Arabidopsis halleri: a perennial model system for studying population differentiation and local adaptation.

Mie N Honjo,Hiroshi Kudoh,Xavier Picó

doi:10.1093/aobpla/plz076

Abstract

Local adaptation is assumed to occur when populations differ in a phenotypic trait or a set of traits, and such variation has a genetic basis. Here, we introduce Arabidopsis halleri and its life history as a perennial model system to study population differentiation and local adaptation. Studies on altitudinal adaptation have been conducted in two regions: Mt. Ibuki in Japan and the European Alps. Several studies have demonstrated altitudinal adaptation in ultraviolet-B (UV-B) tolerance, leaf water repellency against spring frost and anti-herbivore defences. Studies on population differentiation in A. halleri have also focused on metal hyperaccumulation and tolerance to heavy metal contamination. In these study systems, genome scans to identify candidate genes under selection have been applied. Lastly, we briefly discuss how RNA-Seq can broaden phenotypic space and serve as a link to underlying mechanisms. In conclusion, A. halleri provides us with opportunities to study population differentiation and local adaptation, and relate these to the genetic systems underlying target functional traits.

Highlights

One of the most fascinating observations on plants in natural habitats is the spatial co-variation between functional traits and natural environments
Local adaptation refers to the population differentiation that is attributable to adaptation to local biotic and abiotic environments
To confirm whether the observed population differentiation is the result of local adaptation, the presence of home-site advantage needs to be established by performing a reciprocal transplant experiment; plants from a particular local population have a higher fitness than plants from another population in the original habitat (Kawecki and Ebert 2004)

Summary

Introduction

One of the most fascinating observations on plants in natural habitats is the spatial co-variation between functional traits and natural environments. A genome scan study has been conducted using five populations of A. halleri in the Alps, ranging from 790 to 2308 m in altitude, to characterize genetic variation and identify genes associated with climatic variation (Fischer et al 2013) They pooled population samples (20 individual plants per population) for whole-genome sequencing (Pool-Seq) and estimated allele frequency of populations at SNP loci. The knowledge on the actual genes involved in hyperaccumulation and tolerance could provide us with a great advantage in studying population differentiation and local adaptation in A. halleri Epigenetic modifications, such as DNA methylation and posttranscribed histone modification, determine chromatin states that alter gene expression, and can play a critical role in the regulation of phenotypes in response to local environments. It is noteworthy that methods to analyse the epigenome of A. halleri under field conditions have become available; analyses on histone modifications using chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR) or next-generation sequencing (ChIP-Seq), and DNA methylation using bisulphite sequencing (Nishio et al 2016; Ito et al 2019)

Conclusions

Findings

Literature Cited