Phenotypic Screening and Organ-Specific Transcriptomics Unveil Diverse Salt Tolerance Responses at the Seedling Stage in Wheat (Triticum aestivum L.)

Identifying superior salt-tolerant germplasm and resistance genes is crucial, as wheat (Triticum aestivum L.) seedlings are highly vulnerable to salt stress. Here, using an optimized 150 mM NaCl treatment, we screened 137 Chinese wheat accessions via an organ-specific method. Phenotyping analysis revealed extensive organ-specific divergence, with 48.91% of accessions displaying inconsistent performance between shoot and root length. We then performed comparative transcriptomics on three representative phenotypes at the seedling stage: Gaoyou 2018, representing the salt dual-sensitive group; Huapei 5, representing the salt dual-tolerant group; and Jimai 60, representing the divergent group with higher tolerance in shoots rather than in roots. Analysis of overlapping differentially expressed genes (DEGs) across all three accessions revealed a basal stress response—characterized by induced osmotic defense and suppressed primary growth—exemplifying a classical growth–defense trade-off. Genotype-specific DEG profiling demonstrated that the divergent Jimai 60 maintains its shoot advantage by reinforcing physical barriers and inhibiting apoptosis. Conversely, transcriptomic profiling implies that the systemically tolerant Huapei 5 maintains coordinated shoot and root tolerance at the seedling stage by strongly activating below-ground Na+ homeostasis (efflux and compartmentalization) while simultaneously down-regulating non-essential immune responses to optimize defense energy reallocation. Collectively, our findings provide novel insights into the organ-differentiated salt tolerance of wheat, offering well-characterized elite germplasm and compelling genetic targets for future molecular breeding.