Department of Agriculture and Food Western Australia
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Pangenome and pantranscriptome as the new reference for gene-family characterization: A case study of basic helix-loop-helix (bHLH) genes in barley
No full textGenome-wide identification and comparative gene-family analyses have commonly been performed to investigate species-specific evolution linked to various traits and molecular pathways. However, most previous studies have been limited to gene screening in a single reference genome, failing to account for the gene presence/absence variations (gPAVs) in a species. Here, we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups (OGGs). Using the basic helix-loop-helix (bHLH) transcription factor family in barley as an example, we identified 161–176 bHLHs in 20 barley genomes, which can be classified into 201 OGGs. These 201 OGGs were further classified into 140 core, 12 softcore, 29 shell, and 20 line-specific/cloud bHLHs, revealing the complete profile of bHLH genes in barley. Using a genome-scanning approach, we overcame the genome annotation bias and identified an average of 1.5 un-annotated core bHLHs per barley genome. We found that whole-genome/segmental duplicates are predominant mechanisms contributing to the expansion of most core/softcore bHLHs, whereas dispensable bHLHs are more likely to result from small-scale duplication events. Interestingly, we noticed that the dispensable bHLHs tend to be enriched in the specific subfamilies SF13, SF27, and SF28, implying the potentially biased expansion of specific bHLHs in barley. We found that 50% of the bHLHs contain at least 1 intact transposon element (TE) within the 2-kb upstream-to-downstream region. bHLHs with copy-number variations (CNVs) have 1.48 TEs on average, significantly more than core bHLHs without CNVs (1.36), supporting a potential role of TEs in bHLH expansion. Analyses of selection pressure showed that dispensable bHLHs have experienced clear relaxation of selection compared with core bHLHs, consistent with their conservation patterns. We also integrated the pangenome data with recently available barley pantranscriptome data from 5 tissues and discovered apparent transcriptional divergence within and across bHLH subfamilies. We conclude that pangenome-based gene-family analyses can better describe the previously untapped, genuine evolutionary status of bHLHs and provide novel insights into bHLH evolution in barley. We expect that this study will inspire similar analyses in many other gene families and species
Ord River Irrigation Area Stage 2 M2 Supply Channel Compliance Assessment Report 2023 - Statement 938
No full textMinisterial implementation Statement 938 for the Ord River Irrigation Area Stage 2 (M2 Supply Channel) proposal was published on 12 June 2013 pursuant to section 45 of the EP Act. DPIRD administers MS938 on behalf of the Minister for Regional Development
Brome grass and its management in crops
No full textBrome grass (Bromus spp.) is one of the most competitive grass weeds in wheat. Over the last 10 years, brome grass has increased in importance to a greater extent than any other weed species in Australia.
Recent changes in crop production systems, increased conservation tillage, a lack of available selective herbicides, and a decline in system diversity have seen an increase in the importance of this weed in Western Australia (WA).
Seed is the main source of brome grass infestation and, as few seeds remain dormant, the most important aspect of management is to reduce its seed bank
Control small weeds in crops
No full textIn an integrated weed management program, control of weeds should occur in the fallow, pre-sowing, early post-emergent, and in-pasture phases. Weed control can be achieved through killing weeds (particularly seedlings) with cultivation, herbicides, targeted weed control in wide-row cropping, targeted control of small patches of weeds, and biological control tactics
Leaf diseases and their management in oats
No full textLeaf diseases of oats impact on grain yield and quality and reduce hay quality characteristics, such as colour and digestibility. This page outlines the symptoms, factors favouring disease risk and spread, and management.
Major leaf diseases of oats are septoria avenae blotch, stem rust, leaf rust, and barley yellow dwarf virus. Their severity changes with seasons
Loose smut of barley and its management
No full textThe fungal disease loose smut of barley parasitises the host plant and produces masses of soot-like spores that infect the seed head, reducing the yield and quality of harvested grain.
Smut diseases are host specific, meaning that smut of one cereal crop will not infect others (for example, loose smut of barley does not infect wheat or oats).
In many cases grain receival points have low or zero tolerance of smut contaminated grain
Working group on recreational fisheries surveys (WGRFS)
No full textEditors
Estanis Mugerza • Kieran Hyder
Authors
Adam Lejk • Alexander Winkler • Amélie Régimbart • Anastasios Papadopoulos • Anders Kagervall Anna-Marie Winter • Annica de Groote • Antanas Kontautas • Branko Dragicevic • Christian Skov Chun Chen • Chris Bova • Dace Zilniece • David Vertegaal • Diarmuid Ryan • Didzis Ustups Eneko Bachiller • Estanis Mugerza • Evanthia Karasavva • Filipa Duarte • Filipe Freitas Henriques Freya Ivy Palmer • Grace Farrell • Hannah Rudd • Hans Jacob Olesen • Harry Vincent Strehlow Henrik Pärn • Hugo Diogo • Joana Patricio • João Pontes • John Foster • Jules Selles • Karina Ryan Keno Ferter • Kieran Hyder • Krzysztof Radtke • Lara Salvany • Leonardo Venerus • Leonie O\u27Dowd Luca Bolognini • Mafalda Rangel • Marc Simon Weltersbach • Marta Pujol-Baucells • Martín García Asorey • Martín Laporta • Martin Mortensen • Martin Wiech • Martina Scanu • Matthew Farthing Miikka Husa • Mišo Pavesi • Paz Jiménez • Pablo Pita • Paul Venturelli • Pedro Veiga • Pentti Moilanen Qilei Zhao • Sabrina Colella • Samantha Hook • Samira Nuñez • Sean Tracey • Stephen Taylor Thomas Lanssens • Thomas Verleye • Valerio Sbragaglia • Warren Potts • Wendy Edwards Zachary Radford.
