The inland saline-alkali water area in China is large and underutilized. Selecting and breeding new varieties suitable for saline-alkali water aquaculture for promotion is a fundamental and effective way to solve this problem. Grass carp ( Ctenopharyngodon idella ) demonstrate measurable salt tolerance and have the potential for cultivation in saline waters. In this study, whole-genome resequencing and genome-wide association study (GWAS) were conducted to identify single-nucleotide polymorphisms (SNPs) and genes associated with salt tolerance traits in grass carp. In this study, survival time was used as the indicator to evaluate salt tolerance. From 948 grass carp (mean body weight 14.59 ± 2.07 g) exposed to 12 ppt salinity stress, the 50 shortest- and 50 longest-surviving fish were selected for resequencing and salt tolerance trait association analysis. The results showed that after variant detection and quality control, 4754,813 high-quality SNPs were identified. Using the Fixed and random model Circulating Probability Unified (FarmCPU) method, the significance threshold for GWAS was established at 1.00E-06. The GWAS analysis of salt tolerance traits identified 32 significantly associated SNPs, located on 11 chromosomes. The top SNP (Chr20:11444313; p = 2.12E-08) is an intronic variant within traf3ip2a . Annotation of the ± 6.34 kb regions flanking significant SNPs revealed 22 candidate genes, such as traf3ip2a , trpc3 , and loc127502916 , which are involved in calcium signaling, synaptic transmission, motor coordination, immune cell migration and infiltration, hormone regulation, and other processes. Exploration of potential genes and regions associated with salt tolerance in grass carp provides a theoretical foundation for molecular marker-assisted breeding of this trait, supporting early-stage breeding programs. • First GWAS of salt tolerance performance in grass carp. • 32 SNPs were associated with salt tolerance performance, mainly in calcium signaling, synaptic transmission, immune cell migration. • 22 significant genes were annotated, 3 of which were further validated for expression under salt stress.
Zhu et al. (Thu,) studied this question.