Application of second-generation sequencing (SGS) and third generation sequencing (TGS) in aquaculture breeding program

High-throughput sequencing technologies have expanded gene-based to genome-wide research in aquaculture species. Several techniques adopting the Second Generation Sequencing (SGS), Third Generation Sequencing (TGS) platforms and/or hybrid genome assemblies have been widely employed in various aquacu...

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Bibliographic Details
Published in:Aquaculture
Main Authors: Wong, Li Lian, Razali, Siti Aisyah, Deris, Zulaikha Mat, Danish-Daniel, Muhd, Tan, Min Pau, Nor, Siti Azizah Mohd, Ma, Hongyu, Min, Wang, Liang Yantao, Liang Yantao, Asaduzzaman, Md, Sung, Yeong Yik, Liu, Zhanjiang, Sorgeloos, Patrick, Van de Peer, Yves, Afiqah-Aleng, Nor
Format: Article in Journal/Newspaper
Language:English
Published: 2022
Subjects:
Agriculture and Food Sciences
Selective breeding
Genome sequencing
Omics technologies
Population genomics
Next-generation sequencing (NGS)
QUANTITATIVE-TRAIT LOCI
INFECTIOUS PANCREATIC NECROSIS
SINGLE-NUCLEOTIDE POLYMORPHISMS
FLOUNDER PARALICHTHYS-OLIVACEUS
TURBOT SCOPHTHALMUS-MAXIMUS
BULKED-SEGREGANT ANALYSIS
CHARR SALVELINUS-ALPINUS
GENOME-WIDE ASSOCIATION
GROWTH-RELATED TRAITS
ATLANTIC SALMON
Atlantic salmon
Salvelinus alpinus
Scophthalmus maximus
Turbot
Online Access:https://biblio.ugent.be/publication/8738613
http://hdl.handle.net/1854/LU-8738613
https://doi.org/10.1016/j.aquaculture.2021.737633
https://biblio.ugent.be/publication/8738613/file/8738615
Description
Summary:High-throughput sequencing technologies have expanded gene-based to genome-wide research in aquaculture species. Several techniques adopting the Second Generation Sequencing (SGS), Third Generation Sequencing (TGS) platforms and/or hybrid genome assemblies have been widely employed in various aquaculture research areas including general breeding program, disease and health management, sex determination and reproduction biology, environmental stress response, nutrigenomics, morphological appearance, and meat quality/texture. Notably, the application of these novel sequencing technologies has generated Quantitative Trait Loci (QTL) and novel genes associated with commercially important production traits, which are useful for essential processes in selective breeding programs such as population genomics evaluation, Marker-Assisted Selection (MAS) and Genomic Selection (GS). These genomic approaches are also used as genetic traceability tools for seafood fraud assessment and tracking of farm escapees for wild stock conservation. Genomic data generated by these platforms could aid in establishing proper breeding strategies for more profitable and sustainable aquaculture.

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