Genome evolution & adaptation of the multinuclear wheat stripe rust fungus. Animals and plants package their genomes into a single nucleus within each cell. In contrast, millions of fungal species accommodate multiple nuclei containing individual haploid genomes. It is currently unknown what the evolutionary implications are for this unusual genome division into multiple nuclei. Here we explore the evolutionary consequences of genome division into multiple nuclei for the first time by applying c ....Genome evolution & adaptation of the multinuclear wheat stripe rust fungus. Animals and plants package their genomes into a single nucleus within each cell. In contrast, millions of fungal species accommodate multiple nuclei containing individual haploid genomes. It is currently unknown what the evolutionary implications are for this unusual genome division into multiple nuclei. Here we explore the evolutionary consequences of genome division into multiple nuclei for the first time by applying cutting edge genome biology tools and algorithms. The economically significant study system is the devastating wheat stripe rust fungus. This pathogen costs Australian farmers over $100 million a year. New understanding is expected to lead to better disease management, reduced fungicide applications, and increased yields.Read moreRead less
Nuclear RNA surveillance and its connection to splicing quality control. Due to the error-prone nature of RNA splicing, elaborate quality control processes ensure that only correctly spliced transcripts can leave the nucleus. It has long been known that incorrectly spliced mRNA transcripts are degraded by the nuclear RNA surveillance machinery, but how the RNA quality control machinery is connected to nuclear RNA surveillance is not known. This proposal aims to uncover the connection between the ....Nuclear RNA surveillance and its connection to splicing quality control. Due to the error-prone nature of RNA splicing, elaborate quality control processes ensure that only correctly spliced transcripts can leave the nucleus. It has long been known that incorrectly spliced mRNA transcripts are degraded by the nuclear RNA surveillance machinery, but how the RNA quality control machinery is connected to nuclear RNA surveillance is not known. This proposal aims to uncover the connection between these two important processes and will fill a significant gap in our understanding of how splicing quality control and nuclear RNA surveillance work. The project will also identify sequence features that trigger abortive splicing reactions and will thus help to improve the design of synthetic mRNAs.Read moreRead less
Assessment Of The Utility Of Genomics For Sydney Rock Oyster Breeding
Funder
Fisheries Research and Development Corporation
Funding Amount
$620,000.00
Summary
Genomics is routinely used across many livestock and plant breeding industries. It is now practical, within certain considerations, to consider applying genomic selection to aquaculture breeding programs due to significant cost reductions in the last decade. Its use in aquaculture breeding programs is increasing and genomics has already been researched for oyster breeding by USC (Vu et al. 2021a; Vu et al. 2021b).
Genomic selection has the potential to reduce the cost of estimating bre ....Genomics is routinely used across many livestock and plant breeding industries. It is now practical, within certain considerations, to consider applying genomic selection to aquaculture breeding programs due to significant cost reductions in the last decade. Its use in aquaculture breeding programs is increasing and genomics has already been researched for oyster breeding by USC (Vu et al. 2021a; Vu et al. 2021b).
Genomic selection has the potential to reduce the cost of estimating breeding values, which presently is a costly and challenging exercise with SROs and also may potentially increase genetic progress and selection accuracy for the SRO BP. The research proposed in this application will evaluate if it is possible to increase genetic progress for the productivity traits of QX disease resistance and growth as well as the product quality trait of meat condition. Increased QX survival and growth are particularly important traits for the SRO industry at this current time due to Port Stephens, the second largest SRO producing estuary in NSW, reeling from the impact of QX disease outbreaks. Climate change resilience is a new trait being investigated for incorporation into the breeding program for industry to respond to this threat. We would also like to assess whether genomics can provide a pathway to increase selection for resilience.
This project has been developed in line with the Oysters Australia Strategic Plan 2020 and the FRDC R&D Plan 2020-2025. The outcomes from this project will assess the feasibility of increasing selection accuracy for traits that improve productivity (growth and meat condition) as well as reduce impacts caused by QX disease and climate change through breeding for resilience. The outcomes will assess the possibility to improve genetic selections for multiple traits such that oysters can be selected on their ability to adapt to new climate conditions, survive QX disease whilst having faster growth and better meat condition. Additionally, this project will build new knowledge skills and networks through a NSW DPI, The University of the Sunshine Coast and The University of New South Wales alliance as well as create post-doctoral study opportunities. These meet the goals in Program 1, 2 and 3 outlined in the 2020-2025 Oysters Australia Strategic Plan.
With respect to the FRDC R&D Plan 2020-2025, this project will build capacity and create knowledge through developing skills and networks between NSW DPI, The University of the Sunshine Coast and The University of NSW to breed oysters that offer oyster businesses greater profitability, reduced risk and that can adapt to changing environments.
This project will explore alternative methods to what is presently used for SRO breeding to assess feasibility of genomic selection and what might be required today to move towards genomic selection in the future. This project will start compiling a reference library for SROs that can be used in the future and promote innovation in SRO breeding to integrate the technology developed from this project. Moreover, costs associated with genomic selection are reducing which increases the value proposition for incorporation into the future. The ultimate success and transfer of outcomes from this project to end user beneficiaries will be through incorporation of these new technologies into the SRO breeding program. Objectives: 1. Collect tissue samples using non-lethal methods and tagging to identify oysters 2. Sequence the whole genomes of selected individuals at high read depth, which will serve as the genotype resource for the project 3. Identify the associations between genotypes and phenotypes and compile a list of genetic markers and the genes associated with QX survival, whole weight and meat condition to then use modelling (for genomic predictions) to give individuals breeding values Read moreRead less
SCRC: Masters M3.1 Nutritional Genomics And Its Application To Aquaculture (Prof Abigail Elizur; Student Linda Moss)
Funder
Fisheries Research and Development Corporation
Summary
The project aims to address the question: Can different aquaculture diets be assessed and evaluated by examining the expression profiles on known (or newly discovered) candidate genes that are responsible for, or associated with, the digestion and absorption of diet components.
