Retention of embryonic positional identity signatures in the adult sheep tail: evidence from HOXB13 spatial RNA expression gradients

Abstract Body axis patterning in vertebrates is controlled by HOX genes during embryogenesis, with their expression gradients defining spatial identity along the anterior–posterior axis. While the developmental roles of HOX genes in axial patterning are well established, it remains unclear to what extent embryonically defined anterior–posterior HOX expression patterns are retained as transcriptional signatures in adult tissues. Tail length in sheep provides a model for studying the phenotypic effects of HOX gene variants. We used Improved Jezersko–Solčava sheep, which segregate for both tail length and HOXB13 promoter variants, to examine genotype–phenotype associations. The HOXB13 genotype was the main determinant of adult tail length, acting primarily by modulating caudal vertebral number. RNA‑seq and qPCR analyses revealed a clear anterior–posterior HOXB13 expression gradient in adult tail skin and bones, consistent with retained positional patterning, with stronger distal expression in short‑tailed animals. These results provide in vivo evidence that spatially patterned HOX gene expression is retained in adulthood, consistent with residual transcriptional signatures of embryonic anterior–posterior identity.