Genome-wide association study reveals IP6K1 as a critical regulator of salinity tolerance in largemouth bass (Micropterus salmoides)

Given the increasing saturation of freshwater aquaculture space, saline-alkali aquaculture has become a critical strategy to expand fishery space. Largemouth bass ( Micropterus salmoides ) is an ideal candidate for saline-alkali aquaculture due to its strong osmoregulation ability. However, the genetic and mechanistic basis of salt tolerance remains unclear, constraining the breeding efficiency of salt-tolerant strains. In the present study, 1600 fish from 20 families were exposed to a high-salinity challenge (14 ppt), and 242 individuals with extreme survival times were selected for a genome-wide association study. The survival rate of the salinity-tolerant group was more than seven times higher than that of the salinity-sensitive group, indicating considerable phenotypic plasticity in high-salinity tolerance. Eight SNPs were significantly associated with salinity tolerance, and 66 candidate genes were identified within ±100 kb of these SNPs. Functional enrichment analysis showed that these genes were significantly involved in signal transduction, transport and catabolism, and endocrine system-related pathways. Furthermore, the significant association of SNP mutations in the IP6K1 gene with salinity tolerance has been confirmed by Sanger sequencing, which individuals homozygous for the G/G genotype lived over 2.5 times longer under high salinity than those with disadvantageous genotypes. Moreover, differential expression of IP6K1 was also observed between sensitive and tolerant groups. This study will contribute to elucidating the genetic basis associated with salinity-tolerant traits under hyperosmotic conditions, and the identified SNPs and candidate genes can be utilized for genomic selection breeding of salinity-tolerant strains in largemouth bass. • The first GWAS investigation for salinity tolerance in largemouth bass. • Eight SNPs significantly associated with salinity tolerance were identified. • G/G genotype of IP6K1 exhibited significant associations with salinity tolerance. • The expression of IP6K1 significantly differed between sensitive and tolerant groups. • IP6K1 might be a key regulator of salinity tolerance under high-salinity stress.