TY - JOUR
T1 - Combined genomics to discover genes associated with tolerance to soil carbonate
AU - Busoms, Silvia
AU - Tolrà Pérez, Roser
AU - Poschenrieder, Charlotte
AU - Huang, Xin-Yuan
AU - Yant, Levi
AU - Salt, David E.
N1 - Publisher Copyright:
© 2023 The Authors. Plant, Cell & Environment published by John Wiley & Sons Ltd.
PY - 2023/12
Y1 - 2023/12
N2 - 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 and T6 seedlings were grown hydroponically under control (pH 5.9) and bicarbonate conditions (10 mM NaHCO, pH 8.3) to obtain ionomic profiles and conduct transcriptomic analysis. In parallel, A1 and T6 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 versus T6 comparison under bicarbonate stress, mainly involved in iron, nitrogen and carbon metabolism, hormones and glycosylates biosynthesis. Based on A1 and T6 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.
AB - 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 and T6 seedlings were grown hydroponically under control (pH 5.9) and bicarbonate conditions (10 mM NaHCO, pH 8.3) to obtain ionomic profiles and conduct transcriptomic analysis. In parallel, A1 and T6 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 versus T6 comparison under bicarbonate stress, mainly involved in iron, nitrogen and carbon metabolism, hormones and glycosylates biosynthesis. Based on A1 and T6 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.
KW - Arabidopsis
KW - BSA-Seq: transcriptomics
KW - bicarbonate stress
KW - calcareous soil
UR - http://www.scopus.com/inward/record.url?scp=85167683879&partnerID=8YFLogxK
UR - https://www.mendeley.com/catalogue/92f5fa59-3b22-3c8e-87d0-40198f5f9720/
U2 - 10.1111/pce.14691
DO - 10.1111/pce.14691
M3 - Article
C2 - 37565316
SN - 0140-7791
VL - 46
SP - 3986
EP - 3998
JO - Plant, Cell and Environment
JF - Plant, Cell and Environment
IS - 12
ER -