Genome-Wide Association Study in Arabidopsis thaliana of Natural Variation in Seed Oil Melting Point: A Widespread Adaptive Trait in Plants

Abstract

Seed oil melting point is an adaptive, quantitative trait determined by the relative proportions of the fatty acids that compose the oil. Micro- and macro-evolutionary evidence suggests selection has changed the melting point of seed oils to covary with germination temperatures because of a trade-off between total energy stores and the rate of energy acquisition during germination under competition. The seed oil compositions of 391 natural accessions of Arabidopsis thaliana, grown under common-garden conditions, were used to assess whether seed oil melting point within a species varied with germination temperature. In support of the adaptive explanation, long-term monthly spring and fall field temperatures of the accession collection sites significantly predicted their seed oil melting points. In addition, a genome-wide association study (GWAS) was performed to determine which genes were most likely responsible for the natural variation in seed oil melting point. The GWAS found a single highly significant association within the coding region of FAD2, which encodes a fatty acid desaturase central to the oil biosynthesis pathway. In a separate analysis of 15 a priori oil synthesis candidate genes, 2 (FAD2 and FATB) were located near significant SNPs associated with seed oil melting point. These results comport with others' molecular work showing that lines with alterations in these genes affect seed oil melting point as expected. Our results suggest natural selection has acted on a small number of loci to alter a quantitative trait in response to local environmental conditions.

Keywords: GWAS.; adaptation; evolution; fatty acid composition.

Figure 1.

Geographic distribution of the 391 A. thaliana accessions used in this study. Gray circles represent collection locations of: (A) native accessions (N = 356) across Europe, mainland Asia, and northern Africa, (B) non-native accessions from the United States of America (N = 31), and (C) the remaining non-native accessions (N = 4).

Figure 2.

Distribution of seed oil melting points. Histogram of the average melting points for the accessions in the All dataset (N = 391).

Figure 3.

Relative effect of each fatty acid on seed oil melting point. Boxplots (minimum, lower hinge, median, upper hinge, maximum) of the effect each fatty acid had on average seed oil melting point among the 391 accessions. A zero value means the fatty acid has no effect on seed oil melting point because its melting point is equivalent to the seed oil melting point.

Figure 4.

Boxcox transformed melting point regressed on the average minimum temperatures for the months of February through April and September through November. Best fit lines and 95% confidence intervals are shown.

Figure 5.

Scatterplots of the significant associations in the a priori analysis. Negative log P values of all SNPs found within 100kb upstream of the start codon and 100kb downstream of the stop codon of the significant a priori candidate genes (bounded by vertical black lines). Gene locations in each region are represented by striped gray boxes. Significant SNPs are shape coded. Gray triangle = FDR < 0.05, gray circle = FDR < 0.1. (A) Region on chromosome 1 surrounding FATB (AT1G08510), (B) Region on chromosome 3 surrounding FAD2 (AT3G12120).

Figure 6.

GWAS results for boxcox-transformed seed oil melting point in A. thaliana using the EMMA package in R. Scatterplot of the negative log P values for each chromosome. Significant SNPs are shape coded. Gray triangle = FDR < 0.05, gray circle = FDR < 0.1. The vertical black line indicates the position of the a priori candidate gene FAD2 (AT3G12120). Regions of significant association are labeled 1–5. Linkage disequilibrium (r ²) in a 200kb window around the most significant SNP in the genome is shown with a black line graph. (A) Chromosome 1, (B) Chromosome 2, (C) Chromosome 3, (D) Chromosome 4, and (E) Chromosome 5.