ORCID Profile
0000-0002-5862-6335
Current Organisations
Universidade Federal Rural de Pernambuco
,
James Cook University
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Publisher: IEEE
Date: 12-2019
Publisher: Elsevier BV
Date: 12-2011
DOI: 10.1016/J.MARGEN.2011.06.007
Abstract: 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 microsatellites for the silver-lipped pearl oyster, Pinctada maxima, a species of aquaculture importance throughout the Indo-Australian Archipelago for production of the highly valued South Sea pearl. More than 1.2 million Roche 454 expressed sequence tag (EST) reads were screened for microsatellite repeat motifs. A total of 12,604 sequences contained either a di, tri, tetra, penta or hexa microsatellite repeat motif (n ≥ 6), with 6435 of these sequences having sufficient flanking regions for primer development. All identified microsatellites with designed primers were condensed into 2322 unique clusters (i.e., unique loci) of which 360 were shown to be polymorphic based on multiple sequence reads with different repeat motifs. Genotyping of five microsatellite loci demonstrated that in silico evaluation of polymorphism levels was a very useful method for identification of polymorphic loci, with the variation uncovered being a lower bound. Gene Ontology annotations of sequences containing microsatellites suggest that most are derived from a erse array of unique genes. This EST derived microsatellite database will be a valuable resource for future studies in genetic map construction, ersity analysis, quantitative trait loci analysis, association mapping and marker assisted selection, not only for P. maxima, but also closely related species within the genus Pinctada.
Publisher: Wiley
Date: 29-09-2017
DOI: 10.1111/MEC.14333
Abstract: 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 this physiological resilience, we analysed the gill transcriptome of B2 oysters that had been exposed to near-future projected ocean pH over two consecutive generations. Our results suggest that the distinctive performance of B2 oysters in the face of OA is mediated by the selective expression of genes involved in multiple cellular processes. Subsequent high-throughput qPCR revealed that some of these transcriptional changes are exclusive to B2 oysters and so may be associated with their resilience to OA. The intracellular processes mediated by the differentially abundant genes primarily involve control of the cell cycle and maintenance of cellular homeostasis. These changes may enable B2 oysters to prevent apoptosis resulting from oxidative damage or to alleviate the effects of apoptosis through regulation of the cell cycle. Comparative analysis of the OA conditioning effects across sequential generations supported the contention that B2 and wild-type oysters have different trajectories of changing gene expression and responding to OA. Our findings reveal the broad set of molecular processes underlying transgenerational conditioning and potential resilience to OA in a marine calcifier. Identifying the mechanisms of stress resilience can uncover the intracellular basis for these organisms to survive and thrive in a rapidly changing ocean.
Publisher: Elsevier BV
Date: 05-2022
DOI: 10.1016/J.FSI.2022.04.021
Abstract: 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 of traits often leads to low genetic correlation and incorrect estimation of breeding values. In this study, viral hemorrhagic septicemia virus (VHSV) resistance was studied using a genome-wide association study (GWAS), and the genetic parameters were estimated. Genotyping was performed using a high-quality 70 K single nucleotide polymorphism (SNP) Affymetrix® Axiom® myDesign™ Genotyping Array of olive flounder. A heritability of ∼0.18 for resistance to VHSV was estimated using genomic information of the fish. According to the GWAS, significant SNPs were detected in chromosomes 21, 24, and contig AGQT02032065.1. Three SNPs showed significance at the genome-wide level (p < 1 × 10
Publisher: Springer Science and Business Media LLC
Date: 05-08-2020
DOI: 10.1186/S12864-020-06960-W
Abstract: The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between in iduals, uncover the genetic architecture of commercial traits, as well as identify superior in iduals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp ( Penaeus monodon ) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 in iduals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 high-quality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches. Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.
