Molecular basis of complex heritability in natural genotype-to-phenotype relationships

The intrinsic complexity of quantitative traits was evident even before the molecular nature of the gene was understood. Yet we still lack a detailed molecular understanding of complex heritability. Here we alleviated statistical roadblocks to high-resolution genetic mapping by using an inbred population of diploid yeast with very low linkage disequilibrium and more individuals than segregating polymorphisms. We mapped over 18,000 quantitative trait loci, resolving more than 3,300 to single nucleotides. This allowed us to explore the molecular origins of complexity, hybrid vigor, pleiotropy, and gene ´ environment interactions and to rigorously estimate the distribution of fitness effects of natural genetic variation. Our results describe a comprehensive, high-resolution genotype-to-phenotype map and define general principles underlying the complexity of heredity. mRNA-seq performed on 2 parental diploid strains in 3 growth conditions in biological triplicate