The presence of intermuscular bones severely affects the edibility and value-added processing of crucian carp (
Carassius auratus), becoming a constraint to the high-quality development of its industry. Our previous study identified
bmp6 as the key osteogenic regulator and successfully developed a new crucian carp strain lacking intermuscular bones (WUCI) using CRISPR/Cas9 technology. To accelerate its industrialization, we comprehensively assessed WUCI’s growth performance, hematological parameters, antioxidant capacity, innate immunity, and disease resistance. The results demonstrated that the WUCI exhibited significant growth performance compared to the wild-type crucian carp (WT), with significantly higher weight gain (WG) and specific growth rate (SGR) (
p < 0.05) from one month to four months of age. The α-amylase (α-AL) activity of the liver and intestines of WUCI was significantly higher than that of WT. WUCI also displayed enhanced intestinal antioxidant capacity, with superoxide dismutase (SOD) and catalase (CAT) activities significantly higher than those in WT (
p < 0.05). The malondialdehyde (MDA) content in the spleen of WUCI was significantly lower than that of WT (
p < 0.05); no differences were observed in the liver and intestines (
p > 0.05). Additionally, hepatic acid phosphatase (ACP) activity in WUCI was significantly higher than that in WT (
p < 0.05). In contrast, splenic ACP and intestinal alkaline phosphatase (ALP) activities were significantly lower than those in WT (
p < 0.05). Notably, the iron concentration in the serum was significantly higher in WUCI than in the WT (
p < 0.05). Meanwhile, WUCI exhibited significantly lower a expression of
hepcidin,
TF, and
TFR1 mRNA in the liver compared to WT (
p < 0.05), while
FPN mRNA expression was significantly higher (
p < 0.05). Routine blood tests revealed significantly lower WBC in WUCI compared to that of WT (
p < 0.05). Following an
Aeromonas hydrophila challenge, WT demonstrated a rapid transcriptional induction of pro-inflammatory cytokines (
TNF-α,
IL-1β,
IL-6) and immunoregulatory mediators (
IL-10,
TGF-β), with mRNA levels reaching maximal expression at 24 h post-infection (hpi) followed by progressive attenuation. In contrast, WUCI exhibited a delayed immune activation profile characterized by the peak expression of
TNF-α,
IL-1β,
IL-6, and
IL-10 transcripts after 72 hpi, with the maximum transcript abundance remaining lower than corresponding peak values observed in WT at 24 hpi. Finally, we observed that the mortality rate of WUCI was slightly higher post
A. hydrophila infection when compared to WT, but was not significant (
p > 0.05). In conclusion, this study provides a comprehensive evaluation of WUCI, revealing its distinct growth advantages, physiological adaptations, and immune function, presenting its potential for aquaculture breeding applications.
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