Publisher: Springer Science and Business Media LLC
Date: 19-02-2018
DOI: 10.1038/S41588-018-0056-5
Abstract: Stature is affected by many polymorphisms of small effect in humans
Publisher: Elsevier BV
Date: 04-2022
Publisher: Canadian Science Publishing
Date: 09-2023
Abstract: Fish stocking occurs in aquatic systems for conservation purposes, to create or enhance recreational fisheries and to enhance wild-catch commercial fisheries. Identifying and quantifying the contribution of stocking efforts to wild populations is crucial to informing these management objectives. Provenance determination methods trade off accuracy, replicability, and cost-effectiveness at fishery-relevant scales. We present and assess multiple methods for provenance determination using a case study of barramundi ( Lates calcarifer) in the Dry Tropics region of northern Australia. A novel application of near-infrared spectroscopy (NIRS) is compared to two established methods for fish provenance, otolith microchemistry and genetic parentage analysis using microsatellites. The otolith microchemistry method was able to provide extremely high provenance resolution ( % accuracy). The microsatellite parentage analysis method had a slightly lower overall accuracy (95%), likely as a result of genetic introgression in this region. Provenance determination using otolith NIRS had the lowest overall accuracy (76%). Once limitations regarding spectral noise, image resolution, and s le size are addressed, NIRS may have potential for cost-effectively determining provenance in fish.
Publisher: Springer Science and Business Media LLC
Date: 2013
Publisher: FapUNIFESP (SciELO)
Date: 2014
DOI: 10.1590/1807-1929/AGRIAMBI.V18NSUPPS53-S58
Abstract: ABSTRACT This research studied threshold electrolyte concentration (TEC) of irrigation water and its effect on the infiltration rate of two contrasting soils from Pernambuco state, Brazil. The experiment was conducted in the Soil Chemistry and Salinity Laboratory of Federal Rural University of Pernambuco. Each soil was packed in five Buchner funnels, where one funnel from each soil was submitted to treatment with solution of electrical conductivity (EC) of 0.5, 1.0, 2.0, 4.0 or 8.0 dS m-1. For each funnel containing soil, an increasing ratio of NaCl to CaCl2 was applied in a treatment solution to achieve 10 increasing values of sodium adsorption ratio (SAR) from 0 to 100. These solutions were applied through a Mariotte bottle, with a constant hydraulic head of ~2 cm (pressure potential). After a liter of solution had drained, in the flux was collected for a known time interval, until steady state was reached. Darcy’s equation was used to calculate saturated hydraulic conductivity (Ksat) and a mathematical model used to calculate the TEC as a 20% reduction in Ksat. By increasing SAR similar behavior was noted between the two soils, whereby Ksat decreased, although the relativedecrease in Ksat was greater for SAR of 100 in the soil with higher clay content.
Publisher: Frontiers Media SA
Date: 15-10-2020
Publisher: Elsevier BV
Date: 02-2022
Publisher: Frontiers Media SA
Date: 23-01-2019
Publisher: Elsevier BV
Date: 06-2022
Publisher: Springer Science and Business Media LLC
Date: 30-05-2013
DOI: 10.1007/S10126-013-9514-3
Abstract: 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, h ering investigations into identifying genes that regulate important pearl quality traits and unique biological characteristics (i.e. biomineralisation). The silver-lipped pearl oyster, Pinctada maxima, is one species where there is interest in understanding genes that regulate commercially important pearl traits, but presently, there is a dearth of genomic information. The objective of this study was to develop and validate a large number of type I genome-wide single nucleotide polymorphisms (SNPs) for P. maxima suitable for high-throughput genotyping. In addition, sequence annotations and Gene Ontology terms were assigned to a large mantle tissue 454 expressed sequence tag assembly (96,794 contigs) and information on known bivalve biomineralisation genes was incorporated into SNP discovery. The SNP discovery effort resulted in the de novo identification of 172,625 SNPs, of which 9,108 were identified as high value [minor allele frequency (MAF)≥ 0.15, read depth ≥ 8]. Validation of 2,782 of these SNPs using Illumina iSelect Infinium genotyping technology returned some of the highest assay conversion (86.6 %) and validation (59.9 % mean MAF 0.28) rates observed in aquaculture species to date. Genomic resources presented here will be pivotal to future research investigating the biological mechanisms behind biomineralisation and will form a strong foundation for genetic selective breeding programs in the P. maxima pearling industry.
Publisher: Wageningen Academic Publishers
Date: 31-12-2022
Publisher: Wiley
Date: 29-10-2008
DOI: 10.1111/J.1755-0998.2008.02295.X
Abstract: 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 for P. amboinensis using a magnetic bead enrichment protocol. Twenty in iduals from one location were analysed and observed heterozygosities ranged from 0.7 to 0.95. Eight of nine loci were in Hardy-Weinberg equilibrium and no evidence of linkage or null alleles were found.
