Reassessment of a GWAS study of submergence survival in Arabidopsis highlights new genetic hubs and pathways involved in stress tolerance
- 1Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan
- 2Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan
Abstract
Climate change threatens global crop productivity, making it crucial to understand the genetic basis of plant stress tolerance. A decade ago, a genome-wide association study (GWAS) in Arabidopsis thaliana identified genetic loci linked to survival under submergence. Since then, genomic resources have expanded. This study reanalyzes that original phenotypic dataset using updated, high-density SNP databases and other platforms to uncover new genetic components of submergence tolerance. Our reassessment successfully recovered 15 of the 20 previously reported SNPs and identified locus-level concordance for these previously reported SNPs regions and expanded the candidate list with an additional 104 new genes. These genes participate in biological pathways coherent for submergence survival, including cell wall/cytoskeleton remodeling, reactive oxygen species management, hormone signaling (ethylene, auxin, and ABA), and energy-saving metabolic reprogramming involving nucleotide salvage, translational control, and C:N management. Notably, we identify ten overlapping genetic signals between analyses, including a histidyl-tRNA synthetase (HRS1) and an uncharacterized ethylene-responsive factor (ERF17), and signals in the long arm of Chromosome 5, suggesting putative integrative nodes. This study demonstrates that reassessing existing GWAS data with updated models, cross-platform validation, and transcriptional filtering can expand biologically relevant gene lists for future experimental validation and crop improvement.
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BibTeX
@article{zilligutierrez2026reassessment,
title = {{Reassessment of a GWAS study of submergence survival in Arabidopsis highlights new genetic hubs and pathways involved in stress tolerance}},
author = {Saribel Zilli-Gutiérrez and Karla Denisse Abad-Alfonso and Ariana Arlene Huerta-Heredia and Blanca Estela Barrera-Figueroa and Julián Mario Peña-Castro},
journal = {Discover Plants},
year = {2026},
month = oct,
doi = {10.1007/s44372-026-00956-8},
url = {https://doi.org/10.1007/s44372-026-00956-8},
note = {CC BY},
}
RIS
TY - JOUR
TI - Reassessment of a GWAS study of submergence survival in Arabidopsis highlights new genetic hubs and pathways involved in stress tolerance
AU - Saribel Zilli-Gutiérrez
AU - Karla Denisse Abad-Alfonso
AU - Ariana Arlene Huerta-Heredia
AU - Blanca Estela Barrera-Figueroa
AU - Julián Mario Peña-Castro
PY - 2026
DA - 2026/10/25
JO - Discover Plants
DO - 10.1007/s44372-026-00956-8
UR - https://doi.org/10.1007/s44372-026-00956-8
AB - Climate change threatens global crop productivity, making it crucial to understand the genetic basis of plant stress tolerance. A decade ago, a genome-wide association study (GWAS) in Arabidopsis thaliana identified genetic loci linked to survival under submergence. Since then, genomic resources have expanded. This study reanalyzes that original phenotypic dataset using updated, high-density SNP databases and other platforms to uncover new genetic components of submergence tolerance. Our reassessment successfully recovered 15 of the 20 previously reported SNPs and identified locus-level concordance for these previously reported SNPs regions and expanded the candidate list with an additional 104 new genes. These genes participate in biological pathways coherent for submergence survival, including cell wall/cytoskeleton remodeling, reactive oxygen species management, hormone signaling (ethylene, auxin, and ABA), and energy-saving metabolic reprogramming involving nucleotide salvage, translational control, and C:N management. Notably, we identify ten overlapping genetic signals between analyses, including a histidyl-tRNA synthetase (HRS1) and an uncharacterized ethylene-responsive factor (ERF17), and signals in the long arm of Chromosome 5, suggesting putative integrative nodes. This study demonstrates that reassessing existing GWAS data with updated models, cross-platform validation, and transcriptional filtering can expand biologically relevant gene lists for future experimental validation and crop improvement.
SN - 3005-1207
ER -