The genomics and physiology of abiotic stressors associated with global elevation gradients inArabidopsis thaliana

Abstract

Arabidopsis thaliana has a wide elevational range and much of its diversity may be associated with local adaptation to elevation. We took a multi-regional view of the genomics and physiology of elevational adaptation in Arabidopsis, with >200 ecotypes, including 17 newly collected from Africa. We measured plant responses to potential high elevation stressors: low pCO2, high light, and night freezing and conducted genome-wide association studies (GWAS). We found evidence of an adaptive cline in the western Mediterranean with low δ13C/early flowering at low elevations to high δ13C/late flowering at high elevations. By contrast, central Asian high elevation ecotypes flowered earlier. Antioxidants and pigmentation under high light and freezing showed regional differentiation but not elevational clines and may be associated with maladaptive plasticity. We found natural variation in non-photochemical quenching (NPQ) kinetics in response to chilling and fluctuating light, though with an unclear role in local adaptation. There were several candidate genetic loci mapped, including the ascorbate transporter PHT4;4 (associated with antioxidants) that influences the xanthophyll cycle, and may be involved in local adaptation to Morocco. Our study shows how the ecological strategies and genetic loci causing local adaptation to elevation change across regions and contribute to diversity in Arabidopsis.

Climate biogeography ofArabidopsis thaliana:linking distribution models and individual variation

“…We developed a set of high-quality occurrence data ( i.e . species ID verified and location checked, N=4,024) from published research (Durvasula et al, 2017; Hsu et al, 2019; Mandáková et al, 2017; Zeng et al, 2017; Zou et al, 2017), publicly available herbarium and germplasm accessions with known collection locations (Alonso-Blanco et al, 2016; DeLeo et al, 2020), and some of our recent field collections in East Africa (Gamba et al, 2022). These span a period of 1794 - 2018.…”

Estimating scale-specific and localized spatial patterns in allele frequency

“…By contrast, imposing a grid on this landscape, or using national political boundaries to calculate F ST could easily miss the signal as did Horton et al [40]. The climate gradients driving this variation are also complicated and non-monotonic [39, 41], making it challenging for genotype-environment association approaches. At the ∼ 1359 km scale, the #4 locus and SNP (Figure 7B) was on chromosome 5, 648 bp upstream from SNRK2-3, which is in the family of Snf1-related kinases2 and plays an important role in signaling in response to the key abiotic stress response hormone abscisic acid (ABA) [42, 43].…”

“…By contrast, imposing a grid on this landscape, or using national political boundaries to calculate F ST could easily miss the signal as did Horton et al (2012). The climate-allele frequency associations for DOG1 are also complicated and non-monotonic (Gamba et al 2022; Martínez-Berdeja et al 2020), making it challenging for genotype-environment association approaches (Jesse R Lasky, Emily B Josephs, and Morris 2023).…”

Climate biogeography of Arabidopsis thaliana: Linking distribution models and individual variation

“…Zou et al (2017) also did not identify the African refugia (except for a small region in SE Africa) and potential refugia in mountains of SE Asia. Arabidopsis housed in its lower latitude populations (Durvasula et al, 2017;Gamba et al, 2022;Hsu et al, 2019;Lee et al, 2017;Zou et al, 2017) the conservation of these populations could benefit plant biology research.…”