Publisher: Elsevier BV
Date: 2023
Publisher: Elsevier BV
Date: 03-2012
DOI: 10.1016/J.MARGEN.2011.08.006
Abstract: 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 identified and linked to shell biomineralisation in pearl oysters, few studies have determined which of these biomineralisation genes are expressed in the pearl sac and potentially linked to pearl biomineralisation processes. It is also uncertain whether the host or donor oyster is primarily responsible for the expression of biomineralisation genes governing pearl formation, with only two shell matrix proteins previously identified as being expressed by the donor oyster in the pearl sac. To further our understanding of pearl formation, the pearl sac transcriptome of Pinctada maxima and Pinctada margaritifera was each sequenced to an equivalent 5× genome coverage with putative molluscan biomineralisation-related genes identified. Furthermore, the host and donor contribution of these expressed genes within the pearl sac were quantified using a novel approach whereby two pearl oyster species harbouring unique genomes, P. maxima or P. margaritifera, were used to produce xenografted pearl sacs. A total of 19 putative mollusc biomineralisation genes were identified and found to be expressed in the pearl sacs of P. maxima and P. margaritifera. From this list of expressed genes, species-diagnostic single nucleotide polymorphisms (SNP) were identified within seven of these genes Linkine, N66, Perline, N44, MSI60, Calreticulin and PfCHS1. Based on the presence/absence of species diagnostic gene transcripts within xenografted pearl sacs, all seven genes were found to be expressed by the species used as the donor oyster. In one in idual we also found that the host was expressing Linkine. These results convincingly show for the first time that the donor mantle tissue is primarily responsible for the expression of biomineralisation genes in the pearl sac.
Publisher: Elsevier BV
Date: 10-2014
Publisher: Springer Science and Business Media LLC
Date: 03-02-2010
Publisher: Springer Science and Business Media LLC
Date: 04-09-2017
DOI: 10.1038/S41598-017-10515-7
Abstract: 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 measurements and omit potential gains by integrating genetic selection into existing breeding programs. Such integration of genetic information has been hindered by the limited available genomic resources, background genetic parameters and knowledge on the genetic architecture of commercial traits for L . vannamei . This study describes the development of a comprehensive set of genomic gene-based resources including the identification and validation of 234,452 putative single nucleotide polymorphisms in-silico , of which 8,967 high value SNPs were incorporated into a commercially available Illumina Infinium ShrimpLD-24 v1.0 genotyping array. A framework genetic linkage map was constructed and combined with locus ordering by disequilibrium methodology to generate an integrated genetic map containing 4,817 SNPs, which spanned a total of 4552.5 cM and covered an estimated 98.12% of the genome. These gene-based genomic resources will not only be valuable for identifying regions underlying important L . vannamei traits, but also as a foundational resource in comparative and genome assembly activities.
Publisher: Elsevier BV
Date: 07-2021
Publisher: Elsevier BV
Date: 10-2014
Publisher: Elsevier BV
Date: 12-2020
Publisher: Frontiers Media SA
Date: 03-08-2018
Publisher: Elsevier BV
Date: 07-2021
Publisher: Elsevier BV
Date: 06-2020
Publisher: MDPI AG
Date: 04-12-2022
DOI: 10.3390/D14121068
Abstract: 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 Lep-Map3 in linkage map construction. The map length spans 2016.62 cM with an average marker distance of 0.85 cM. Integration of the recent H. maculosa genome allowed 1151 scaffolds comprising 34% of the total genomic sequence to be orientated and/or placed using 1278 markers across all 47 LG. The linkage map generated provides a new perspective on HOX gene distribution in octopods. In the H. maculosa linkage map three (SCR, LOX4 and POST1) of six identified HOX genes (HOX1/LAB, SCR, LOX2, LOX4, LOX5, POST1) were located within the same LG (LG 9). The generation of a linkage map for H. maculosa has provided a valuable resource for understanding the evolution of cephalopod genomes and will provide a base for future work.
Location: Brazil
Location: Australia
No related grants have been discovered for David Jones.