Genetic architecture of regulatory variation in Arabidopsis thaliana

Abstract

Studying the genetic regulation of expression variation is a key method to dissect complex phenotypic traits. To examine the genetic architecture of regulatory variation in Arabidopsis thaliana, we performed genome-wide association (GWA) mapping of gene expression in an F(1) hybrid diversity panel. At a genome-wide false discovery rate (FDR) of 0.2, an associated single nucleotide polymorphism (SNP) explains >38% of trait variation. In comparison with SNPs that are distant from the genes to which they were associated, locally associated SNPs are preferentially found in regions with extended linkage disequilibrium (LD) and have distinct population frequencies of the derived alleles (where Arabidopsis lyrata has the ancestral allele), suggesting that different selective forces are acting. Locally associated SNPs tend to have additive inheritance, whereas distantly associated SNPs are primarily dominant. In contrast to results from mapping of expression quantitative trait loci (eQTL) in linkage studies, we observe extensive allelic heterogeneity for local regulatory loci in our diversity panel. By association mapping of allele-specific expression (ASE), we detect a significant enrichment for cis-acting variation in local regulatory variation. In addition to gene expression variation, association mapping of splicing variation reveals both local and distant genetic regulation for intron and exon level traits. Finally, we identify candidate genes for 59 diverse phenotypic traits that were mapped to eQTL.

Figure 1.

GWA for gene expression. (A) The middle position of the mapped genes was plotted against the chromosome position of the associated SNPs detected at FDR < 0.2. The intensity of the points indicates the effect (r²) of the corresponding association. (Black circles) Centromeres. (B) The length distribution of LD blocks surrounding locally (solid lines) and distantly (dashed lines) associated SNPs, detected at different FDR thresholds. LD block length was defined as the distance between the first two flanking SNPs, with which focal SNP r² < 0.1. (Black line) Randomly sampled 20,000 SNPs without local or distant association. The small peak between 8 and 12 kb for the distant associations included 470 associations, 126 of which were with the largest trans hot spot located at 14,423,393 bp on chromosome 4. (C) The frequency distribution of the derived alleles of locally (solid line) and distantly (dashed line) associated SNPs, detected at different FDR thresholds. (Black line) Randomly sampled 50,000 SNPs without local or distant association.

Figure 2.

Allelic heterogeneity of local regulatory variation. (A) Associated SNPs detected at different FDR thresholds from GWA of gene expression were grouped to local and distant regulatory regions. At FDR < 0.2, for example, 1238 genes (67.4%) were associated with a single distant region (1 dist), 82 genes (4.5%) were associated with multiple distant regions (>1 dist), 444 genes (24.2%) were only locally associated (local), and an additional 74 genes (4.0%) were associated with both local and distant regions (local & dist). (B) For associations detected at FDR < 0.2 from GWA of gene expression, the number of genes that have single eQTL within local regulatory region (local 1), multiple eQTL within local regulatory region (local >1), single eQTL within distant regulatory region (dist 1), and multiple eQTL within distant regulatory region (dist >1). Associated SNPs within a regulatory region were clustered at different LD thresholds. (C) Distribution of eQTL from local scan. Proportion of eQTL (the number of eQTL after clustering by r² > 0.8/[the number of SNPs tested]) was plotted along 500-bp bins for 25 kb upstream and 25 kb downstream. Within genes, the positions were binned to five positional quantiles. (Gray bars) The proportion of associated SNPs before LD clustering. (s) Transcriptional start site; (e) transcriptional stop site. (D) The P-value distribution of the F-tests for model comparison. Associated SNPs were clustered at different LD thresholds. (Dashed line) P-value of 0.05.

Figure 3.

An example of cis-acting, locally associated SNP. (A) The relative gene expression levels were plotted against the genotypes at the associated SNP, located at 3,041,799 bp on chromosome 1. (C) Col allele; (N) non-Col allele. (B) The log allele ratios (LARs) of the sense strain were plotted against LARs of antisense strain for the transcribed SNP, located at 3,041,022 bp on chromosome 1. An explanation of legends follows: (CC at transcribed SNP) lines for which transcribed SNP is homozygous Col allele; (NN at transcribed SNP) lines for which transcribed SNP is homozygous non-Col allele; (C-C/C-N or N-C/N-N) lines for which transcribed SNP is heterozygous but the regulatory SNP is homozygous; (C-C/N-N) lines for which transcribed SNP is heterozygous and the regulatory SNP is in phase with transcribed SNP. In this case, the non-Col allele at the regulatory SNP up-regulates gene expression.

Figure 4.

Additive (A) and dominant (B) associations detected at FDR < 0.2 in GWA for genetic inheritance of gene expression. The middle position of the associated genes was plotted against the chromosome position of the associated SNPs. The intensity of the points indicates the effect (r²) of the corresponding association. In B, cross points represent Col allele dominant, while diamond points represent non-Col allele dominant.

Figure 5.

Genetic regulation of splicing variation. The middle position of the mapped introns (A) and exons (B) was plotted against the chromosome position of the associated SNPs, detected in GWA at FDR < 0.2. The intensity of the points indicates the effect (r²) of the corresponding association. (Black circles) Centromeres. The distribution of intron (C) and exon (D) splicing QTL from local scan. Proportion of splicing QTL (the number of splicing QTL after clustering by r² > 0.8/[the number of SNPs tested]) was plotted along 100-bp bins for 5 kb upstream and 5 kb downstream from the mapped introns or exons. Within introns or exons, the positions were binned to five positional quantiles. (Gray bars) The proportion of associated SNPs before LD clustering. (s) Start position of intron or exon; (e) end position of intron or exon.