Quantitative analysis of gene expression domains and investigation of relationships between gene expression and developmental and phenotypic outcomes are central to advancing our understanding of the genotype–phenotype map. Gene expression domains typically have smooth but irregular shapes lacking homologous landmarks, making it difficult to analyze shape variation with the tools of landmark-based geometric morphometrics. In addition, 3D image acquisition and processing introduce many artifacts that further exacerbate the problem. To overcome these difficulties, this paper presents a method that combines optical projection tomography scanning, a shape regularization technique and a landmark-free approach to quantify variation in the morphology of Sonic hedgehog expression domains in the frontonasal ectodermal zone (FEZ) of avians and investigate relationships with embryonic craniofacial shape. The model reveals axes in FEZ and embryonic-head morphospaces along which variation exhibits a sharp linear relationship at high statistical significance. The technique should be applicable to analyses of other 3D biological structures that can be modeled as smooth surfaces and have ill-defined shape.
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We acknowledge funding from the National Science Foundation Grant DBI-1052942 (WM) and National Institutes of Health Grants 3R01DE021708 (BH, RSM and WM) and F32DE02214 (RMG). We thank the anonymous reviewers for their comments.
Conflict of interest
The authors declare that they have no conflict of interest.
All experiments comply with the current laws of the United States of America and Canada.
Software Accessibility Matlab code for the shape regularization method developed in this paper is available for free use at https://github.com/qx0731/Mesh-Regularization-/.
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Xu, Q., Jamniczky, H., Hu, D. et al. Correlations Between the Morphology of Sonic Hedgehog Expression Domains and Embryonic Craniofacial Shape. Evol Biol 42, 379–386 (2015). https://doi.org/10.1007/s11692-015-9321-z
- Gene expression domains
- Facial shape
- Sonic hedgehog
- Frontonasal ectodermal zone (FEZ)
- Genotype–phenotype map