Collaborative research: edge FGT: revolutionizing the poeciliid model system for the genome editing age

The National Science Foundation's Division of Integrative Organismal Systems awarded $1,526,917 to The Leland Stanford Junior University under the Biological Sciences program (CFDA 47.074) on September 15, 2025, for a collaborative research project to develop genome editing tools and genomic resources for poeciliid fishes (guppies, mollies, and swordtails). The project, extending through August 31, 2029, will establish immortalized cell lines from multiple poeciliid species, optimize transfection protocols to enable CRISPR-based DNA editing both in vitro and in vivo, and generate high-quality, telomere-to-telomere genome assemblies with functional annotation resources. These genomic tools will be made publicly accessible through a genome browser to facilitate broad research adoption.

Beyond advancing functional genomics capabilities in this important model system for studying human diseases such as melanoma and metabolic disorders, the project will deliver significant educational and workforce development benefits. Deliverables include hands-on research opportunities for undergraduate students, public outreach activities, and training programs to build a community of researchers proficient in these new genome editing techniques. A sub-award was issued to Universidad de Los Andes (Bogota, Colombia) on December 5, 2025, as part of this collaborative research effort, expanding the project's international research capacity.

Abstract

This project aims to unlock the full scientific potential of a group of small, colorful fish commonly found in home aquariums?guppies, mollies, and swordtails. These fish have already allowed scientists to uncover important insights on human diseases such as melanoma and metabolic disorders, as well as in studies of animal behavior and development. However, scientists currently lack the tools to precisely modify their DNA, which limits how much we can learn from them. This project will develop new methods to enable DNA editing in these fish, opening the door to discoveries that could benefit both medicine and biology. In addition to advancing science, the project will provide hands-on research opportunities for undergraduate students and engage the public through outreach activities. IT will also train other scientists in these new techniques, helping to build a community of researchers equipped to study health and disease using these powerful animal models. Poeciliid fishes are a key model system in integrative organismal biology, yet their utility has been constrained by the lack of DNA editing tools, largely due to their viviparous reproduction. This proposal addresses that GAP by developing a suite of biotechnological tools to enable functional genomics in poeciliids. The project will begin by establishing immortalized cell lines from multiple species and optimizing transfection protocols to enable crispr-based DNA editing in vitro. Building on recent success in culturing embryos EX vivo, the team will adapt these protocols for in vivo gene editing. Concurrently, the project will generate high-quality, telomere-to-telomere genome assemblies and functional annotation resources to support downstream applications. These genomic tools will be made publicly accessible via a genome browser, facilitating broad adoption. Together, these efforts will establish a robust platform for genetic manipulation in poeciliids, enabling mechanistic studies of development, physiology, and disease. The research will result in new biotechnology. 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.- subawards are planned for this award.