Natural genetic variation quantitatively regulates heart-rate and -dimension.

Development and function of the heart are crucially controlled by individual genetic factors determining the continuum from health to disease. A prime example of a quantitative pathological phenotype is left ventricular hypoplasia, affecting the left ventricle (LV) and its associated inflow and outflow structures and reducing its size to varying degrees 1 . Current models suggest polygenic contributions on heart development and disease, but we are just beginning to understand the impact of naturally occurring sequence variations. Here we show how natural genetic variants exert cumulative, environment-sensitive effects on both embryonic heart development as well as adult heart function. We addressed this in embryos of five inbred strains of the Japanese rice fish medaka ( Oryzias latipes 2 and Oryzias sakaizumii 3 ), analyzing heart rates as a functional proxy to capture combined characteristics of the conduction system and structural morphology. We identified one strain, HO5 2 , with embryonic hypoplastic ventricles, fast heart rates, and significantly impaired cardiac function and overall fitness in adults. We created an interpopulation cross of the divergent HO5 strain to HdrR, which exhibits a morphologically normal heart and comparably slow heart rates, to leverage segregation variance in the second filial generation (F2) for genetic mapping. The correlation of 1192 individually phenotyped F2 embryos (heart rate) with the corresponding whole-genome sequences established a single nucleotide polymorphism-based linkage map. Integrated analysis of parental cardiac transcriptomes highlighted 59 loci containing genes prominently linked to human cardiovascular phenotypes. In vivo knockout models of the top 12 candidate genes demonstrated a causal and differential impact on heart development, ventricular size, and heart rate, evidencing the polygenic nature of heart phenotypes and establishing new loci for genetic diagnostics of human congenital heart disease. The controllable and scalable genetics and experimental validation in inbred vertebrate models complement and expand human association studies to provide novel and unique insights into the role of natural genetic variation in the mechanism of cardiac disease and allow to identify genetic susceptibility in individual human subjects.