Abstract
BackgroundNatural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits. A collection of 54 A. thaliana natural accession-derived lines were subjected to deep genotyping through Single Feature Polymorphism (SFP) detection via genomic DNA hybridization to Arabidopsis Tiling 1.0 Arrays for the detection of selective sweeps, and identification of associations between sweep regions and growth-related metabolic traits.ResultsA total of 1,072,557 high-quality SFPs were detected and indications for 3,943 deletions and 1,007 duplications were obtained. A significantly lower than expected SFP frequency was observed in protein-, rRNA-, and tRNA-coding regions and in non-repetitive intergenic regions, while pseudogenes, transposons, and non-coding RNA genes are enriched with SFPs. Gene families involved in plant defence or in signalling were identified as highly polymorphic, while several other families including transcription factors are depleted of SFPs. 198 significant associations between metabolic genes and 9 metabolic and growth-related phenotypic traits were detected with annotation hinting at the nature of the relationship. Five significant selective sweep regions were also detected of which one associated significantly with a metabolic trait.ConclusionsWe generated a high density polymorphism map for 54 A. thaliana accessions that highlights the variability of resistance genes across geographic ranges and used it to identify selective sweeps and associations between metabolic genes and metabolic phenotypes. Several associations show a clear biological relationship, while many remain requiring further investigation.
Highlights
Natural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits
A threshold of -1.5 (2.8-fold decrease in signal) was applied to the log2-fold change based on the plots as it produced a suitable False Discovery Rate (FDR - the proportion of false positives among the called Single Feature Polymorphism (SFP)) across the 12 accessions
The False Negative Rates (FNRs defined as the proportion of false negatives among all polymorphic probes) were estimated to be between 60% and 70% when compared to the 2010 dataset
Summary
Natural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits. Natural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation in morphological, developmental, metabolic, resistance and reproductive traits [6]. Major candidate genes controlling flowering time and vernalisation response have been identified and allelic variation segregating at these loci shows evidence of positive Darwinian selection [10,11,12]. A similar variation in flowering time was observed in other species, indicating that latitudinal pattern does not result from past historical processes like the re-colonization of glacial habitats and the fixation of new mutations by genetic drift, but resembles local adaptation. Genes that mediate resistance to pathogens (R genes) are well known to be highly polymorphic in A. thaliana [13] and indications of various modes of selection acting on these genes have been obtained [13,14,15,16,17,18,19,20]
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