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

The evolution of body shape in vertebrates is typically achieved through changes in the number of vertebrae or vertebral fusion, and different taxonomic groups often exhibit distinct patterns of divergent evolution. In this study, we compared the body shape differences between the Hebao red carp (HB, Cyprinus carpio Wuyuanensis) and the Yellow River carp (YR, Cyprinus carpio haematopterus). Although both possess the same number of vertebrae (35), the altered body shape of the HB arises from skeletal developmental abnormalities, characterized by marked vertebral shortening and fusion. To elucidate the genetic basis underlying the distinctive morphology in the HB, we conducted GWAS and population genetic analyses using genotypic data from two generations (F1 and F2) of hybrid offspring. There were 231 significant selective sweep regions identified on chromosomes A06, A08, A16, B05 and B06. Notably, the 15.99 - 16.39 Mb region on chromosome A08 showed a strong association with body shape traits. Further transcriptomic analysis revealed a significant haplotype-dependent expression gradient of the rflna within this region, suggesting that rflna may play a critical role in body shape regulation. Targeted gene knockout of rfln in the cyprinid model organism zebrafish (Danio rerio) reproduced skeletal abnormalities, including rounded abdomen, vertebral shortening, spinal kyphosis and vertebral fusion. Together, this study elucidates the morphological and molecular mechanisms underlying the unique body shape of the HB and provides new insights into the regulation of skeletal development and body shape variation in fish.