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

• 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

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.