The completeness and stratification in yeast genotype-phenotype space

Genotype and phenotype are two themes of modern biology. While the running principles in genotype has been well understood (e.g., DNA double helix structure, genetic code, central dogma, etc.), much less is known about the rules in phenotype. In this study we examine a yeast phenotype space that is represented by 405 quantitative traits. We show that the space is convergent with limited latent dimensions, which form surprisingly long-distance chains such that all traits are interconnected with each other. As a consequence, statistically uncorrelated traits are linearly dependent in the multi-dimensional phenotype space and can be precisely inferred from each other. Meanwhile, the performance is much poorer for similar trait inferences but from the genotype space (including DNA and mRNA), highlighting the dimension stratification between genotype space and phenotype space. Since the world we’re living is primarily phenotypic and what we truly care is phenotype, these findings call for phenotype-centered biology as a complement for the cross-space genetic thinking in current biology.