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.

The European perch (Perca fluviatilis) is highly susceptible to heat stress, limiting its sustainable aquaculture. While single-organ thermal responses are partially understood, the systemic, multi-organ cooperative survival mechanisms under acute heat stress remain poorly characterized. To elucidate the underlying tolerance mechanisms and provide genetic markers for breeding, this study investigated the multi-organ responses of European perch (n = 90; body length: 13.15 ± 1.75 cm; body weight: 30.54 ± 7.17 g) transferred from 24 °C to an acute heat stress challenge (31 °C) at an increasing rate of 2 °C/h, and the histopathological changes (liver and gill), hepatic biochemical biomarkers (CAT, SOD, GSH-Px, GST, LDH, and MDA), and transcriptomic changes (liver and kidney) were evaluated over a 24 h period. Heat stress induced progressive structural damage, including gill lamellar edema and hepatocyte necrosis, accompanied by significant hepatic oxidative stress and lipid peroxidation. RNA-seq transcriptome profiling uncovered distinct sets of genes with significant expression changes, comprising 1343 DEGs in liver tissue and 722 DEGs in kidney samples. Both organs shared a systemic endoplasmic reticulum stress response but exhibited highly divergent survival strategies. The liver underwent severe metabolic reprogramming towards anaerobic glycolysis and gluconeogenesis, coupled with vesicle-mediated membrane repair attempts and apoptosis. Conversely, the kidney adopted a strict “energy triage” strategy, suppressing highly energy-consuming immune and osmoregulatory functions while actively silencing pro-apoptotic signals. These findings highlight organ-specific adaptations and identify potential metabolic markers for the future breeding of new heat-tolerant varieties.

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.

Grass carp is an important aquaculture fish species in China that is affected by severe diseases, especially haemorrhagic disease caused by grass carp reovirus (GCRV). However, the mechanisms of GCRV invasion and infection remain to be elucidated. In the present study, Ctenopharyngodon idellus kidney (CIK) cells were infected with GCRV, harvested at 0, 8, 24, and 72 h post infection, respectively, and then subjected to transcriptomics sequencing. Each sample yielded more than 6 Gb of clean data and 40 million clean reads. To better understand GCRV infection, the process was divided into three phases: the early (0–8 h post infection), middle (8–24 h post infection), and late (24–72 h) stages of infection. A total of 76 (35 up-regulated, 41 down-regulated), 553 (463 up-regulated, 90 down-regulated), and 284 (150 up-regulated, 134 down-regulated) differently expressed genes (DEGs) were identified during the early, middle, and late stages of infection, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that DEGs were mainly involved in carbohydrate biosynthesis, transport, and endocytosis in the early stage, phagocytosis and lysosome pathways were mainly enriched in the middle stage, and programmed cell death, apoptosis, and inflammation were largely associated with the late stage. These results suggest GCRV infection is a gradual process involving adsorption on the cell surface, followed by endocytosis into cells, transport by lysosomes, and eventually resulted in cell necrosis and/or apoptosis. Our findings provide insight into the mechanisms of grass carp reovirus infection.

Integrin β-1 (ITGB1) is a transmembrane protein belonging to the integrin family and it plays an important role in viral entry. In this study, the itgb1b gene of the rare minnow, Gobiocypris rarus, was cloned and analyzed. To investigate the possible role of itgb1b on grass carp reovirus (GCRV) infection, we generated an ITGB1b-deficient rare minnow (ITGB1b^−/−) using the CRISPR/Cas9 system. Following stimulation with GCRV, the survival time of the -ITGB1b^−/− rare minnows was extended in comparison to the wild-type minnows. Moreover, the relative copy number of GCRV and the level of clathrin-mediated endocytosis-associated and apoptosis-related gene expression in the ITGB1b^−/− rare minnows was significantly lower than that of the wild-type minnows. These results suggested that the absence of itgb1b reduced viral entry efficiency and the expression of apoptosis-related genes. Moreover, the data suggested that itgb1b played an important role in mediating the entry of viruses into the cells via clathrin. Therefore, these findings provide novel insight into the function of itgb1b in the process of GCRV infection.