Genetic Basis and Identification of Candidate Genes for Alkalinity Tolerance Trait in Spotted Sea Bass (Lateolabrax maculatus) by Genome-Wide Association Study (GWAS)

Given the challenges of overcrowded coastal aquaculture spaces and insufficient production, utilizing saline-alkaline water areas represents a vital strategy to alleviate these bottlenecks. Spotted sea bass (Lateolabrax maculatus), with its formidable osmoregulatory capabilities, is an ideal candidate to develop a saline-alkaline tolerant strain. In our study, genotypic and phenotypic data from 287 L. maculatus individuals exposed to carbonate alkaline conditions were collected, and a genome-wide association study (GWAS) conducted to elucidate genetic basis related to carbonate alkalinity tolerance trait. Results showed that 14 SNPs and 8 InDels were markedly related to carbonate alkalinity tolerance trait, and 404 candidate genes were pinpointed within a ± 300-kb region surrounding these variants. Notably, the most significant SNP (SNP_05_17240108), along with two adjacent SNPs (SNP_05_17240102 and SNP_05_17240340) and two InDels (InDel_05_17240228 and InDel_05_17240231), was situated in the intron region of trio gene that could play vital roles in cell remodeling, and cell junction and activity of aquaporins to deal with carbonate alkalinity stress. Furthermore, candidate genes were significantly involved in pathways associated with carbohydrate metabolism, cell remodeling, ion transport, and RNA degradation, which were consistent with RNA-Seq analysis results of gills and kidneys in response to alkalinity stress. Our study will contribute to elucidate the genetic basis of alkalinity tolerance and the identified SNPs and InDels could be used for marker-assisted selection (MAS) and genomic selection (GS) for alkalinity tolerance trait in the breeding programs of spotted sea bass.