Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast

Gene expression varies between individuals and corresponds to a key step linking genotypes to phenotypes. However, our knowledge regarding the species-wide genetic control of protein abundance, including its dependency on transcript levels, is very limited. Here, we have determined quantitative proteomes of a large population of 942 diverse natural Saccharomyces cerevisiae yeast isolates. We found that mRNA and protein abundances are weakly correlated at the population gene level. While the protein co-expression network recapitulates major biological functions, differential expression patterns reveal proteomic signatures related to specific populations. Comprehensive genetic association analyses highlight that genetic variants associated with variation in protein (pQTL) and transcript (eQTL) levels poorly overlap (3.6%). Our results demonstrate that transcriptome and proteome are governed by distinct genetic bases, likely explained by protein turnover. It also highlights the importance of integrating these different levels of gene expression to better understand the genotype-phenotype relationship. HighlightsO_LIAt the level of individual genes, the abundance of transcripts and proteins is weakly correlated within a species ({rho} = 0.165). C_LIO_LIWhile the proteome is not imprinted by population structure, co-expression patterns recapitulate the cellular functional landscape C_LIO_LIWild populations exhibit a higher abundance of respiration-related proteins compared to domesticated populations C_LIO_LILoci that influence protein abundance differ from those that impact transcript levels, likely because of protein turnover C_LI