Building a Portuguese Water Dog Reference Genome to Unlock Breed-Specific Health Insights

The Portuguese Water Dog Foundation is very excited to join with Drs. Jaime Modiano VMD, PhD and Steven Friedenberg DVM, PhD, DACVECC in a project to improve the lives and well-being of PWDs. The team of Drs. Modiano and Friedenberg will lead a project creating a reference genome specific to PWDs, which will improve our ability to identify genetic drivers of common inherited disorders in the PWD. This project is fully funded by your donations to the PWD Foundation. Once completed, this high-quality reference genome will be made available to the public, allowing researchers from around the world to access this cutting-edge resource that will enhance the breed’s welfare.

Background of Canine Genome

Both Addison’s disease and hemangiosarcoma impose serious health burdens on Portuguese Water Dogs (PWDs). Other conditions – for example hip dysplasia, dilated cardiomyopathy, inflammatory bowel disease, and hypothyroidism – also disproportionately affect the breed. Efforts to pinpoint the genetic drivers of these disorders have been limited by reliance on canine reference genomes built from other dog breeds, such as the Boxer (CanFam 3.0) and German Shepherd (CanFam 4.0), which miss PWD-specific variation, particularly in complex or repetitive regions of the genome. Human genome studies have shown that relying on a single reference can omit up to 10% of a species’ genetic content – hundreds of millions of bases and the majority of structural variants – highlighting just how much PWD-specific information may be lost without a dedicated genome assembly.

How This Project Will Make a Difference

This project will generate a high-quality, telomere-to-telomere reference genome combining the latest technologies, to produce a PWD genome assembly of unprecedented accuracy and completeness. Crucially, this assembly will be released publicly so that researchers everywhere can align existing and future PWD sequencing data directly to the correct reference. Additionally, this assembly will enable researchers to compare PWD genomes with those of other breeds – unlocking insights into inherited variation that governs morphology, disease risk, and longevity.

This breed-specific framework will immediately accelerate discovery of genetic variants underlying Addison’s, hemangiosarcoma, and the full spectrum of PWD-predisposed conditions. Existing whole-genome and targeted sequencing datasets can be reanalyzed at once, and all future studies will benefit from a precise, breed-specific scaffold for variant calling, functional annotation, and the development of diagnostic tests. By funding a PWD reference genome, the Foundation will help create a lasting, community-wide resource that transforms research, informs breeding decisions, and ultimately improves the healthspan of PWDs.

The Team Behind the Project

The research team will be co-led by Dr. Steven Friedenberg, DVM, PhD, and Dr. Jaime Modiano, VMD, PhD. Together, Drs. Friedenberg and Modiano are uniquely positioned to complete this work because of their deep knowledge of PWDs and complementary skill set. Dr. Friedenberg brings years of experience studying Addison’s disease in Portuguese Water Dogs along with deep bioinformatics expertise, while Dr. Modiano, a world-renowned cancer biologist, has spearheaded hemangiosarcoma research in the breed. Bioinformatics analyses will be driven by Dr. Friedenberg’s graduate student Hayden Hamsher, who already has two years of pipeline development experience, and the project will benefit from the guidance of Dr. Jonah Cullen, whose postdoctoral work on the horse pangenome will provide invaluable genome assembly knowledge. They have also enlisted collaborators at UC Santa Cruz, the University of Washington, and the BC Cancer Research Centre – each contributing specialized expertise in long-read sequencing, Omni-C scaffolding, and Strand-seq methodologies. Together, this multidisciplinary team combines breed-specific veterinary insight, advanced computational skills, and world-class sequencing know-how to ensure the success of the PWD reference genome.