Vertebral morphological changes driven by rflna lead to body shape differentiation in carp

Body shape evolution in vertebrates frequently involves modifications in vertebral number or patterns of vertebral fusion, with distinct lineages displaying divergent trajectories. This study investigated the morphological and genetic basis of body shape variation between Hebao red carp (HB, Cyprinus carpio wuyuanensis) and Yellow River carp (YR, Cyprinus carpio haematopterus). Although both subspecies share an identical vertebral count (35), the compressed morphology of HB was attributable to skeletal anomalies, including vertebral shortening and fusion. Genome-wide association and population genetic analyses were performed on F1 and F2 hybrid cohorts to identify loci associated with this phenotype. A total of 231 selective sweep regions were detected across chromosomes A06, A08, A16, B05, and B06, with a prominent locus on chromosome A08 (15.99–16.39 Mb) strongly correlated with body shape traits. Transcriptomic analysis revealed haplotype-dependent expression of rflna within this interval, implicating rflna in axial skeletal patterning. Functional validation using CRISPR/Cas9-mediated knockout of rfln in zebrafish (Danio rerio) induced vertebral malformations, including axial shortening, kyphosis, fusion, and a rounded abdominal profile. These results delineate the morphological and molecular framework governing axial remodeling in HB and highlight a conserved regulatory role for rflna in teleost skeletal development.