Elizabethkingia miricola (E. miricola) is a significant pathogen that causes the crooked head disease in black spotted frogs. This disease has plagued numerous frog farms in China and has resulted in substantial losses to the frog farming industry. Nonetheless, the exact mechanism that causes the disease in frogs remains unknown. In this study, transcriptomic and microbiomic analyses were conducted to analyze frog samples infected with E. miricola to reveal the infection mechanism of the pathogen. Liver transcriptomic analysis indicated that the livers of infected frogs had 1469 differentially expressed genes when compared with an uninfected group. These DEGs are mainly involved in immunity and metabolism, including neutrophil extracellular trap formation, the NOD-like receptor signaling pathway, leukocyte transendothelial migration, chemokine signaling pathway, Fc gamma R-mediated phagocytosis, and “metabolism”-related pathways such as the pentose phosphate pathway, carbon metabolism, glycerophospholipid metabolism, and glycerolipid metabolism. Similarly, 4737 DEGs were found in the kidney of infected frogs. These DEGs are mainly involved in immunity, including neutrophil extracellular trap formation, the NOD-like receptor signaling pathway, B cell receptor signaling pathway, C-type lectin receptor signaling pathway, complement and coagulation cascade, and Toll-like receptor signaling pathway. Ten immune-associated DEGs were screened in liver and kidney DEGs, respectively. And it was hypothesized that E. miricola infection could influence the host immune response. Microbiome analysis results showed that some opportunistic pathogens such as Citrobacter, Shigella, and Providencia were significantly elevated (p < 0.05) in infected frogs. Additionally, functional prediction confirmed that most of the microbiota in infected frogs were linked to metabolism-related KEGG pathways. In this study, the screened genes linked to immunity showed an association with the gut microbiome. The majority of these genes were found to be linked with the abundance of opportunistic pathogens. The results showed that E. miricola infection led to the downregulation of immune and metabolic-related genes, which led to the inhibition of immune function and metabolic disorder, and then increased the abundance of opportunistic pathogens in the gut microbiota. The findings of this study offer a preliminary foundation for comprehending the pathogenic processes of E. miricola infection in black spotted frogs.

Growth traits are economically important in bighead carp (Hypophthalmichthys nobilis), but their genetic basis remains unclear. We conducted whole-genome association analyses in 298 fish using 2,891,492 single-nucleotide polymorphisms and linear mixed models controlling for population structure and genomic relatedness. Five variants reached the per-trait genome-wide threshold. The strongest body-weight association occurred at 13:40990738:C:T on linkage group 13 (LG13) (p = 5.09 × 10⁻¹⁰; effect = 5.50 ± 0.87 g). Two LG04 variants were associated with body weight, while two adjacent LG14 variants were associated with head height (lead p = 8.34 × 10⁻⁹; effect = 2.59 ± 0.44 mm). However, associations with head dimensions were substantially attenuated after body-length adjustment, indicating that head-specific genetic effects were not established. Regional linkage disequilibrium and conditional analyses distinguished compact LG13 and LG14 signals from a complex LG04 pattern, and complementary sensitivity analyses supported their robustness. Sanger sequencing confirmed all 118 tested LG13 genotypes. The LG13 body-weight association was reproduced in an independent population of 268 fish and remained significant after body-length adjustment. Genotype-stratified reverse-transcription quantitative polymerase chain reaction assays detected higher expression of mchr2-like gene13.20, syngr1-like gene32.45, and cacng2-like gene32.46 in effect-allele carriers after multiple-test correction. These findings provide independent support for the LG13 body-weight association, while LG14 and LG04 remain discovery-stage candidate regions requiring independent replication and functional investigation before potential breeding applications can be considered.

Reliable marker–trait associations can support genetic improvement of growth and body conformation in bighead carp (Hypophthalmichthys nobilis). We investigated eight traits in 569 fish assigned to 34 inferred consensus full-sib groups. Genotypes at 89,684 reference-consistent SNP positions were recalled from sequencing alignments and filtered by read depth, genotype quality, and heterozygote-allele balance. Common-mask validation of 274,566 genotype cells supported a 60% pre-imputation call-rate threshold, achieving 94.17% overall, 90.26% non-reference, and 89.04% heterozygote concordance, with hard-dosage r² = 0.859. The final imputed matrix contained 32,304 SNPs; 9086 LD-pruned SNPs were used to estimate population structure and genomic covariance. Primary mixed-model scans used recalled genotype inputs before Beagle imputation and identified 18 suggestive trait–marker combinations. Candidate analyses using actual observed genotypes supported 17 combinations at within-group permutation FDR < 0.05, representing 16 markers. Grouping, model, and group-omission sensitivity analyses characterized their robustness. Prioritized regions contained developmentally relevant genes, including sulf1, dmrt2, cyp24a1, chst12, efcab7, and anapc7. These family-supported candidates provide targets for replication and functional investigation and may inform genetic improvement and new-variety development in bighead carp.