- and -regulatory Effects on Gene Expression in a Natural Population of .

• and -regulatory mutations are important contributors to transcriptome evolution. Quantifying their relative contributions to intraspecific variation in gene expression is essential for understanding the population genetic processes that underlie evolutionary changes in gene expression. Here, we have examined this issue by quantifying genome-wide, allele-specific expression (ASE) variation using a crossing scheme that produces F hybrids between 18 different strains sampled from the Genetic Reference Panel and a reference strain from another population. Head and body samples from F adult females were subjected to RNA sequencing and the subsequent ASE quantification. - and -regulatory effects on expression variation were estimated from these data. A higher proportion of genes showed significant -regulatory variation (∼28%) than those that showed significant -regulatory variation (∼9%). The sizes of -regulatory effects on expression variation were 1.98 and 1.88 times larger than -regulatory effects in heads and bodies, respectively. A generalized linear model analysis revealed that both - and -regulated expression variation was strongly associated with nonsynonymous nucleotide diversity and tissue specificity. Interestingly, -regulated variation showed a negative correlation with local recombination rate. Also, our analysis on proximal transposable element (TE) insertions suggested that they affect transcription levels of ovary-expressed genes more pronouncedly than genes not expressed in the ovary, possibly due to defense mechanisms against TE mobility in the germline. Collectively, our detailed quantification of ASE variations from a natural population has revealed a number of new relationships between genomic factors and the effects of - and -regulatory factors on expression variation.