Uniqueness of Heilongjiang Mandarin Fish (Siniperca chuatsi): Identifying Growth-Related Functional Loci Through Whole-Genome Analysis Across Four Geographic Populations

To analyze growth trait differences and genetic characteristics of <i>Siniperca chuatsi</i> from distinct geographic populations, whole-genome resequencing was performed on 90 samples from Heilongjiang (HLJ), Hubei (HB), Hunan (HN), and Anhui (AH), and for the first time, population-unique growth-related loci were detected. Population structure analysis indicated that the four populations were genetically distinct (K = 4). A preliminary Genome-Wide Association Study (GWAS) revealed 26 significant growth-related SNPs linked to 158 potential functional genes, which were primarily enriched in Metabolic pathways, the NOD-like receptor signaling pathway, and Necroptosis, suggesting their possible roles in growth regulation. Non-tag SNP capture within functional genes yielded 24 known significant loci and 118 potentially linked loci. On this basis, one-way ANOVA ultimately identified 13 SNPs significantly associated with growth, and their advantageous genotypes were characterized. Notably, this study revealed, for the first time, that the HLJ population possesses six population-unique genotypes significantly linked to superior growth traits, which may represent population-restricted candidate markers associated with growth-related variation. The results of this study provide new candidate molecular markers and supporting data that may inform future breeding strategies pending further validation.