Nutrition is a key significant consideration in aquaculture operations and absorption of molecular components of feed is the main factor contributing to nutrition in fish. An innovative alternative to feed trials ....The project aims to address the question: Can different aquaculture diets be assessed and evaluated by examining the expression profiles on known (or newly discovered) candidate genes that are responsible for, or associated with, the digestion and absorption of diet components.
Nutrition is a key significant consideration in aquaculture operations and absorption of molecular components of feed is the main factor contributing to nutrition in fish. An innovative alternative to feed trials is the use of nutritional genomics, where the specific response to the various diet at a gene expression level can potentially predict the quality of the diet and its suitabilty for optimum aquaculture use.
Candidate genes for such studies include genes associated with the digestion and absorption of nutrients i.e. trypsin, aminopeptidase, bile salt-activated lipase, insulin, glucagon and cholecstokinin. This project is expected to also lead to the discovery of a novel suite of genes whose expression is diet dependant, leading to the discovery of suitable markers for diet effectiveness, reducing the necessity and costs of feed trials.
The research done during the project is expected to greatly enhance our knowledge of the molecular processes with feed digestion, absorption and feed development, thus not only offereing an attractive testing alternative to diet development, but also explore the animal's response to different diets.Read moreRead less
Stock Identification And Discrimination Of Commercially Important Whitings (Teleostii; Sillaginidae) In Australian Waters Using Genetic Criteria [later Sillago Maculata And S. Bassensis Were Added]
Funder
Fisheries Research and Development Corporation
Summary
Objectives: 1. To investigate the population structure of the commercially important whitings, Sillago ciliata, S. maculata, S. robusta, S. bassensis and Sillagonides punctatus, using allozymes detected by electrophoresis as genetic markers. NSW, Vic, Tas, SA
Regulation Of Haemopoietic And Immune Cells In Health And Disease
Funder
National Health and Medical Research Council
Funding Amount
$19,924,984.00
Summary
This Program brings together a team of researchers with world-class multidisciplinary skills in biomedical discovery and an established track record of clinical and commercial translation of research discoveries. This Program will result in the creation of new knowledge regarding the control of blood and immune cell production and function and provide new avenues for the treatment of people suffering from cancers of the blood, inflammatory and immune disorders.
BCA: Identification Of A Y-chromosome Marker In Atlantic Salmon (extension To FRDC 95/80)
Funder
Fisheries Research and Development Corporation
Funding Amount
$5,272.01
Summary
Genetic variation The results we have obtained in the current project are encouraging for SALTAS, as they confirm the earlier allozyme results of little loss of genetic variation. However, the results are also suggestive of a potential long term trend in loss of genetic variation. A sample collected and analysed in January 1997 (1993 year-class parents) would provide evidence to substantiate this trend or indicate whether the current results were a sampling artifact. The analysis of a 1997 ....Genetic variation The results we have obtained in the current project are encouraging for SALTAS, as they confirm the earlier allozyme results of little loss of genetic variation. However, the results are also suggestive of a potential long term trend in loss of genetic variation. A sample collected and analysed in January 1997 (1993 year-class parents) would provide evidence to substantiate this trend or indicate whether the current results were a sampling artifact. The analysis of a 1997 sample would be the second of a proposed regular 4 to 5 year assessment of the status of the Tasmanian stock, and would help to describe the nature and speed of any long term trends.
SALTAS, as the principal Atlantic salmon hatchery in Australia, has a long term requirement to maintain industry and investor confidence in their product, and the ability to confirm the reliability of its breeding practices is important for the sustainability of the industry.
Loss of genetic variation in a cultured population will provide an early indicator of potential inbreeding, which could have grave consequences as deleterious recessive genes are exposed and stocks lose vigour dependent on genetic variance. Any loss of genetic variation in Tasmanian Atlantic salmon could be difficult or impossible to recover due to the restrictions on importation of new broodstock.
Y-chromosome marker A number of molecular genetic techniques for trait or marker screening have been developed since the original proposal was submitted. We propose to apply some of these new techniques to the screening of Atlantic salmon DNA for a potential Y-chromosome marker. These approaches will greatly increase our chances of finding such a marker.
The new techniques we propose include: Representational Difference Analysis (RDA); PCR-Select cDNA Subtraction Technique; the application of other modified subtractive hybridization and differential display techniques that have proved useful in other species; AFLP (amplified fragment polymorphism) technique; and the application of a number of commercial RAPD (random amplified polymorphic DNA) primers.
We have also established contact, and will collaborate during the proposed project extension, with workers who have a Y-chromosome marker for brook trout and arctic char, and other workers in this field working with other teleosts.
We believe that a continuation of the current project (95/80) is the best approach to further tackle this Y-chromosome marker issue. It will allow us to best utilise the expertise and momentum we have established on this problem, rather than completed our current objectives and then revisit this issue in a year or two.
If we are successful in locating a Y-chromosome marker either during the remainder of the current schedule or early in the 1997 grant extension, resources will then be directed to isolate and further characterize that marker. Objectives: 1. To locate a Y-chromosome marker in Atlantic salmon by applying a range of molecular genetic techniques. 2. To establish the rate of change in genetic variation in Tasmanian Atlantic salmon by comparing the genetic (microsatellite and allozyme) variation expressed in progeny from 1993 year-class parents with that present in 1989 year-class parents and the parental Nova Scotia population. Read moreRead less