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Combined genomics to discover genes associated with tolerance to soil carbonate
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  • Charlotte Poschenrieder,
  • Silvia Busoms,
  • Laura Pérez-Martín,
  • Joana Gelabert,
  • Xin-Yuan Huang,
  • Levi Yant,
  • Roser Tolrà,
  • David Salt E
Charlotte Poschenrieder
Universitat Autonoma de Barcelona Departament de Biologia Animal de Biologia Vegetal i d'Ecologia

Corresponding Author:[email protected]

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Silvia Busoms
Universitat Autonoma de Barcelona Departament de Biologia Animal de Biologia Vegetal i d'Ecologia
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Laura Pérez-Martín
Universitat Autonoma de Barcelona Departament de Biologia Animal de Biologia Vegetal i d'Ecologia
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Joana Gelabert
Universitat Autonoma de Barcelona Departament de Biologia Animal de Biologia Vegetal i d'Ecologia
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Xin-Yuan Huang
Nanjing Agricultural University State Key Laboratory of Crop Genetics and Germplasm Enhancement
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Levi Yant
University of Nottingham School of Life Sciences
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Roser Tolrà
Universitat Autonoma de Barcelona Departament de Biologia Animal de Biologia Vegetal i d'Ecologia
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David Salt E
University of Nottingham School of Biosciences
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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 NaHCO 3, 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 (DEGs) in A1 (c+) vs 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.
27 Jul 2023Submitted to Plant, Cell & Environment
28 Jul 2023Submission Checks Completed
28 Jul 2023Assigned to Editor
28 Jul 2023Review(s) Completed, Editorial Evaluation Pending
01 Aug 2023Editorial Decision: Accept