Full species-wide leaf and seed ionomic diversity of Arabidopsis thaliana

Abstract

Summary Soil is a heterogenous reservoir of essential elements needed for plant growth and development. Plants have evolved mechanisms to balance their nutritional needs based on availability of nutrients. This has led to genetically-based variation in the elemental composition ‘ionome’, of plants, both within and between species. We explore this natural variation using a panel of wild-collected, geographically widespread Arabidopsis thaliana accessions from the 1001 Genomes Project including over 1,135 accessions, and the 19 parental accessions of the Multi-parent Advanced Generation Inter-Cross (MAGIC) panel, all with full-genome sequences available. We present an experimental design pipeline for high-throughput ionomic screenings and analyses with improved normalisation procedures to account for errors and variability in conditions often encountered in large-scale, high-throughput data collection. We report quantification of the complete leaf and seed ionome of the entire collection using this pipeline and a digital tool-IonExplorer to interact with the dataset. We describe the pattern of natural ionomic variation across the A. thaliana species and identify several accessions with extreme ionomic profiles. It forms a valuable resource for exploratory QTL, GWA studies to identify genes underlying natural variation in leaf and seed ionome and genetic adaptation of plants to soil conditions.

Plant phenotyping relevance

大規模植物イオノーム取得のための高スループット実験・正規化パイプラインとデジタルツールを開発し、再利用可能なデータ資源として提示しているため、測定法が中心的です。

Code and data availability

The paper's species-wide leaf and seed ionomic dataset for 1,135 A. thaliana accessions is made publicly accessible through the authors' interactive web tool Ion Explorer, which allows filtering, analysis, and download of the complete dataset as .csv files. This is a paper-specific, public, actionable asset. No author-