Large variation in body weight poses a major challenge to the development and industrialization of formulated-feed aquaculture in Siniperca chuatsi. Breeding varieties that combine formulated-diet adaptation, rapid growth, and uniform body weight is therefore important for improving production efficiency. However, the genetic architecture of body weight and optimal genomic selection (GS) strategies remain poorly understood. Here, whole-genome resequencing was performed on 522 formulated-diet-adapted individuals. Genome-wide association study (GWAS) identified 21 significant loci, with candidate genes associated with lipid metabolism, endocrine regulation, and neuroendocrine signaling. Genomic prediction was evaluated using genome-wide single-nucleotide polymorphisms (SNPs) and GWAS-prioritized SNP panels with Bayesian and machine-learning models. Prediction accuracy increased with marker number and generally plateaued at approximately 30,000 SNPs. Random forest using GWAS-prioritized markers achieved the highest accuracy, improving prediction accuracy by 4.8% over genome-wide genomic best linear unbiased prediction (GBLUP) while using fewer markers. These findings demonstrate the potential of GWAS-informed marker prioritization to reduce marker requirements and improve GS efficiency for body weight in formulated-diet-adapted S. chuatsi.

Masu salmon (Oncorhynchus masou) is an ecologically and economically important cold-water salmonid in East Asia that exhibits diverse life-history forms. To compare population-level genomic variation and patterns of homozygosity among fish from different sources, we analyzed whole-genome resequencing data from 465 individuals representing one field-collected Tumen River population (TM) and two landlocked cultured populations from Chicheng (CC) and Yanji (YJ). After quality control, 6,220,980 high-quality SNPs were retained. Population-specific filtering identified 5,589,828, 3,545,209, and 4,975,751 polymorphic SNPs in CC, TM, and YJ, respectively; although SNP numbers differed, approximately 91% of variants in each population were located in intronic or intergenic regions. Principal component analysis, ADMIXTURE, and distance-based neighbor-joining analysis clearly distinguished the three populations, with CC and YJ showing the closest genetic relationship. Pairwise $F_{\mathrm{ST}}$ was lowest between CC and YJ and highest between TM and YJ. CC exhibited the highest linkage disequilibrium, whereas TM showed the fastest LD decay and the lowest nucleotide diversity and heterozygosity. Runs of homozygosity (ROH) burden was highest in TM, intermediate in CC, and lowest in YJ. TM had the highest number of ROHs, cumulative ROH length, and $F_{\mathrm{ROH}}$, and ROHs longer than 5 Mb were detected only in this population. CC had an intermediate ROH burden dominated by short segments, whereas YJ had the lowest ROH-based genomic inbreeding. The high and heterogeneous ROH burden in TM indicates elevated genome-wide homozygosity among the sampled fish but does not, by itself, demonstrate recent inbreeding throughout the population. Candidate ROH islands and their annotated genes showed limited overlap among populations. Candidate genes in TM were primarily associated with ion regulation, neural processes, and energy metabolism, whereas those in CC and YJ shared broad functional categories involving development, muscle organization, nutrient transport, and neural regulation but differed in most specific genes. These regions and genes should be regarded as exploratory, hypothesis-generating candidates rather than evidence of selection or causality. Overall, this study reveals distinct population genomic characteristics and ROH patterns among masu salmon populations of different origins and provides a basis for future germplasm conservation and genetic management.