Executive summary
The ICES Working Group on Recreational Fisheries Surveys (WGRFS) is tasked with compiling and validating data from European marine recreational fisheries (MRF) to support ICES assessment and advisory processes. In 2024, WGRFS undertook a wide range of activities focused on MRF, including the consolidation and assessment of national survey programs, the validation of novel methodologies, and the provision of guidance regarding data availability, quality, and use. Additional responsibilities included facilitating regional data collection and storage, exploring human dimensions of MRF, and conducting assessments of workshops hosted by the group. These sessions emphasized information exchange, national survey program evaluation, intersessional activities, and strategies for scientific publication. Discussions covered a diverse set of topics, such as the launch and outcomes of new national survey initiatives across various regions, including China, Sweden, Azores, Croatia, and Australia. Updates on MRF were also provided by the European Commission and angling community representatives. Findings from the Regional Coordination Groups were shared, along with approaches to include MRF in assessment and advisory processes. ICES have been tasked with providing advice on MRF, so an ICES roadmap has been developed giving key recommendations. MRF can be important as a food source, so the impact of this for food safety and human health was considered. The core focus of the meeting centred on evaluating progress, developing strategies, and the intersessional groups (ISGs). The ISGs are the primary mechanism for WGRFS activities addressing areas including governance, survey methodology, quality assurance, regional coordination and data storage, catch-and-release practices, animal welfare, stock assessment and reconstruction, novel methods, human dimensions, and communication and engagement. Given the extensive scope of discussions and outcomes, a comprehensive summary is not possible here; however, detailed information is presented in the main text
Pilbara Demersal Scalefish Resource Recovery Plan 2023- 2043 (Phase 1)
No full textThe Pilbara Demersal Scalefish Resource (PDSR) includes over 60 demersal scalefish species. The resource is accessed by the Pilbara Trap Managed Fishery, Pilbara Fish Trawl (Interim) Managed Fishery, and the Pilbara Line Fishery (PTMF, PFTIMF & PLF respectively) as well as the recreational and charter fisheries.
The PDSR is managed in accordance with the North Coast Demersal Scalefish Resource Harvest Strategy (Harvest Strategy). The sustainability objectives of the PDSR are set out in the Harvest Strategy and monitored via the use of an indicator species approach, whereby the status of key species is considered representative of the status of the resource. Under this approach the spawning biomass level of red emperor (Lutjanus sebae), bluespotted emperor (Lethrinus punctulatus) and rankin cod (Epinephelus rankini) are monitored against target, threshold, and limit reference levels.
Assessments of the status of other key non-indicator species, such as goldband snapper (Pristipomoides multidens), are also undertaken periodically. In November 2023, the Department of Primary Industries and Regional Development (DPIRD) finalised the Assessment of the Status of the Pilbara Demersal Scalefish Resource (Fisheries Research Report (FRR) No. 338).
The 2023 PDSR stock assessment indicated that the relative female spawning biomass of: red emperor (indicator species) had breached the limit reference level and is classified a depleted stock; bluespotted emperor (indicator species) was above the threshold reference level and is classified a sustainable stock; goldband snapper (retained non-indicator species) was between the limit and the threshold reference level and is classified a depleting stock; and rankin cod (indicator species) was not assessed but will be included in the next periodic stock assessment for the PDSR scheduled for completion in 2026.
In accordance with the Harvest Strategy, where the status of an indicator species (or non-indicator species) breaches the threshold or limit reference level, a review is undertaken, and a management response is implemented to recover the resource within two generations (or a maximum of 20 years). A resource is considered to have recovered when the spawning biomass level of all indicator species is above the threshold reference level and being managed to the target reference level.
Model projections outlined the 2023 stock assessment estimated that the catch of red emperor needs to be reduced by at least 38% (from 2022 levels) to recover the stock to above the threshold reference level within 20 years. Given the outcomes of the 2023 stock assessment, the indicator species approach has been applied such that red emperor (high sustainability risk) is considered an indicator for the suite of species with similar biological characteristics (e.g. late maturation relative to selection by fishing gear, relatively long lived). These species include goldband snapper (also high sustainability risk), saddletail snapper (Lutjanus malabaricus), crimson snapper (Lutjanus erythropterus), and other species that share similar life history characteristics.
Similarly, bluespotted emperor (medium/acceptable sustainability risk) is considered an indicator for the suite of species with similar biological characteristics (e.g., early maturation relative to selection by fishing gear, shorter lived), including brown-striped snapper (Lutjanus vitta)
Western Australia Pastoral Land Tenure - Gascoyne Region
No full textA map of the Gascoyne region of Western Australia showing the pastoral lease boundaries and names and their tenure. Includes an index of pastoral leases.https://library.dpird.wa.gov.au/gis_maps/1019/thumbnail.jp
Annual pasture quantity and quality in South West Western Australia
No full textThe productivity of sheep is largely governed by the amount of pasture they eat and this is influenced by the quantity of the pasture on offer and its quality. Assessing pasture quantity and quality throughout the growing season gives managers the information they need to manage animal performance and pasture condition.
The Department of Primary Industries and Regional Development provides this information for farmers to help improve the productivity and profitability of the livestock industry in Western Australia