Aquaculture is becoming an increasingly important source of fish protein available for human consumption. Brendan mcandrew, genetics and reproduction research group, institute of aquaculture, university of stirling, stirling fk9 4la. The production of fish and shellfish through aquaculture is an increasingly important source of highquality animal protein, with a worldwide production of 66. Caird rexroad serves as the ars national program leader. The upcoming of hts techniques has led to emergence of metagenomics, nutrigenomics, epigenetics and other omics technologies in aquaculture in the last decade.
Choose from the readily available fixed content arrays or collaborate with neogens highly experienced custom array design team to build a custom content array for your focused research project or breeding program. Cordesb athe fish molecular genetics and biotechnology laboratory, department of fisheries and allied aquacultures, and program of cell and molecular biosciences, aquatic genomics unit, auburn university, 203 swingle hall, auburn, al 36849, usa. Jan 31, 2015 although no chapters of this book describe novel genome technologies that have originated from or are unique to aquaculture or fisheries species, almost every chapter deals with how genome technologies can be used for aquaculture and fisheries, or for agricul tural sciences in general. Genome, made up of a 3 billion sequence code, contains the blueprint for every cell in our body. The aquaculture industry has often been innovative and visionary in their application of new technologies to improve production. Aquaculture genome technologies is edited by an international leader in the field of aquaculture genome research, with contributions from an international team of leading researchers. Applications of modern genetics and genomic technologies. Fishes are the largest vertebrate group, with more than 30,000 species, and provide a major role in feeding global economies and people. Recently, genomesequencing efforts have been made beyond model species and reached into the field of aquaculturerelated genomes. Current status of genome sequencing and its applications in. Recently, genome sequencing efforts have been made beyond model species and reached into the field of aquaculture related genomes. Recent developments in dna marker technologies, in particular the emergence of single nucleotide polymorphism snp discovery, have rendered some of the traditional methods of genetic research outdated. With the rapid advance of ngs technologies and bioinformatics analysis of large sequencing data, the development of whole genome sequencing in aquaculture is very quick. Edited by an international leader in aquaculture genome research with contributions from leaders in the field, this book will provide a tour through the aquaculture genomics process providing basic principles and detailed methodologies as to how to use genome technologies to study the.
Fish aquaculture is considered to be one of the most sustainable sources of protein for humans. Choose from the readily available fixed content arrays or collaborate with neogens highly experienced custom array design team to build a custom content. The draft wholegenome sequences of over 24 species have been published, and served as reference genomes for downstream studies on important issues related to aquaculture. Dna marker technologies and their applications in aquaculture. Jul 31, 2017 despite this, dbc as a methodology still has much use in fish aquaculture and barcoding along with other dna marker technologies have helped revolutionize aquaculture research. Despite this, dbc as a methodology still has much use in fish aquaculture and barcoding along with other dna marker technologies have helped revolutionize aquaculture research.
Gene expression studies in aquaculture have slowly evolved from the traditional reductionist approach of single gene sequencing to high throughput sequencing hts techniques able to sequence entire genomes of living organisms. Nagrp aquaculture genomics annual report for 2018 jan. Aquaculture genomics, genetics and breeding in the united. Genomics for fisheries and aquaculture genome canada. Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. Aug 28, 2007 aquaculture genome technologies is edited by an international leader in the field of aquaculture genome research, with contributions from an international team of leading researchers. This book contains 29 chapters written by wellknown scientists from all over the world. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. This site is designed to enhance collaboration, cooperation, communication, and coordination among aquaculture genome research community members. Wenbiao chen vanderbilt university school of medicine, dr. Current status of genome sequencing and its applications. The rapid development of sequencing technologies has revolutionized biological sciences, and supplied necessary tools to tackle these challenges in aquaculture and thus ensure its sustainability and profitability.
Applications of modern genetics and genomic technologies to. Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. Catfish genomics nrsp8 species coordinator sylvie quiniou research molecular biologist, sylvie. Genome wide association studies have be able to link. Zhanjiang john liu is a distinguished alumni professor, department of fisheries and allied aquacultures and program of cell and molecular biosciences, and director, aquatic genomics unit at auburn. It is also realised that there is distinct difference between fish and animal genetics and that aquaculture candidate species present greater genetic variability. Dna marker technologies and their applications in aquaculture genetics z. Aquaculture genome technologies university of dhaka. Genomics in aquaculture is a concise, musthave reference that describes current advances within the field of genomics and their applications to aquaculture. Whole genome sequencing and assembly the genomes of several major aquaculture species in the united states, especially those under the usda national research support project 8 nrsp8. Current advances in functional genomics in aquaculture. Genetics and genomics are powerful biological tools for studying fish and fish populations. Their enriched experience in both genomics and aquaculture and fisheries allowed them to provide discussions of genome technologies with unique angles.
Cordesb athe fish molecular genetics and biotechnology laboratory, department of fisheries and allied aquacultures, and program of cell and molecular biosciences, aquatic genomics unit, auburn university. We apply it to the four genomes from the assemblathon competitions and show it. So far, draft genomes have been published in over 24 aquaculture species, and used to address important issues related to aquaculture. Advances of genotypingbysequencing in fisheries and. Keywords genome sequencing ngs technologies transcriptome microarray nutrigenomics introduction aquaculture is becoming an increasingly important source of. Review dna marker technologies and their applications in aquaculture genetics z. Striped bass transcriptome sequence contigs database 20092010 rainbow trout est contigs characterized 2010 2011 tools. Review dna marker technologies and their applications in. Although aquaculture management becomes challenging because of overuse, pollution and human activities reduced resources and genetic variations, current developments in molecular technology and genome programs have created an enormous evidence to be used for the genetic advancement of aquaculture. The major potential applica tions of genome technologies, primarily in. This is driving growth, productivity, commercialization and global competitiveness, while finding solutions to environmental sustainability problems. General introduction aquaculture production has continued to grow at an ever increasing rate from less. Aquaculture genome technologies linkedin slideshare. Advances of genotypingbysequencing in fisheries and aquaculture.
