Pan-genomic analysis of Cation/H+ exchanger (CAX) family variation in soybean reveals structural and functional insights into heavy metal stress response

Pan-genomic analysis of Cation/H+ exchanger (CAX) family variation in soybean reveals structural and functional insights into heavy metal stress response

Cadmium (Cd), a pervasive environmental toxicant, jeopardizes ecosystem integrity and human health. The cation/H+ exchanger (CAX) family, a key class of metal transporters, mediates Cd uptake, translocation, and detoxification in plants. Despite extensive soybean genomic studies, systematic pan-geno...

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Bibliographic Details
Main Authors: Yonggang Gao, Cheng Zhao
Format: Article
Language:English
Published: Elsevier 2025-10-01
Series:Journal of Agriculture and Food Research
Subjects:
Glycine max
CAX gene family
Structural variation
Pan-genome
Heavy metal stress
Gene expression
Online Access:http://www.sciencedirect.com/science/article/pii/S2666154325005800
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Summary:Cadmium (Cd), a pervasive environmental toxicant, jeopardizes ecosystem integrity and human health. The cation/H+ exchanger (CAX) family, a key class of metal transporters, mediates Cd uptake, translocation, and detoxification in plants. Despite extensive soybean genomic studies, systematic pan-genomic exploration of CAX genes remains limited. Here, we conducted a comprehensive pan-genome analysis across 35 high-quality soybean genomes, identifying 30 CAX genes implicated in stress response, including 2 core genes conserved in all accessions. Genomic structural variation (SV) analysis revealed 299 SVs overlapping with 22 CAX loci and their flanking regions (±2 kb). Notably, SVs significantly modulated NCL2 expression (P < 0.05). Structural dissection of NCL2 showed that 53 % of soybean genomes retain domains identical to the reference (Wm82.a4), while atypical variants exhibit expanded exons and motifs. Expression profiling demonstrated that CAX5, NCL2, CCX2, and CCX8 transcripts were significantly elevated in typical vs. atypical structural genomes (P < 0.01). Furthermore, CCX7, CAX1, CAX5, and CAX6 displayed dynamic responses to dehydration/salt stress. Our findings propose a TF-CAX regulatory module fine-tuning heavy metal stress adaptation, providing a foundational resource for soybean functional genomics and stress-resilient crop design.
ISSN:2666-1543

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