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Avocado (Persea americana cv. ‘Hass’) Fruit Mineral Composition at Canopy Level towards Sustainable Quality
Get PDFSustaining avocado fruit quality is crucial to maintain customer satisfaction and confidence. Among fruit qualities, mineral nutrient composition is an important contributor to postharvest robustness. Towards better understanding and addressing variability within the plant canopy, ‘Hass’ fruit from across seven orchard blocks were individually characterised. From five representative trees in each block, five fruit were harvested (one from each of five positions: top (sun-exposed), bottom (shaded), middle (shaded), East (sun-exposed), and West (sun-exposed)). Fruit dry matter was significantly higher (p ≤ 0.001) in fruit from the top, East, and West sun-exposed positions. No significant (p > 0.05) effect of position was discerned for fruit weight at harvest or for either stem end rot (SER) or body rot (BR) incidence at eating soft. Shaded fruit had significantly higher (p ≤ 0.05) [N], [K], [Mg], N:Ca, K:Ca, and K + Mg:Ca in their flesh. Significant negative linear correlations (p ≤ 0.001) were obtained between fruit DM and flesh [N] (r = −0.75), [K] (r = −0.67), and N:Ca (r = −0.57). SER and BR incidence were significantly positively correlated (p ≤ 0.01) with flesh and skin mineral ratios of N:Ca, K:Ca, Mg:Ca, and K + Mg:Ca. Skin and flesh [Ca] were significantly negatively correlated with SER (r = −0.51, p ≤ 0.01) and BR (r = −0.74, p ≤ 0.001) incidences. Soil cation (Ca, Mg, K) availability (%base saturation of cation exchange capacity (CEC)) was not (p > 0.05) correlated with skin or flesh mineral concentrations or ratios. Considered collectively, results suggest that selective harvest of sun-exposed fruit with inherently lower mineral nutrient ratios yields relatively robust fruit. Such fruit lots should better tolerate the rigours of harvest and postharvest treatment and handling. In this context, they should better maintain quality upon passage through long, in terms of accumulated time-temperature increments, export supply chains. In contrast, shaded fruit could be directed into shorter domestic supply chains. As a harvest strategy, segregating fruit lots from harvest could underpin the quality offered to consumers at the end of ‘short’ and ‘long’ supply chains
Underwater hyperspectral imaging technology has potential to differentiate and monitor scallop populations
Get PDFAccurate and low-impact monitoring of scallop abundance is critical for stock assessment, especially in sensitive habitats. The possibility of using low-impact hyperspectral imaging (HSI) for differentiating scallop species in the marine environment was investigated. Live saucer (Ylistrum balloti) and mud (Ylistrum pleuronectes) scallops (N = 31) were scanned inside a sea simulator using a visible to near infrared (400–1000 nm) line-scanner HSI camera. Partial least square discriminant analysis (PLS-DA) was trained to distinguish between the species using their spectral signatures. Important wavelengths were identified and new models were developed using these wavelengths to reduce the model complexity and potentially increase the imaging speed when applied under at-sea conditions. The PLS-DA model distinguished between saucer and mud scallops using any area of the left valve that was exposed above the sediments, with 90.73% accuracy when all 462 available wavelengths were used. Using the subset of important wavelengths (N = 13) reduced the classification accuracy to 84%. Overall, our results showed that HSI has potential for detecting, distinguishing and counting commercially important saucer scallops for low-impact monitoring and resource management, and to complement RGB imaging that relies solely on morphological properties
Multidisciplinary approach to the diagnosis of Contracaecum magnipapillatum infections in Australian black noddies, Anous minutus (Charadriiformes: Laridae)
Get PDFWe provide the incidental necropsy findings associated with anisakid nematode infections of black noddy terns, Anous minutus Boie, 1844 (Charadriiformes: Laridae), from offshore islands in the southern Great Barrier Reef, Queensland, Australia. Specimens collected from the proventriculi were identified morphologically as Contracaecum magnipapillatum Chapin, 1925 (Rhabditida: Anisakidae), using light and scanning electron microscopy (SEM). The entire nuclear ribosomal DNA internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) was amplified by polymerase chain reaction (PCR) and sequenced to provide reference sequences for morphologically well-identified voucher specimens. Interestingly, after an alignment with closely related taxa using