Combined genomics to discover genes associated with tolerance to soil carbonate

Busoms, Silvia; Pérez‐Martín, Laura; Terés, Joana; Huang, Xin‐Yuan; Yant, Levi; Tolrà, Roser; Salt, David E.; Poschenrieder, Charlotte

Abstract

Carbonate‐rich soils limit plant performance and crop production. Previously, local adaptation to carbonated soils was detected in wild Arabidopsis thaliana accessions, allowing the selection of two demes with contrasting phenotypes: A1 (carbonate tolerant, c+) and T6 (carbonate sensitive, c−). Here, A1(c+) and T6(c−) seedlings were grown hydroponically under control (pH 5.9) and bicarbonate conditions (10 mM NaHCO3, pH 8.3) to obtain ionomic profiles and conduct transcriptomic analysis. In parallel, A1(c+) and T6(c−) parental lines and their progeny were cultivated on carbonated soil to evaluate fitness and segregation patterns. To understand the genetic architecture beyond the contrasted phenotypes, a bulk segregant analysis sequencing (BSA‐Seq) was performed. Transcriptomics revealed 208 root and 2503 leaf differentially expressed genes in A1(c+) versus T6(c−) comparison under bicarbonate stress, mainly involved in iron, nitrogen and carbon metabolism, hormones and glycosylates biosynthesis. Based on A1(c+) and T6(c−) genome contrasts and BSA‐Seq analysis, 69 genes were associated with carbonate tolerance. Comparative analysis of genomics and transcriptomics discovered a final set of 18 genes involved in bicarbonate stress responses that may have relevant roles in soil carbonate tolerance.

Citation

Busoms, S., Pérez‐Martín, L., Terés, J., Huang, X., Yant, L., Tolrà, R., …Poschenrieder, C. (2023). Combined genomics to discover genes associated with tolerance to soil carbonate. Plant, Cell and Environment, 46(12), 3986-3998. https://doi.org/10.1111/pce.14691

• Journal Article Type: Article
• Acceptance Date: Aug 1, 2023
• Online Publication Date: Aug 11, 2023
• Publication Date: 2023-12
• Deposit Date: Oct 18, 2023
• Publicly Available Date: Oct 18, 2023
• Journal: Plant, Cell & Environment
• Print ISSN: 0140-7791
• Electronic ISSN: 1365-3040
• Publisher: Wiley
• Peer Reviewed: Peer Reviewed
• Volume: 46
• Issue: 12
• Pages: 3986-3998
• DOI: https://doi.org/10.1111/pce.14691
• Keywords: bicarbonate stress, BSA‐Seq: transcriptomics, calcareous soil, Arabidopsis
• Public URL: https://nottingham-repository.worktribe.com/output/24414600
• Publisher URL: https://onlinelibrary.wiley.com/doi/10.1111/pce.14691
• Additional Information: © 2023 The Authors. Plant, Cell & Environment published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.