The overall aim of this project is to improve equine health and welfare by identifying causative mutations for inherited diseases and performance traits to aid informed breeding of healthy horses. We use a comparative genomics approach, combining Whole Genome Sequencing (WGS) and bioinformatics with state-of-the-art clinical diagnosis of disease phenotypes. The objectives of this on-going study are to: 1. clinically define monogenic diseases with various inheritance patterns, 2. further develop our general framework for identifying disease causing mutation with a bioinformatics pipeline for whole-genome sequencing, 3. develop a plan for breeding advise in different scenarios of inheritance patterns, and severity of the disease. In the first part of the project a general framework for mutation-detection of equine monogenetic diseases was developed by WGS of to date, eight family trios. The initial focus was on anophthalmia and microphthalmia, potentially autosomal recessive disease/s, recently observed among Swedish Warmblood horses. The bioinformatic pipeline is up and running for variant calling of SNVs, indels, and larger structural variants. The called variants are further analyzed for different inheritance patterns. The first part of the project will be followed by further WGS of 20 horses to discover a potential genetic background to extreme joint laxity. The collection of these samples was delayed because of difficulties in sample collection due to the Covid pandemic, and the following post-pandemic endeavors, but we have now collected most of the samples to do this during 2024. We aim to confirm and validate association of putative genomic regions with highly flexible locomotion in horses, by genotyping, whole genome sequencing, and re-sequencing. We will pay special attention to chromosomal regions and genes known to be associated with hypermobility and connective tissue disorders in other species. In the planned study, we will describe the association between equine performance and phenotypes seen in collagen deficiencies and joint laxity syndromes. Identification of genetic markers or causative mutations in such regions could provide new tools in horse breeding to select for healthy, sustainable, and better performing horses.