BLAST, sequences of the ITS1 and ITS2 were 100% identical to the sequences assigned to Contracaecum septentrionale Kreis, 1955, from a razorbill, Alca torda Linnaeus, 1758 (Charadriiformes: Alcidae), from Spain. These results either raise questions about the ITS as a genetic marker for some members of Contracaecum, or the identity of the specimens assigned to C. septentrionale, given that no supporting morphological data was associated with them. We highlight the need for a combined morphological and molecular approach to parasite diagnostics and the use of multiple genetic loci to resolve the molecular taxonomy of cryptic species. Morphological identifications should be taxonomically robust, transparent and precede the deposition of molecular barcodes in public repositories. The gross and histopathological findings of our investigation concur with previous reports of widespread Contracaecum infections in black noddies and support the contention that Contracaecum spp. are an unlikely primary cause of mortality
Genomic variation in pepper vein yellows viruses in Australia, including a new putative variant, PeVYV-10
Get PDFSince the first identification and full sequence of the polerovirus pepper vein yellows virus in Australia in 2016, virus surveys of crops and weeds have sporadically identified PeVYV in different hosts and locations. Genomic comparisons of 14 PeVYV-like isolates using RT-PCR products spanning the 3’ end of the RdRp region (ORF 2), the intergenic region, ORF 3a, ORF 4, and ORF 3 (1388 nt) showed that four of the PeVYV isolates might be a new variant or PeVYV-like virus. From six PeVYV-positive plants, eight PeVYV-like sequences were obtained by high-throughput sequencing, as two hosts, 5352 and 5634, contained two slightly different PeVYV-like isolates. Three of the PeVYV-like isolates were most closely related to PeVYV-6 and PeVYV-5, and two isolates were closely related to PeVYV-9 and PeVYV-2. The other three isolates shared only 69-74% nucleotide sequence identity across the whole genome with any of the other PeVYVs, despite sharing 73-98%, 87-91%, and 84-87% amino acid sequence identity in ORF 3a, ORF 3, and the RdRp (ORF 2), respectively, suggesting that this virus is a new PeVYV-like virus, which we have tentatively called PeVYV-10. This is also the first report of a PeVYV-like virus infecting garlic
Genetic Diversity and Candidate Genes for Transient Waterlogging Tolerance in Mungbean at the Germination and Seedling Stages
Get PDFMungbean [Vigna radiata var. radiata (L.) Wilczek] production in Asia is detrimentally affected by transient soil waterlogging caused by unseasonal and increasingly frequent extreme precipitation events. While mungbean exhibits sensitivity to waterlogging, there has been insufficient exploration of germplasm for waterlogging tolerance, as well as limited investigation into the genetic basis for tolerance to identify valuable loci. This research investigated the diversity of transient waterlogging tolerance in a mini-core germplasm collection of mungbean and identified candidate genes for adaptive traits of interest using genome-wide association studies (GWAS) at two critical stages of growth: germination and seedling stage (i.e., once the first trifoliate leaf had fully-expanded). In a temperature-controlled glasshouse, 292 genotypes were screened for tolerance after (i) 4 days of waterlogging followed by 7 days of recovery at the germination stage and (ii) 8 days of waterlogging followed by 7 days of recovery at the seedling stage. Tolerance was measured against drained controls. GWAS was conducted using 3,522 high-quality DArTseq-derived SNPs, revealing five significant associations with five phenotypic traits indicating improved tolerance. Waterlogging tolerance was positively correlated with the formation of adventitious roots and higher dry masses. FGGY carbohydrate kinase domain-containing protein was identified as a candidate gene for adventitious rooting and mRNA-uncharacterized LOC111241851, Caffeoyl-CoA O-methyltransferase At4g26220 and MORC family CW-type zinc finger protein 3 and zinc finger protein 2B genes for shoot, root, and total dry matter production. Moderate to high broad-sense heritability was exhibited for all phenotypic traits, including seed emergence (81%), adventitious rooting (56%), shoot dry mass (81%), root dry mass (79%) and SPAD chlorophyll content (70%). The heritability estimates, marker-trait associations, and identification of sources of waterlogging tolerant germplasm from this study demonstrate high potential for marker-assisted selection of tolerance traits to accelerate breeding of climate-resilient mungbean varieties
A metagenomic investigation of phytoplasma diversity in Australian vegetable growing regions
