Transposon-associated polymorphisms of stress-responsive gene promoters in natural variants of Arabidopsis thaliana

Abstract

Genetic diversity caused by transposable element movement can play an important role in plant adaptation to local environments. Regarding genes, transposon-induced alleles were mostly related to gene bodies and a few of them to promoter areas. In this study, the promoter regions of 9 stress-related genes were searched for transposable element insertions in 12 natural variants of A. thaliana. The promoter screening was performed via PCR amplification with primers designed to flank transposable element insertions in the promoter areas of the reference accession Col-0. Transposable element -associated insertion/deletion (indel) polymorphisms were identified in 7 of the 12 promoter loci across studied accessions that can be developed further as molecular markers. The transposable element absence in the promoter regions of orthologous genes in A. lyrata indicated that the insertion of these transposable elements in A. thaliana lineage had occurred after its divergence from A. lyrata. Of the genes having indel polymorphic promoters, two genes CML41 (Calmodulin-like protein 41) and CHAP (chaperone protein dnaJ-related) were further analyzed in the accessions Col-0, Ws, Shahdara and Pirin. The observed promoter indel polymorphisms were linked to altered gene expression patterns in the four accessions that were laboratory-grown at 21°C and 36°C. The collected data can be a starting point for gene expression profiling studies under conditions resembling the natural habitats of accessions.