Genomic Insights into Genetic Diversity of Coilia nasus Across Wild Ecotypes and Farmed Populations in China

Coilia nasus is a migratory fish in China, inhabiting oceanic waters and spawning in rivers and lakes, and exhibiting various ecotypes. Following a technological breakthrough in artificial breeding of this species from wild migratory form, a stock enhancement and release program was initiated to replenish its natural resources. However, comprehensive genomic comparisons among the migratory form and farmed populations remain limited. Here, we employed 2b-RAD sequencing to investigate genetic diversity of wild migratory form across marine, estuarine, migratory-route populations in comparison with the farmed populations. In total, 835 high-quality single nucleotide polymorphisms (SNPs) were detected, with the highest proportion (28.1%) located in exon regions. Significant genetic differences (P < 0.01) were observed between the farmed and wild populations, corresponding to a moderate level of differentiation based on pairwise Fst values (0.082–0.091). Population structure clearly separated the two groups: the farmed populations showed distinct genetic components, while the wild populations displayed only minor compositional differences. Phylogenetic analyses further distinguished the farmed from wild populations. Functional enrichment analyses revealed that elevated SNP frequencies in the farmed population were linked to genes related to growth, metabolism, and intestinal immunity, likely reflecting adaptation to nutrient-rich conditions and growth demands under captive environments. Additionally, 12 SNPs were validated for distinguishing farmed from wild individuals by PCR combined with sequencing. These findings provide genomic insights into the artificial breeding effects on C. nasus and offer practical tools for stock management and germplasm conservation of this ecologically important fish.