Next Generation Sequencing And Whole Genome Selection In Aquaculture Pdf

next generation sequencing and whole genome selection in aquaculture pdf

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Published: 02.05.2021

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Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers.

This study aimed at investigating growth-related, EST-derived microsatellite markers in Nile tilapia O. The link between alleles and genotypes of these makers was particularly examined, as well as the growth performances of the samples of offspring produced from the broodstocks of 5 different fishery stations in Thailand. A total of 25 families of offspring were reared to observe the growth performance for a period of 83 days. Then, the fins of the fish samples were employed to perform DNA analysis.

Current Advances in Functional Genomics in Aquaculture

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 of biological and economic importance. We discuss the technical advances, practical requirements, and commercial applications that have made genomic selection feasible in a range of aquaculture industries, with a particular focus on molluscs pearl oysters, Pinctada maxima and marine shrimp Litopenaeus vannamei and Penaeus monodon. The use of low-cost genome sequencing has enabled cost-effective genotyping on a large scale and is of particular value for species without a reference genome or access to commercial genotyping arrays. We highlight the pitfalls and offer the solutions to the genotyping by sequencing approach and the building of appropriate genetic resources to undertake genomic selection from first-hand experience.

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 marker-assisted selection in fisheries and aquaculture. High-throughput variant discovery has been made possible in multiple species by the recent advent of next-generation DNA sequencing technologies. New genotyping methods that are high-throughput, accurate, and inexpensive are urgently needed for gaining full access to the abundant genetic variation of organisms. This approach is known as genotyping-by-sequencing GBS , which holds great promise as a research tool because of its ability to allow simultaneous marker discovery and genotyping at low cost and with a simple molecular biology workflow for fisheries and aquaculture studies. This review summarizes the genotyping methodologies, recent advances in next-generation DNA sequencing technologies to achieve GBS, and the promises this approach holds as a genome-wide genotyping application in fisheries and aquaculture.

Advances of genotyping-by-sequencing in fisheries and aquaculture

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. The upcoming of HTS techniques has led to emergence of metagenomics, nutrigenomics, epigenetics and other omics technologies in aquaculture in the last decade. Metagenomics analyses have accelerated the speed at which emerging pathogens are being discovered, thereby contributing to the design of timely disease control strategies in aquaculture. Using metagenomics, it is easy to identify and monitor microbial communities found in different ecosystems. In vaccine production, genomic studies are being used to identify cross neutralizing antigens against variant strains of the same pathogens. In genetics and epigenetics, genomics traits have been identified that are beginning to gain commercial applications in aquaculture. Overall, herein, we have shown that functional genomics provide multifaceted applications ranging from monitoring microbial communities in aquatic environments to optimizing production systems in aquaculture.


Genomic Selection for Aquaculture: Principles and Procedures (Pages: ) · Summary · PDF · References · Request permissions.


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 of biological and economic importance. We discuss the technical advances, practical requirements, and commercial applications that have made genomic selection feasible in a range of aquaculture industries, with a particular focus on molluscs pearl oysters, Pinctada maxima and marine shrimp Litopenaeus vannamei and Penaeus monodon.

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