Grass carp (Ctenopharyngodon idella), a globally important aquaculture species, exhibits protein-dependent growth plasticity, requiring genetic improvement for sustainable production. This study integrates genome-wide association analysis (GWAS) and genomic selection (GS) to unravel the genetic architecture of four growth traits, body weight, body length, body height, and body depth, in grass carp fed with diets of varying protein levels (20%, 25%, 30%, and 35%). Using a 21K liquid SNP array, we identified 62,736 high-quality SNPs across 24 chromosomes, with 90 SNPs significantly associated with growth traits. Notably, three SNPs (SLG14_24417024, SLG14_24417039, SLG24_30276273) exhibited pleiotropic effects on multiple traits. Functional annotation of 276 candidate genes near significant SNPs revealed enrichment in keratinocyte development, septin cytoskeleton organization, and heat acclimation pathways. Genomic prediction achieved accuracies up to 0.79 for body weight traits using 1533 optimal markers. This study provides the first comprehensive SNP resource for grass carp growth traits with different dietary treatments, bridging GWAS and genomic prediction to accelerate marker-assisted selection. Our findings not only advance genetic breeding strategies but also inform protein diet optimization, minimizing economic and environmental costs in aquaculture.

The grass carp (Ctenopharyngodon idella) is highly susceptible to infections caused by Aeromonas species, particularly A. hydrophila and A. veronii. However, the immunological mechanisms underlying co-infection by these pathogens remain largely uncharted. This study investigated the pathogenesis and host immune response in grass carp following concurrent infection with A. hydrophila and A. veronii. Mortality was observed as early as 24 h post-infection, with cumulative mortality reaching 68%. Quantitative analysis demonstrated significantly elevated bacterial loads in hepatic tissue at 3 days post-infection (dpi). Histopathological evaluation revealed severe hepatic lesions characterized by cellular necrosis, cytoplasmic vacuolization, and hemorrhagic manifestations. Comparative transcriptomic analysis of hepatic tissues between co-infected and control specimens identified 868 and 411 differentially expressed genes (DEGs) at 1 and 5 dpi, respectively. Gene ontology and KEGG pathway analyses revealed significant enrichment of immune-related genes primarily associated with Toll-like receptor signaling and TNF signaling cascades. Notably, metabolic pathways showed substantial suppression while immune responses were significantly activated after infected. These findings provide novel insights into the host–pathogen interactions during Aeromonas co-infection in grass carp, which may facilitate the development of effective prevention and control strategies.

Grass carp (Ctenopharyngodon idella), a key species in freshwater aquaculture, is particularly vulnerable to opportunistic pathogens, including Aeromonas hydrophila and Aeromonas veronii. While the pathogenic mechanisms of individual infections have been extensively characterized, the host immune responses during co-infection remain poorly understood. This research explored the renal pathological alterations and transcriptomic shifts in grass carp subjected to simultaneous infection by A. hydrophila and A. veronii. Mortality occurred as early as 24 h post-challenge, ultimately reaching a cumulative death rate of 65%. Quantitative analysis of renal bacterial burden revealed a marked increase in colonization at 3 days post-infection (dpi). The histopathological assessment showed progressive kidney damage, including tubular collapse, epithelial necrosis, interstitial edema, and widespread epithelial desquamation, with the most severe lesions observed at 5 dpi and partial signs of recovery by 7 dpi. A total of 1106 and 472 genes were found to be differentially expressed at 1 and 5 dpi, respectively, based on transcriptome profiling. The functional enrichment analysis indicated that the differentially expressed genes (DEGs) were mainly involved in the complement and coagulation cascade pathways. Notably, the immune-related genes exhibited a biphasic trend, with predominant downregulation at 1 dpi followed by marked upregulation by 5 dpi, indicating dynamic changes in immune modulation during co-infection. These results provide new insights into host responses during dual bacterial infections in fish and may inform disease prevention strategies in aquaculture.