Genome-Wide Association Study Reveals Growth-Related SNPs and Candidate Genes in Largemouth Bass (Micropterus salmoides) Adapted to Hypertonic Environments

Sustainable development of the largemouth bass industry is hindered by limited freshwater resources. Consequently, the expansion of farming space by brackish and saline water aquaculture has become imperative. Largemouth bass is an economically important freshwater fish species. However, there is presently a lack of germplasm resources with the capacity to adapt to hypertonic environments and maintain rapid growth. A genome-wide association study is a technique used for the detection of genetic variants associated with specific phenotypic traits. In this study, we firstly applied this technique to explore the potential single-nucleotide polymorphism (SNP) locus and candidate genes associated with rapid growth and adaptation to the hypertonic environment of largemouth bass. A total of 10 potential growth-related SNPs were obtained on chromosome 16, and SNP16:4120214 was a significant SNP peak. Based on these SNPs, 23 candidate genes were annotated in the genome, including <i>Nkcc1</i>, <i>Mapkap1</i>, <i>Hmgcs1</i>, <i>Slc27a6,</i> and <i>Shroom3</i>. <i>Shroom3</i> expression was significantly higher in individuals enriched for the most growth-advantageous genotypes. <i>Shroom3</i> upregulation is beneficial for fish growth in hyperosmotic environments. This study provides insight into the genetic basis of rapid growth in hypertonic environments and foundational information for the future breeding of salt-tolerant largemouth bass.