Identification of Growth-Related SNPs and Genes Through Genome-Wide Association Studies in Pseudobagrus ussuriensis

Pseudobagrus ussuriensis is a widely cultured bagrid fish known for its delicious tastes and high nutrition values in China. As growth performances of this fish significantly declined in recent years, the breeding of new germplasm with excellent growth traits is urgently needed. In the present study, the genome-wide association study (GWAS) method was used to identify genetic sites significantly associated with five growth traits in a population with 183 individuals. A total of 2,408,557 high-quality SNPs were identified across the 26 chromosomes of the genome. Among these, 31 SNPs were found to be significantly associated with growth traits, including 12 SNPs on Chr08, Chr17 and Chr21 associated with body length, 9 SNPs from Chr07, Chr08, Chr16, Chr22 and Chr25 associated with head length, 8 SNPs on Chr03 and Chr08 associated with body weight, and 4 SNPs from Chr03, Chr04, Chr08 and Chr15 associated with condition factor. One SNP, Chr08:20667021, located at the upstream region of the pld1 gene, was significantly associated with body length, head length and body weight, and it was also validated using Sanger sequencing in 100 individuals. Within a 50 kb range upstream and downstream of the 31 significant SNPs, 71 candidate genes were identified, with 28 of them being considered as more probable growth-associated candidate genes. The results of this study showed that the majority of growth related SNPs and candidate genes clustered on Chr08, which may be dominant in the process of growth regulation. These findings provide valuable insights into the genetic mechanisms of growth and useful tools for marker-assisted selection breeding in P. ussuriensis.