Quantitative trait loci and candidate genes underlying genotype by environment interaction in the response of Arabidopsis thaliana to drought

Drought stress was imposed on two sets of Arabidopsis thaliana genotypes grown in sand under short-day conditions and analysed for several shoot and root growth traits. The response to drought was assessed for quantitative trait locus (QTL) mapping in a genetically diverse set of Arabidopsis accessions using genome-wide association (GWA) mapping, and conventional linkage analysis of a recombinant inbred line (RIL) population. Results showed significant genotype by environment interaction (GxE) for all traits in response to different watering regimes. For the RIL population, the observed GxE was reflected in 17 QTL by environment interactions (QxE), while 17 additional QTLs were mapped not showing QxE. GWA mapping identified 58 single nucleotide polymorphism (SNPs) associated with loci displaying QxE and an additional 16 SNPs associated with loci not showing QxE. Many candidate genes potentially underlying these loci were suggested. The genes for RPS3C and YLS7 were found to contain conserved amino acid differences when comparing Arabidopsis accessions with strongly contrasting drought response phenotypes, further supporting their candidacy. One of these candidate genes co-located with a QTL mapped in the RIL population. Genome wide association studies and traditional recombinant inbred line quantitative trait loci (QTL) mapping were used to genetically dissect genotype by environment interactions of the Arabidopsis response to water availability. Many candidate genes were identified, of which two genes showed conserved differences in amino acid sequences between drought tolerant and drought sensitive accessions, supporting their candidacy. One of those two genes, associated with variation for drought related root length, co-located with a QTL for the same trait.