year to year, differing with geographical region. With few exceptions, all four environment types occurred in most seasons, for each location, management system and genotype. * Applications of such environment characterization are proposed to assist breeding and research to focus on germplasm, traits and genes of interest for target environments. The method was applied at a continental scale to highly variable environments and could be extended to other crops, to other drought-prone regions around the world, and to quantify potential changes in drought patterns under future climates.

Population genetics of Australian white sharks reveals fine-scale spatial structure, transoceanic dispersal events and low effective population sizes

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 6 nuclear-encoded microsatellite loci. MtDNA population structure was found between the eastern and southwestern coasts (F-ST = 0.142, p < 0.0001), implying female reproductive philopatry. This concurs 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 micro satellite markers (F-ST = 0.009, p < 0.05), suggesting that males may also exhibit some degree of reproductive philopatry; 5 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 close to thresholds at which adaptive potential may be lost. For a variety of reasons, these contemporary estimates were at least 1, possibly 2, orders of magnitude below our historical effective size estimates. 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.

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

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

First complete genome sequence of a capsicum chlorosis tospovirus isolate from Australia with an unusually large S RNA intergenic region

The first complete genome sequence of capsicum chlorosis virus (CaCV) from Australia was determined using a combination of Illumina HiSeq RNA and Sanger sequencing technologies. Australian CaCV had a tripartite genome structure like other CaCV isolates. The large (L) RNA was 8913 nucleotides (nt) in length and contained a single open reading frame (ORF) of 8634 nt encoding a predicted RNA-dependent RNA polymerase (RdRp) in the viral-complementary (vc) sense. The medium (M) and small (S) RNA segments were 4846 and 3944 nt in length, respectively, each containing two non-overlapping ORFs in ambisense orientation, separated by intergenic regions (IGR). The M segment contained ORFs encoding the predicted non-structural movement protein (NSm; 927 nt) and precursor of glycoproteins (GP; 3366 nt) in the viral sense (v) and vc strand, respectively, separated by a 449-nt IGR. The S segment coded for the predicted nucleocapsid (N) protein (828 nt) and non-structural suppressor of silencing protein (NSs; 1320 nt) in the vc and v strand, respectively. The S RNA contained an IGR of 1663 nt, being the largest IGR of all CaCV isolates sequenced so far. Comparison of the Australian CaCV genome with complete CaCV genome sequences from other geographic regions showed highest sequence identity with a Taiwanese isolate. Genome sequence comparisons and phylogeny of all available CaCV isolates provided evidence for at least two highly diverged groups of CaCV isolates that may warrant re-classification of AIT-Thailand and CP-China isolates as unique tospoviruses, separate from CaCV.

Integrating Rapid Phenotyping and Speed Breeding to Improve Stay-Green and Root Adaptation of Wheat in Changing, Water-Limited, Australian Environments

Temperatures have increased and in-crop rainfall decreased over recent decades in many parts of the Australian wheat cropping region. With these trends set to continue or intensify, improving crop adaptation in the face of climate change is particularly urgent in this, already drought-prone, cropping region. Importantly, improved performance under water-limitation must be achieved while retaining yield potential during more favourable seasons. A multi-trait-based approach to improve wheat yield and yield stability in the face of water-limitation and heat has been instigated in northern Australia using novel phenotyping techniques and a nested association mapping (NAM) approach. An innovative laboratory technique allows rapid root trait screening of hundreds of lines. Using soil grown seedlings, the method offers significant advantages over many other lab-based techniques. Another recently developed method allows novel stay-green traits to be quantified objectively for hundreds of genotypes in standard field trial plots. Field trials in multiple locations and seasons allow evaluation of targeted trait values and identification of superior germplasm. Traits, including yield and yield components are measured for hundreds of NAM lines in rain fed environments under various levels of water-limitation. To rapidly generate lines of interest, the University of Queensland “speed breeding” method is being employed, allowing up to 7 plant generations per annum. A NAM population of over 1000 wheat recombinant inbred lines has been progressed to the F5 generation within 18 months. Genotyping the NAM lines with the genome-wide DArTseq molecular marker system provides up to 40,000 markers. They are now being used for association mapping to validate QTL previously identified in bi-parental populations and to identify novel QTL for stay-green and root traits. We believe that combining the latest techniques in physiology, phenotyping, genetics and breeding will increase genetic progress toward improved adaptation to water-limited environments.

