Genome-wide Association Study Reveals Novel Growth-related SNPs and Candidate Genes in Grass Carp (Ctenopharyngodon idella) Adapted to Hyper-salinity Stress.

Given the increasing saturation of freshwater aquaculture space, saline-alkali aquaculture has become a critical direction to expand fishery space. Grass carp (Ctenopharyngodon idellus) is an ideal candidate for saline-alkali aquaculture because of its strong osmoregulation ability. However, the mechanism and genetic basis of salt tolerance are unclear, which restricts the breeding efficiency of salt-tolerant and fast-growing strains. In the present study, body weight was used as a key indicator to measure growth traits, and 98 individuals of maximal and minimal grass carp under hypersaline stress were collected for the first time for a genome-wide association study. The results showed that 14 SNPs were significantly correlated with the body weight of grass carp under high-salinity stress, and intron mutations were the main type of variation. The most significant SNP is upstream of the UBL5 gene. Notably, three SNPs were located in the intron region of the GNG7 gene, which might regulate grass carp growth by regulating cell proliferation and differentiation, transmembrane signal transduction, and immune processes. The results of genotyping verification of UBL5, GNG7 and SLC16A2 further showed that there were significant differences between extremely large and extremely small individuals. In addition, the candidate genes were significantly involved in growth regulation, signal transduction and osmotic regulation-related pathways. In conclusion, this work will help to elucidate the genetic basis associated with fast-growth traits under a hyperosmotic environment, and the identified SNPs and candidate genes can be used for genomic selection breeding of salt-tolerant fast-growing strains in grass carp.