Collaborative Research: EDGE CMT: A four-dimensional genotype-phenotype map of poison frog skin color

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Coloration plays important ecological roles in animals, including mate choice, thermoregulation, and avoiding predation. However, the understanding of how animals produce coloration is based on only a few species and large gaps in knowledge remain. For example, very little is known about how amphibians, one of the major groups of vertebrate animals, produce their beautiful array of colors and patterns. This project will leverage recent advances in genomic and developmental biology to identify the genes that control color and color patterning in three species of poison frogs that represent some of the most colorful and charismatic vertebrates. The development of poison frogs as a model system for the study of coloration will identify key biological mechanisms that contribute to coloration, and open new avenues of research into genetics of color in other animals. The proposed research will also train undergraduate students, graduate students, and postdoctoral researchers in cutting-edge genomic techniques. Project personnel will communicate research results to the public using visual displays of live frogs, children’s books written in Spanish, and a virtual field experience based on scientific field work which will be made available freely online. The proposed research will create a four-dimensional genotype-to-phenotype map of poison frog skin coloration using methods that link color and pattern to their underlying genetics. Color and pattern phenotypes will be examined using a combination of computational analysis of images, spectrophotometry, metabolomics and their genetic underpinnings will be examined using genome sequencing of several genera, species and populations, genome wide association studies, and RNAseq. Results will be synthesized using in-situ hybridization to track the expression of candidate genes over the course of development and spatial RNA sequencing to track gene expression in specific skin regions of the frogs, both of which will then be mapped onto images of skin structure obtained using transmission electron microscopy (TEM). Finally, key candidate patterning genes will be validated using CRISPR. Results will be integrated into a four-dimensional map connecting genetic variants and spatial gene expression with phenotypic variation in color, color patterning, and pigment organization, and visualized using TEM images. This holistic approach, focusing on three independent origins of spot and stripe patterning, will provide key insights into general mechanisms underlying color variation in vertebrates. Furthermore, poison frogs are known for having large, complex genomes, so this work will provide a guide to future investigators on how to connect genotype to phenotype in difficult systems.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.