A high-throughput, fully automated morphometric method to discover the genes controlling shape differences in the Faroese mice

Yingguang Frank Chan, William H. Beluch, Rémi Blanc - Friedriech Miescher Laboratory of the Max Planck Society, Tübingen, Germany

The Faroe Islands are a group of islands in the North Atlantic that are known for its natural beauty, Viking culture and a special population of house mouse. The Faroese house mouse from the most remote island of the Faroese, Mykines (population: 10 people), looked so distinct when it was discovered that it was declared a subspecies, Mus musculus faeroenesis. These mice are large-bodied and showed an extreme form of left-right asymmetry in its skull. Our research group has brought back these mice and made a large (>800) genetic cross to perform genetic mapping, with the goal to find the genes that control the remarkable shape of these Faroese house mouse. Using whole-body microCT scans, we have obtained high-resolution data for the skeletons of around than 700 mice. This is a far larger dataset than most microCT datasets in image analysis. In order to analyze this data efficiently, we have developed a fully automated pipeline in collaboration with Thermo Fisher Scientific/FEI.

How Amira-Avizo Software is used

The fully automated pipeline developed in collaboration with Thermo Fisher Scientific/FEI takes the whole-body microCT volume and combined registration with guided segmentations to computationally take apart the skeleton into individual bones such as the cranium, left and right mandibles, femur, etc. Then we apply surface-based methods to quantify shape differences in each bone from individual to individual. Coupled with the genetic information we can then determine the effect of each gene on specific shape changes in a bone.  This detailed dataset offers us the opportunity to discover how the Faroese mice have become so special since they have made it to the remote Faroe Islands.