Genome loci with selection signatures revealed in a domesticated mandarin fish population

Artificial selection enables the targeted alteration of allele frequencies within a population, leading to the consolidation and enhancement of beneficial variations and the stable genetic development of new varieties. Mandarin fish (Siniperca chuatsi) is a commercially important freshwater fish species in China. Through four generations of artificial selection targeting growth rate and survival rate as key traits, our team developed the new variety “Guangqing No. 1”. To identify the genomic loci subjected to selection during the artificial selection process, we conducted whole-genome resequencing on 150 individuals, comprising two wild populations of S. chuatsi (HN and AH) as the base populations and the selectively bred population “Guangqing No. 1”. A total of 3.90 million high-quality SNPs were identified across the three groups. Analysis of population structure and genetic diversity revealed that the individuals were divided into three groups, consistent with their geographical origins. Moreover, the selectively bred population was subjected to more intensive selection and exhibited reduced genetic diversity. Using Fst, Pi ratio, and XP-EHH, this study identified 71 significantly selected regions in S. chuatsi populations, along with 424 candidate genes potentially under selection. Among the candidate genes identified through selection loci analysis, some are closely associated with key economic traits such as growth, immunity, reproduction, and feeding (e.g., pfkp, igf1, Ig, il4i1, npy2r, omp, lrat, c2orf71, sept12). In this study, we identified valuable candidate genes and selection markers for the artificial selection of S. chuatsi, offering valuable insights and guidance for future aquatic breeding efforts.