Although aquaculture management becomes challenging because of overuse, pollution and human activities reduced resources and genetic variations, current developments in molecular technology and genome programs have created an enormous evidence to. Aquaculture genome technologies will fill just this gap. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. Molecular markers and their applications in aquaculture. Aquaculture is the farming of aquatic organisms, including fish, molluscs, crustaceans, etc. The national aquaculture genome project is a part of the national animal genome research project. Potential practical application of omics technologies in genetic programs for aquaculture species 1. However, the aquaculture of these fishes is seriously hampered by the scarce knowledge on their biology. Application of proteome and transcriptome analysis in the molecular biological studies in marine finfish. Just as genetic techniques are used in agriculture to select for and breed crops or animals with desired traits, these tools can be used in aquaculture. When wild fish are moved to aquaculture settings, a new set of selective pressures comes into play that often changes gene frequencies.
The final two sections look forward toward sequencing. By coupling genome mapping technologies with aquaculture trait evaluations, quantitative trait locus qtl. In the northeast atlantic area, there exist a total of 11 relevant species for fisheries belonging to the teleost order pleuronectiformes. Development of transgenic technologies in marine finfish. Zhanjiang liu at auburn university of usa, together with more than 40 aquaculture genomics experts in the world, edited a highly technical and comprehensive book aquaculture genome. Aquaculture genome technologies is an essential reference for anyone with an interest in aquaculture genetics. Barcoding, nucleic acid sequencing are powerful resources. Next generation sequencing and whole genome selection in. Advances in genomics for flatfish aquaculture genes. Although the chemical composition is highly dependent on the species, age, sex, environment, migratory behaviour or season, fish proteins represent a. John buchanan center for aquaculture technologies, dr.
Written in an accessible manner for anyonenonspecialists to experts alikethis book provides indepth coverage of genomics spanning from genome sequencing, to transcriptomics and proteomics. Marta gomezchiarri infectious diseases have a serious impact on shellfish and finfish, constraining the expansion of aquaculture and endangering wild fisheries. Barcoding, nucleic acid sequencing are powerful resources for. Microarray analysis of fish genomic data for enhancing. Genomics present another major opportunity, and the research published in this special issue provides several excellent examples of their potential or realized application. As the field expands a book is needed to bridge the gap between basic genomic technology and how to systematically apply this information to aquaculture genomes. Lessons from the application of genomic selection to. Neogen offers whole aquaculture genome, genotyping or copy number variation analysis service based on illuminas infinium chemistry or affymetrix axiom technology. The plant and animal genome pag aquaculture workshop will be held in san diego january 1415, 2012. Many different species are cultured worldwide, but among them, marine flatfishes comprise a group of teleosts of high commercial interest because of their highly prized white flesh. Aquaculture genome technologies will fill just this. Considering the continuously growing global human population and increasing demand for fish products, improvements in the scale, efficiency, and sustainability of aquaculture are essential. Disease reduction in aquaculture with genetic and genomic.
Reduction in the occurrence and severity of disease in aquaculture would improve the productivity, profitability, efficiency and welfare of aquacultural fish. Fish meal is characterized by its high content in proteins and lipids carbohydrates represent lower than 0. Next generation sequencing and whole genome selection in aquaculture comprehensively covers the current state of research in whole genome selection and applies these. Next generation sequencing and whole genome selection in aquaculture comprehensively covers the current state of research in whole genome selection and applies these discoveries to the aquaculture industry specifically. We then propose a set of priorities for future research in aquaculture genomics, genetics, and breeding. Aquaculture genome technologies provides the reader with a tour through the aquaculture genomics process. Aquaculture genome technologies zhanjiang john liu auburn university 3. The aquaculture genomics workshop that took place at pag in san diego on saturday, january. Methods and practical considerations 165 ashok ragavendran and william m. Aquaculturomics use of genomic technologies and their scientific products to enhance the health of. The use of genotyping has enabled the characterization and mapping of genes and the study of stock identification, population genetics, evolution, ecological speciation, and invasion, as well as genomic evaluation, sex control and sex determination, nutrition, biomarkers for disease, and quantitative trait loci mapping for markerassisted selection in fisheries and aquaculture. Genome technologies have been developed to study genome structure, organization, expression and function, and to select and modify genomes of interest to increase benefits to humans. Current status of aquaculture genetics domestication and strain evaluation. Aquaculture 2 plant and animal genome xx conference.
Aquaculture 2 pag 2012 aquaculture genomics workshop. Application of the microarray technology in the studies of fish biology. Genetic linkage analysis, quantitative trait locus qtl mapping, genomewide association studies gwas to detect genes for traits of economic importance in commercial selective breeding programs 2. The dramatic development of molecular genetics since the first widespread use of allozymes in the 1970s, and currently exemplified by the human genome project and other equally ambitious undertakings, has laid the groundwork for genomics. Thus an organism better suited for the aquaculture environment begins to evolve. Genome canada and the six regional genome centres across the country are working to harness the transfor. Comparison of index selection, blup, mas, and whole genome selection 185 zhenmin bao index 219. Overall, aquaculture genome technologies gives a good and comprehensive overview of the principles of genomic tools covering both classical and modern methods, combining clarity and depth despite. Molecular markers and their applications in aquaculture and. Aquaculture neogen genomics offers whole aquaculture genome, genotyping or copy number variation analysis service based on illuminas infinium chemistry or affymetrix axiom technology. New genomics technologies and their impact on finfish and shellfish functional genomics.