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 will use a comparative genomics approach, combining whole-genome sequencing (WGS) and bioinformatics with state-of-the-art clinical diagnosis of disease phenotypes. In the first part project a general framework for mutation-detection of equine monogenetic diseases will planned to WGS family trios with offspring affected by microphthalmia. A potentially autosomal recessive disease, recently observed among Swedish Warmblood horses. The objectives of this part of the study are to: 1. clinically define monogenic diseases with autosomal recessive inheritance, 2. develop a 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. During this first phase we have now sequenced and analyzed whole-genome sequence data from ten individual horses included in a family material of two trios (healthy mother and father, and affected offspring), and two duos (healthy mother and affected offspring). We compared these ten individual sequences with three previously sequenced individuals, and a sequenced pool of 20 horse samples. These 23 individuals are all sampled from healthy stallions. We will now initiate the second part of this storage project including sequencing and analysis of whole-genome sequence data from another 20 individual horses to discover a potential genetic background of extreme joint laxity. The sampling was delayed due to the Covid-19 pandemic, and will instead be conducted during spring of 2022. The generated sequences from these 20 individuals will also be used as controls to the family material sequenced in the first part of the project. 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.