Expression Quantitative Trait Locus Mapping across Water Availability Environments Reveals Contrasting Associations with Genomic Features in Arabidopsis      

Abstract

The regulation of gene expression is crucial for an organism's development and response to stress, and an understanding of the evolution of gene expression is of fundamental importance to basic and applied biology. To improve this understanding, we conducted expression quantitative trait locus (eQTL) mapping in the Tsu-1 (Tsushima, Japan) × Kas-1 (Kashmir, India) recombinant inbred line population of Arabidopsis thaliana across soil drying treatments. We then used genome resequencing data to evaluate whether genomic features (promoter polymorphism, recombination rate, gene length, and gene density) are associated with genes responding to the environment (E) or with genes with genetic variation (G) in gene expression in the form of eQTLs. We identified thousands of genes that responded to soil drying and hundreds of main-effect eQTLs. However, we identified very few statistically significant eQTLs that interacted with the soil drying treatment (GxE eQTL). Analysis of genome resequencing data revealed associations of several genomic features with G and E genes. In general, E genes had lower promoter diversity and local recombination rates. By contrast, genes with eQTLs (G) had significantly greater promoter diversity and were located in genomic regions with higher recombination. These results suggest that genomic architecture may play an important a role in the evolution of gene expression.

Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana

“…Our analysis of the parental genomes (sequences were published in Lowry et al, 2013) revealed that the chloroplast genomes of TSU and KAS were identical and only 16 SNPs existed in the mitochondrial genome. These results differed from published TSU-1 (SRX246442) and KAS-1 (SRX246466) sequences (http://www.ncbi.…”

“…Only AT2G03140 had any sequence polymorphism between the TSU and KAS parental accessions (Supplemental Table 6). While gene function can easily be affected by polymorphism outside of the coding region, genes that are conserved between the widely divergent genomes of TSU and KAS may be less likely to contribute to quantitative genetic divergence than those with sequence, and especially protein, divergence (Lowry et al, 2013).…”

“…For example, over half of the published sequenome SNPs that are polymorphic in our mapping population are monomorphic between NCBI TSU-1 and KAS-1 (http://naturalvariation.org/hapmap). It is important to note that, while well suited for the characterization of SNPs, the short read sequencing and reference-based alignment used by Lowry et al (2013) to sequence the mapping parents TSU and KAS may be unable to detect genomic rearrangements. As large-scale rearrangements are characteristic of the Arabidopsis mitochondrial genome (Davila et al, 2011), it is possible that these sequence variants are augmented by other undetected polymorphisms.…”

“…We downloaded high-depth resequencing of both parental lines (Lowry et al, 2013). Sequence comparisons revealed that the chloroplast genomes of TSU and KAS had identical DNA sequences.…”

“…First, all genes with significant gene expression polymorphism were extracted (for each QTL interval) by including only genes with significant cis-eQTLs (mapped in a recent study using the same gene expression data set; Lowry et al, 2013). Second, we ran QTL scans in which expression of each gene was iteratively added (and subsequently removed) as an additive covariate to the previously generated multiple-QTL model.…”