Get PDFIn this study, metagenomic sequence data was used to investigate the phytoplasma taxonomic diversity in vegetable-growing regions across Australia. Metagenomic sequencing was performed on 195 phytoplasma-positive samples, originating either from historic collections (n=46) or during collection efforts between January 2015 and June 2022 (n=149). The sampled hosts were classified as crop (n=155), weed (n=24), ornamental (n=7), native plant (n=6), and insect (n=3) species. Most samples came from Queensland (n=78), followed by Western Australia (n=46), the Northern Territory (n=32), New South Wales (n=17), and Victoria (n=10). Of the 195 draft phytoplasma genomes, 178 met our genome criteria for comparison using an average nucleotide identity approach. Ten distinct phytoplasma species were identified and could be classified within the 16SrII, 16SrXII (PCR only), 16SrXXV, and 16SrXXXVIII phytoplasma groups, which have all previously been recorded in Australia. The most commonly detected phytoplasma taxa in this study were species and subspecies classified within the 16SrII group (n=153), followed by strains within the 16SrXXXVIII group (‘Ca. Phytoplasma stylosanthis’; n=6). Several geographic- and host-range expansions were reported, as well as mixed phytoplasma infections of 16SrII taxa and ‘Ca. Phytoplasma stylosanthis’. Additionally, six previously unrecorded 16SrII taxa were identified, including five putative subspecies of ‘Ca. Phytoplasma australasiaticum’ and a new putative 16SrII species. PCR and sequencing of the 16S rRNA gene was a suitable triage tool for preliminary phytoplasma detection. Metagenomic sequencing, however, allowed for higher-resolution identification of the phytoplasmas, including mixed infections, than was afforded by only direct Sanger sequencing of the 16S rRNA gene. Since the metagenomic approach theoretically obtains sequences of all organisms in a sample, this approach was useful to confirm the host family, genus, and/or species. In addition to improving our understanding of the phytoplasma species that affect crop production in Australia, the study also significantly expands the genomic sequence data available in public sequence repositories to contribute to phytoplasma molecular epidemiology studies, revision of taxonomy, and improved diagnostics
All‐in‐one Xylella detection and identification: A nanopore sequencing‐compatible conventional PCR
Get PDFXylella fastidiosa is a plant-pathogenic bacterium that poses a serious threat to the production of economically important plant species including grapes, almonds, olives and a broad range of amenity plants, causing significant economic losses worldwide. While multiple molecular detection assays have been developed for X. fastidiosa, there is a lack of molecular tools available for detection and differentiation of the closely related pear pathogen, Xylella taiwanensis. In this study, we present a novel conventional PCR assay with primers that can amplify both Xylella species. The amplified product could be sequenced and used for discrimination between the two species and the subspecies within the fastidiosa species. This PCR assay was designed using a genome-informed approach to target the ComEC/Rec2 gene of both Xylella species, ensuring a higher specificity than other previously developed PCR assays. A test performance study across five national plant diagnostic laboratories in Australia and New Zealand demonstrated this assay's high sensitivity and specificity to all known species and subspecies within the Xylella genus. This PCR assay can be used for Xylella identification at the species and subspecies level and is compatible with Sanger sequencing and nanopore sequencing for rapid turnaround time. The newly developed conventional PCR assay presented here offers rapid detection and accurate identification of both Xylella species from plant, insect vector or bacterial samples, enabling timely implementation of biosecurity measures or disease management responses
Total allowable commercial catch review for Queensland spanner crab (Ranina ranina), with data to December 2023
Get PDFThis report was prepared to inform on the total allowable commercial catch (TACC) of spanner crabs in managed area A for the forthcoming two quota years 1 July 2024 to 30 June 2025 and 1 July 2025 to 30 June 2026.
The harvest strategy used standardised commercial (sCPUE) and fishery independent survey (sFIS) catch rates from two years, compared against target rates, to calculate TACC. The average 2022–2023 catch rate indicators from two years, standardised using generalised linear models, were: sCPUE = 0.754 kilograms per dilly-net lift and sFIS = 5.913 crab per ground-line.
