David Jones

James Cook University · Centre for Sustainable Tropical Fisheries and Aquaculture

Genetic linkage maps provide a useful resource for non-model genomes and can aid in genome reassembly to form more contiguous pseudo-chromosomes. We present the first linkage map of any cephalopod, H. maculosa, composed of 47 linkage groups (LG). A total of 2166 single nucleotide polymorphisms and 2455 presence–absence variant loci were utilised by...

The giant black tiger shrimp (Penaeus monodon) is an important aquaculture and fishery species and is the second most farmed penaeid shrimp species globally. Genomic resources available in giant black tiger shrimp research are growing rapidly. However, considering the large number of animals that would require SNP genotyping for commercial applicat...

Transformer-based models, such as the Vision Transformer (ViT), can outperform onvolutional Neural Networks (CNNs) in some vision tasks when there is sufficient training data. However, (CNNs) have a strong and useful inductive bias for vision tasks (i.e. translation equivariance and locality). In this work, we developed a novel model architecture t...

Traits linked to growth performance in farmed fish are major drivers of profitability in aquaculture systems. Given the importance of growth-related traits, there have been efforts to unravel the genomic architecture of growth traits and to identify key genes or genomic regions useful as selection markers in various species. Such markers would incr...

In flounder aquaculture, selective breeding plays a vital role in the development of disease-resistant traits and animals with high growth rates. Moreover, superior animals are required to achieve high profits. Unlike growth-related traits, disease-resistant experiments need to be conducted in a controlled environment, as the improper measurement o...

Due to the high revenues generated by the pearl industry, interest in developing breeding programs is increasing. The traditional approach for collecting DNA for pedigree analyses in breeding programs for the silver-lipped pearl oyster (Pinctada maxima) involves tissue excision from the muscular foot and/or mantle. Tissue excision causes injury and...

Barramundi (Lates calcarifer) is a tropical species of increasing aquaculture interest. In efforts to accumulate genetic gains through selection, the species is now subject to several pedigree-based breeding programs globally; however, these breeding programs would further benefit from the implementation of genomic selection methodologies. Here we...

The silver-lipped pearl oyster, Pinctada maxima, is an important aquaculture species extensively farmed in tropical Australia and Southeast Asia to produce “South Sea” pearls. The pearling industry in Australia is in the process of implementing breeding programs targeting improved disease resistance, growth and pearl quality, and as a result geneti...

To enable cumulative increases in aquaculture productivity, structured and efficient selective breeding programs are required. These are contingent on the management of genetic resources within the breeding population though the attainment of accurate pedigree information which can be provided by DNA-based parentage analysis. This study developed a...

Domestication to captive rearing conditions, along with targeted selective breeding have genetic consequences that vary from those in wild environments. Nile tilapia (Oreochromis niloticus) is one of the most translocated and farmed aquaculture species globally, farmed throughout Asia, North and South America, and its African native range. In Egypt...

Background: The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic...

The white-leg shrimp, Litopenaeus vannamei, is the most widely farmed shrimp species globally. In recent years, interest in developing selective breeding programs and identifying the mechanisms controlling sex determination in L. vannamei has increased in the hope that improvements can be made on productivity efficiency. L. vannamei exhibits sexual...

Background The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic pr...

Within aquaculture industries, selection based on genomic information (genomic selection) has the profound potential to change genetic improvement programs and production systems. Genomic selection exploits the use of realized genomic relationships among individuals and information from genome-wide markers in close linkage disequilibrium with genes...

Elucidating the underlying genetic drivers of production traits in agricultural and aquaculture species is critical to efforts to maximize farming efficiency. “Omics” based methods (i.e., transcriptomics, genomics, proteomics, and metabolomics) are increasingly being applied to gain unprecedented insight into the biology of many aquaculture species...

The Pacific whiteleg shrimp, Litopenaeus vannamei, is the most farmed aquaculture species worldwide with global production exceeding 3 million tonnes annually. Litopenaeus vannamei has been the focus of many selective breeding programs aiming to improve growth and disease resistance. However, these have been based primarily on phenotypic measuremen...

Some populations of marine organisms appear to have inherent tolerance or the capacity for acclimation to stressful environmental conditions, including those associated with climate change. Sydney rock oysters from the B2 breeding line exhibit resilience to ocean acidification (OA) at the physiological level. To understand the molecular basis of th...

The silver-lipped pearl oyster, Pinctada maxima, is of high economic importance to the global pearling industry. However, pearling industries worldwide have reported declines in gross pearl production values over the last decade, leading to the establishment of several genetic breeding programmes aiming to improve commercially important pearl produ...

Pearl oysters are commercially farmed for their gemstone quality pearls worldwide and are an important animal model for understanding bivalve biology. However, despite their economic and scientific significance, limited quantitative genetic studies have been undertaken to identify genes that regulate important pearl quality traits and unique biolog...

The silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species extensively farmed for the highly sought "South Sea" pearls. Traditional breeding programs have been initiated for this species in order to select for improved pearl quality, but many economic traits under selection are complex, polygenic and confounded wi...

Pearl oysters are not only farmed for their gemstone quality pearls worldwide, but they are also becoming important model organisms for investigating genetic mechanisms of biomineralisation. Despite their economic and scientific significance, limited genomic resources are available for this important group of bivalves, hampering investigations into...

Cultured pearl production is a complex biological process involving the implantation of a mantle graft from a donor pearl oyster along with a bead nucleus into the gonad of a second recipient host oyster. Therefore, pearl production potentially involves the genetic co-operation of two oyster genomes. Whilst many genes in the mantle tissue have been...

Pearls are an important export commodity for the Australian aquaculture industry with a production value of ~$113 million per annum. However, due to the large variation in pearl quality, there is the need for product improvement. Marker Assisted Selection (MAS) is one genetic approach that has great potential to increase the number of highly valuab...

Molecular stock improvement techniques such as marker assisted selection have great potential in accelerating selective breeding programmes for animal production industries. However, the discovery and application of trait/marker associations usually requires a large number of genome-wide polymorphic loci. Here, we present 2322 unique microsatellite...

Pearls are an important export commodity for Australian aquaculture with a production value of $113 million per annum. However, there is large variation in pearl quality from farm harvests which advocates scope for product improvement through genetic approaches, including Marker Assisted Selection (MAS). MAS breeding programs have great potential t...

Understanding patterns of connectivity in marine species is vital for the management and conservation of marine biodiversity. Here, the population genetic structure of a common and abundant tropical reef damselfish, Pomacentrus amboinensis, is reported. Using nine polymorphic microsatellite loci, the genetic structure at both small (i.e., around Li...

The relatively long pelagic larval duration of Pomacentrus amboinensis, a tropical fish, suggests the potential for long-distance dispersal; however, several nongenetic studies have found substantial self-recruitment at one location. To analyse patterns of connectivity of this species, primers for nine independent microsatellite loci were developed...