Enhanced genome integrity maintenance and few large stress-mitigating changes in Arabidopsis halleri extreme-habitat local adaptation

Heavy metal-rich toxic soils and ordinary soils are both natural habitats of Arabidopsis halleri, different from closely related plant species including A. thaliana. Here we demonstrate enhanced Cd hypertolerance and attenuated Cd accumulation in plants originating from the most highly heavy metal-contaminated A. halleri site in Europe at Ponte Nossa (Noss/IT), compared to A. halleri from non-metalliferous (NM) sites at a small and a larger phylogenetic distance. In the two populations from NM sites, hundreds of Cd-responsive transcripts mostly reflect the activation of Fe deficiency responses, whereas no single transcript showed differential abundance between Cd-exposed and untreated control plants from the metalliferous (M) site Noss. Among thousands of transcripts exhibiting between-population differential abundance in vegetative stage tissues, meiotic cell cycle functions were overrepresented, with an activation in plants from Noss. Between-population differences in transcript levels were highest for ARGONAUTE 9 (AGO9) and the synaptonemal complex transverse filament protein-encoding genes ZYP1a/b, which are pre-meiosis- and meiosis-specifically expressed, respectively, in A. thaliana. Moreover, transcript levels of IRON-REGULATED TRANSPORTER 1 (IRT1) were much lower in Noss and those of HEAVY METAL ATPASE 2 (HMA2) were far higher compared to both Pais and Wall, largely explaining between-population differences in Cd handling. Immunoblots for ZYP1 and IRT1 validated our observations at the protein level. In summary, plant adaptation to extreme abiotic stress is associated with globally enhanced somatic genome integrity maintenance including previously unsuspected gene functions, as well as a small number of constitutive alterations in stress-related functional networks.