Genome resequencing of the orange-spotted grouper (Epinephelus coioides) for a genome-wide association study on ammonia tolerance

The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome

“… † Closest candidate gene to lowest p-value variant, but not well supported. * Genes related to ammonia tolerance [ 102 ]. …”

“…Three candidate genes: complement C3, carboxypeptidase A6, and plexin A2 were previously identified as candidate genes for ammonia tolerance in orange-spotted grouper ( Epinephelus coioides ) [ 102 ]. All three of these candidate genes were established in previous studies identifying outlier loci between kokanee and sockeye populations (plexin A2-like and complement C3 outlier loci were within 200 kbp of the current associations and the carboxypeptidase A6 outlier locus was within 1 Mbp, RAD tag: 14532 [ 17 ]).…”

“…� Immunoglobulin heavy chain variable gene cluster.�� Similar to immunoglobulin gene. † Closest candidate gene to lowest p-value variant, but not well supported.https://doi.org/10.1371/journal.pone.0240935.† Closest candidate gene to lowest p-value variant, but not well supported.� Genes related to ammonia tolerance[102]. https://doi.org/10.1371/journal.pone.0240935.t002…”

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

“…These research were conducted to study the population structure and candidate genes related to economically important traits for selective breeding programs such as sex determination, growth, immunity, reproduction, shell shape and morphological deformities. In addition, SNPs associated with stressors tolerance such as ammonia in orange-spotted grouper, Epinephelus coioides (Xu et al, 2019b) and heat stress in Pacific abalone were identified using whole genome resequencing and were implemented in GWAS for Marker Assisted Selective (MAS) breeding programs. In addition, genome of pikeperch was also used to generate ultra-high density linkage map for quantitative trait locus (QTL) analysis (de Los Ríos-Pérez et al, 2020).…”

“…Considering that disease is one of the major challenges and bottlenecks in aquaculture, QTL analysis on disease resistance was conducted through pathogenic challenge tests towards many species (Gilbey et al, 2006;Houston et al, 2008). QTL for resistance to particular diseases have been identified and mapped, such as MSX and Dermo in the eastern oyster, Crassostrea virginica (Yu and Guo, 2006), Bonamiosis in European flat oyster, Ostrea edulis (Lallias et al, 2009), salmonid alphavirus in Atlantic salmon (Gonen et al, 2015), infectious pancreatic necrosis (IPN) in Atlantic salmon (Moen et al, 2009), columnaris disease and ESC in channel catfish (Geng et al, 2015;Zhou et al, 2017), whirling disease and bacterial cold water disease in rainbow trout (Baerwald et al, 2011;Palti et al, 2015), haemorrhagic septicaemia in turbot (Rodríguez-Ramilo et al, 2011), Vibrio anguillarum in Japanese flounder (Wang et al, 2014a), fish pasteurellosis in gilthead sea bream (Massault et al, 2011) and viral nervous necrosis disease in Asian seabass (Liu et al, 2016b) and V. anguillarum-resistant in turbot (Zhang et al, 2019b).…”