Genetic regulation of transcriptional variation in natural 1 Arabidopsis thaliana accessions 2 3

1 2 An increased knowledge of the genetic regulation of expression in Arabidopsis 3 thaliana is likely to provide important insights about the basis of the plant's extensive 4 phenotypic variation. Here, we reanalysed two publicly available datasets with 5 genome-wide data on genetic and transcript variation in large collections of natural A. 6 thaliana accessions. Transcripts from more than half of all genes were detected in the 7 leaf of all accessions, and from nearly all annotated genes in at least one accession. 8 Thousands of genes had high transcript levels in some accessions but no transcripts at 9 all in others and this pattern was correlated with the genome-wide genotype. In total, 10 2,669 eQTL were mapped in the largest population, and 717 of them were replicated 11 in the other population. 646 cis-eQTLs regulated genes that lacked detectable 12 transcripts in some accessions, and for 159 of these we identified one, or several, 13 common structural variants in the populations that were shown to be likely 14 contributors to the lack of detectable RNA-transcripts for these genes. This study thus 15 provides new insights on the overall genetic regulation of global gene-expression 16 diversity in the leaf of natural A. thaliana accessions. Further, it also shows that 17 strong cis-acting polymorphisms, many of which are likely to be structural variations, 18 make important contributions to the transcriptional variation in the worldwide A. 19 thaliana population.