Whole-genome re-sequencing reveals genetic diversity, population structure, and selection signals of different geographic populations in Ctenopharyngodon idella

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Characterizing genomic variation is essential for understanding local adaptation and optimizing breeding programs. Whole-genome resequencing of 439 wild-caught and hatchery grass carp ( Ctenopharyngodon idella ) yielded 28.6 million high-quality SNPs, providing a comprehensive overview of genetic diversity, population structure, and putative selective sweeps across the Yangtze and Pearl River systems. Whole-genome analyses revealed relatively low overall genetic polymorphism in grass carp (average PIC < 0.25). Notably, wild-caught populations maintained higher genetic diversity, faster linkage disequilibrium (LD) decay, and fewer runs of homozygosity (ROH) compared to hatchery strains. Furthermore, distinct genetic divergence was observed between the Yangtze and Pearl River systems, reflecting long-term geographic isolation. In contrast, hatchery populations formed independent clusters driven by founder effects and genetic drift. Selective sweep analyses using multiple methods identified basin and region-specific adaptive signals. The Yangtze River population exhibits selective signals in genes related to lipid transport, temperature-sensing regulation, vitamin absorption, and osteoclast differentiation, suggesting potential adaptations to persistent winter cold and turbulent currents through mechanisms likely involving membrane fluidity maintenance and skeletal remodeling. Meanwhile, the Pearl River population shows selection on genes associated with lipid synthesis and storage, thyroid hormone signaling pathways, and immune responses, adapting to subtropical high temperatures and high pathogen loads. Further regional comparisons within river systems revealed fine-scale adaptive signals linked to vision, growth, immunity, and metabolism. Together, our results provide a genome-wide perspective on grass carp population differentiation and environmental adaptation, offering valuable insights for germplasm conservation and sustainable breeding programs.