Origin-associated transcriptomic signatures across the reproductive axis of Solea senegalensis

Understanding how captive conditions impair reproduction remains a major challenge in vertebrate biology and aquaculture. In Senegalese sole ( Solea senegalensis ), this problem is especially evident in captive-bred males, which are widely reported to show impaired mating behaviour and reduced production of functional sperm. To characterize gene expression variation in tissues involved in reproductive regulation, we performed RNA-seq profiling across the hypothalamic-pituitary-gonadal (HPG) axis in adult wild-bred and captive-bred males and females at the end of the spawning season. Tissue identity was the main driver of transcriptional variation, with sex-biased differences concentrated in the gonad and origin-associated differences more pronounced in central neuroendocrine tissues, particularly the pituitary. In males, integrated analyses identified candidate networks enriched in captive-bred individuals and containing genes related to neuroendocrine signalling, steroid metabolism and reproductive regulation. These results provide a transcriptomic framework for understanding how origin-associated differences across the HPG axis may be relevant to the reproductive phenotype previously described in captive-bred Senegalese sole.