The stock indices were the ratio of the indicators compared to their targets. The calculated stock indices were less than 1, signalling catch rates were below target: sCPUE ratio = 0.546 and sFIS ratio = 0.567. The pooled index was 0.556 (average of the two stock indices). The pooled index means that the fishery was at 56% of its target
Management strategy for serpentine leafminer, Liriomyza huidobrensis
Get PDFThe project commenced with a focus on Serpentine leafminer (SLM – Liriomyza huidobrensis), initially detected in western Sydney, New South Wales, October 2020 and soon after in the Fassifern Valley west of Brisbane, Queensland. The American serpentine leafminer (ASLM – Liriomyza trifolii) followed suit arriving in far north QLD, NT and Kununurra WA 2021. With the Vegetable leafminer (VLM – Liriomyza sativae) already in Australia since 2015 in far north QLD, Project MT16004 ‘RD&E program for control, eradication and preparedness for vegetable leafminer’. These introduced Liriomyza leafminers can significantly impact a wide range of commercial crops (vegetables, broadacre, ornamentals and non-commercial hosts); and categorised as high priority pests and considered a serious threat to these industries.
This multi-industry, QLD DAF led collaboration incorporates organisations with recent, relevant R&D into leafminers as well as field scientists located in affected regions. The multidisciplinary team developed and delivered specific Liriomyza information with emphasis on the species found within the regions and facilitated a targeted communication program, which is critical if susceptible horticultural industries are to better understand and manage these pests.
Key outputs have been a refinement for the eDNA assays for L. sativae, L. trifolii and L. huidobrensis (Sooda et al. 2017) and L. brassicae (Pirtle et al. 2021). This test can now determine the presence of 2 additional leafminers, L bryoniae, L chinensis. Real-time qPCR assays were compared with a small portable qPCR machine for use in the field. This was done for L. brassicae and L. huidobrensis in the field with results for flies and larvae comparable to those achieved in the laboratory. This project developed 2 LAMP (Loop-Mediated Isothermal Amplification) tests that are highly sensitive and specific for serpentine leafminer identification using Genie III machine. For direct visualization of the test result in field, this project evaluated a colorimetric method for identification.
The grower guide “Monitoring for serpentine leafminer in Australia”, provides information for conducting effective and efficient monitoring of these pests in Australia. Four grower guides (Vegetable, Potatoes, Melons and Onions) address the differences in management considerations that will occur between different cropping systems. An Industry Management Plan (IMP) includes many aspects of managing these pests by the industry, engaging with relevant stakeholders to ensure effective business and trade continuity.
Extension efforts have been broad ranging, delivering 16 workshops, 3 webinars, 2 field days, 4 grower and agronomist meetings, 2 conferences, 2 melon roadshows and visiting 46 farms. The key outcomes of this project have increased awareness and significance of these 3 leafminer pests, their host range, how they are suited to various regions, what to look out for, and the significance of beneficial insects in managing them and how to look after these beneficial insects by selectively using insecticides.
This project has developed a number of documents which will are available on the Ausveg website MT20005 – Management Strategy for serpentine leafminer (Liriomyza huidobrensis) | AUSVEG as well as 2 publications on the spread of these leafminers and using LAMP as a diagnostic tool to help identify at least SLM
Development of a rapid, accurate, and field deployable LAMP-CRISPR-Cas12a integrated assay for Xylella fastidiosa detection and surveillance
Get PDFXylella fastidiosa is an aggressive plant pathogenic bacterium of significant quarantine concern. Accurate and reliable detection tools are essential to minimise the risk of the pathogen’s spread and for outbreak control, as limited post-infection management strategies are possible. Here, we report the development of a specific and potentially field-deployable assay combining a pre-existing Loop-Mediated Isothermal Amplification (LAMP) assay and a Cas12a-based DNA Endonuclease-Targeted (DETECTR) Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) trans reporter for X. fastidiosa detection. The LAMP-CRISPR-Cas12a integrated assay detected the amplified target region of the X. fastidiosa specific rimM gene at the low femto-molar range within 10 min of initiation. The assay detected varied X. fastidiosa sub-species in a range of naturally infected and economically relevant host material, with no non-target amplification recorded. The results show integration of LAMP with CRISPR-based detection is a specific, sensitive and a potentially field-adaptable strategy for the detection of X. fastidiosa and has the potential for further operationally focused improvements