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Systems-Level Developmental Reprogramming Under Waterlogging Stress in Cowpea Revealed by Integrated Phenotypic,
Mohammad A Ghanbari1, Omolayo J Olorunwa2, Mohit Verma1,3
1Institute for Genomics, Biocomputing & Biotechnology, Mississippi State, Mississippi, USA.
Plant, Cell & Environment
|June 25, 2026
Summary
Cowpea genotypes show varying waterlogging tolerance, with the tolerant UCR369 genotype exhibiting superior physiological recovery and dynamic transcriptional adjustments. These findings provide a framework for breeding climate-resilient cowpea varieties for waterlogged regions.
Area of Science:
- Plant Biology
- Genetics
- Agronomy
Background:
- Cowpea (Vigna unguiculata (L.) Walp.) is a vital climate-resilient legume, crucial for global food security.
- Increasing climate-driven flooding and waterlogging threaten cowpea productivity and seed quality in vulnerable regions.
Purpose of the Study:
- To investigate the transcriptional responses of different cowpea genotypes to waterlogging across various growth stages.
- To identify key genes, pathways, and molecular mechanisms underlying waterlogging tolerance in cowpea.
Main Methods:
- RNA-sequencing (RNA-seq) to analyze gene expression profiles under waterlogging stress.
- Integration of phenotypic, physiological, biochemical, yield, and seed-quality data with transcriptomic analysis.
- Utilized differential expression analysis, KEGG pathway enrichment, transcription factor profiling, WGCNA, and XGBoost machine learning.
Main Results:
- The tolerant genotype UCR369 showed enhanced physiological recovery and transcriptional dynamism compared to EpicSelect.4.
- Waterlogging induced stage- and genotype-dependent alterations in metabolic pathways (phenylpropanoid, flavonoid, carbohydrate, lipid biosynthesis) and physiological traits.
- Key transcription factor families (MYB, bHLH, ERF/AP2, WRKY, HD-ZIP, HSF) were differentially activated, suggesting roles in stress signaling and protection.
Conclusions:
- A systems-level framework for cowpea waterlogging tolerance was established, highlighting cuticle/barrier remodeling, carbohydrate/redox reprogramming, and stress signaling.
- Identified specific genes (LTP3, CER1/CER22, CASPL1D1, NIA2/NR2, ICL, SAG12, HSP21, ACS6) as potential targets for breeding.
- Findings provide biologically grounded targets for marker development and functional validation to enhance cowpea resilience in waterlogged environments.
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