Maize yield determination in the Northern Region: Hybrid by environment by management interactions

In Maize, as with most cereals, grain yield is mostly determined by the total grain number per unit area, which is highly related to the rate of crop growth during the critical period around silking. Management practices such as plant density or nitrogen fertilization can affect the growth of the crop during this period, and consequently the final grain yield. Across the Northern Region maize is grown under a large range of plant populations under high year-to-year rainfall variability. Clear guidelines on how to match hybrids and management across environments and expected seasonal condition, would allow growers to increase yields and profits while managing risks. The objective of this research was to screen the response of commercial maize hybrids differing in maturity and prolificity (i.e. multi or single cobbing) types for their efficiency in the allocation of biomass into grain.

Coronavirus Infection and Diversity in Bats in the Australasian Region

Following the SARS outbreak, extensive surveillance was undertaken globally to detect and identify coronavirus diversity in bats. This study sought to identify the diversity and prevalence of coronaviruses in bats in the Australasian region. We identified four different genotypes of coronavirus, three of which (an alphacoronavirus and two betacoronaviruses) are potentially new species, having less than 90% nucleotide sequence identity with the most closely related described viruses. We did not detect any SARS-like betacoronaviruses, despite targeting rhinolophid bats, the putative natural host taxa. Our findings support the virus-host co-evolution hypothesis, with the detection of Miniopterus bat coronavirus HKU8 (previously reported in Miniopterus species in China, Hong Kong and Bulgaria) in Australian Miniopterus species. Similarly, we detected a novel betacoronavirus genotype from Pteropus alecto which is most closely related to Bat coronavirus HKU9 identified in other pteropodid bats in China, Kenya and the Philippines. We also detected possible cross-species transmission of bat coronaviruses, and the apparent enteric tropism of these viruses. Thus, our findings are consistent with a scenario wherein the current diversity and host specificity of coronaviruses reflects co-evolution with the occasional host shift.

First complete genome sequence of a capsicum chlorosis tospovirus isolate from Australia with an unusually large S RNA intergenic region

The first complete genome sequence of capsicum chlorosis virus (CaCV) from Australia was determined using a combination of Illumina HiSeq RNA and Sanger sequencing technologies. Australian CaCV had a tripartite genome structure like other CaCV isolates. The large (L) RNA was 8913 nucleotides (nt) in length and contained a single open reading frame (ORF) of 8634 nt encoding a predicted RNA-dependent RNA polymerase (RdRp) in the viral-complementary (vc) sense. The medium (M) and small (S) RNA segments were 4846 and 3944 nt in length, respectively, each containing two non-overlapping ORFs in ambisense orientation, separated by intergenic regions (IGR). The M segment contained ORFs encoding the predicted non-structural movement protein (NSm; 927 nt) and precursor of glycoproteins (GP; 3366 nt) in the viral sense (v) and vc strand, respectively, separated by a 449-nt IGR. The S segment coded for the predicted nucleocapsid (N) protein (828 nt) and non-structural suppressor of silencing protein (NSs; 1320 nt) in the vc and v strand, respectively. The S RNA contained an IGR of 1663 nt, being the largest IGR of all CaCV isolates sequenced so far. Comparison of the Australian CaCV genome with complete CaCV genome sequences from other geographic regions showed highest sequence identity with a Taiwanese isolate. Genome sequence comparisons and phylogeny of all available CaCV isolates provided evidence for at least two highly diverged groups of CaCV isolates that may warrant re-classification of AIT-Thailand and CP-China isolates as unique tospoviruses, separate from CaCV.