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.
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Data availability
RNA-Seq data were deposited into the Gene Expression Omnibus database under accession number GSE311823 and are available at the following URL: [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE311823].
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Acknowledgements
At the University of Ljubljana, Biotechnical Faculty, we thank Ana Petek, Ana Jakopič, Ana Brunčič, Stane Karner, Domen Drašler, Marko Bizjak, Gregor Šen, and Dušan Birtič for their valuable technical assistance with animal measurements and sampling procedures at the slaughterhouse. Funding: core grant P4-0220 from Slovenian Research and Innovation Agency (ARIS). We are also thankful to the DAAD funding programs for supporting our work through the project number DAAD ID-57514909.
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S.H.: original draft preparation. S.H., I.M., M.S., C.F.: conceptualization, methodology, supervision. R.E., M.Č., U.D., S.K., N.P., M.U. V.B., M.F.: investigation, methodology. All authors read, contributed to the article and approved the submitted version.
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Horvat, S., Ellenrieder, R., Simčič, M. et al. Retention of embryonic positional identity signatures in the adult sheep tail: evidence from HOXB13 spatial RNA expression gradients. Sci Rep (2026). https://doi.org/10.1038/s41598-026-42438-7
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DOI: https://doi.org/10.1038/s41598-026-42438-7
