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Hoxd13 ,  Tbx2 ,  Tbx3 ,  Sall1  and  Sall3  genes are candidates for encoding antero-posterior positional values in the developing chick wing and specifying digit identity. In order to build up a detailed profile of gene expression patterns in cell lineages that give rise to each of the digits over time, we compared 3 dimensional (3D) expression patterns of these genes during wing development and related them to digit fate maps. 3D gene expression data at stages 21, 24 and 27 spanning early bud to digital plate formation, captured from  in situ  hybridisation whole mounts using Optical Projection Tomography (OPT) were mapped to reference wing bud models. Grafts of wing bud tissue from GFP chicken embryos were used to fate map regions of the wing bud giving rise to each digit; 3D images of the grafts were captured using OPT and mapped on to the same models. Computational analysis of the combined computerised data revealed that  Tbx2  and  Tbx3  are expressed in digit 3 and 4 progenitors at all stages, consistent with encoding stable antero-posterior positional values established in the early bud;  Hoxd13  and  Sall1  expression is more dynamic, being associated with posterior digit 3 and 4 progenitors in the early bud but later becoming associated with anterior digit 2 progenitors in the digital plate.  Sox9  expression in digit condensations lies within domains of digit progenitors defined by fate mapping; digit 3 condensations express  Hoxd13  and  Sall1 , digit 4 condensations  Hoxd13 ,  Tbx3  and to a lesser extent  Tbx2 .  Sall3  is only transiently expressed in digit 3 progenitors at stage 24 together with  Sall1  and  Hoxd13 ; then becomes excluded from the digital plate. These dynamic patterns of expression suggest that these genes may play different roles in digit identity either together or in combination at different stages including the digit condensation stage.

Comparative Analysis of 3D Expression Patterns of Transcription Factor Genes and Digit Fate Maps in the Developing Chick Wing