An increased understanding of how genetics contributes to expression variation in natural Arabidopsis thaliana populations is of fundamental importance to understand adaptation. Here, we reanalyse data from two publicly available datasets with genome-wide data on genetic and transcript variation from whole-genome and RNA-sequencing in populations of wild-collected A. thaliana accessions. We found transcripts from more than half of all genes (55%) in the leaf of all accessions. In the population with higher RNA-sequencing coverage, transcripts from nearly all annotated genes were present in the leaf of at least one of the accessions. Thousands of genes, however, were found to have high transcript levels in some accessions and no detectable transcripts in others. The presence or absence of particular gene transcripts within the accessions was correlated with the genome-wide genotype, suggesting that part of this variability was due to a genetically controlled accession-specific expression. This was confirmed using the data from the largest collection of accessions, where cis-eQTL with a major influence on the presence or absence of transcripts was detected for 349 genes. Transcripts from 172 of these genes were present in the second, smaller collection of accessions and there, 81 of the eQTLs for these genes could be replicated. Twelve of the replicated genes, including HAC1, are particularly interesting candidate adaptive loci as earlier studies have shown that lack-of-function alleles at these genes have measurable phenotypic effects on the plant. In the larger collection, we also mapped 2,320 eQTLs regulating the expression of 2,240 genes that were expressed in nearly all accessions, and 636 of these replicated in the smaller collection. This study thus provides new insights to the genetic regulation of global gene-expression diversity in the leaf of wild-collected A. thaliana accessions and in particular illustrate that strong cis-acting polymorphisms are an important genetic mechanisms leading to the presence or absence of transcripts in individual accessions.