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.

Wheat starch granule size distribution is a critical determinant of processing quality and end-use functionality. However, conventional methods for characterizing starch granules are labor-intensive, require relatively large sample quantities, and may preferentially lose small B-type granules during starch extraction. To address these limitations, we developed SSDSG (Determination of Starch Size Distribution in Single Grains), a novel, high-throughput, image-based method for in situ and non-destructive phenotyping of starch granule size distribution at the single grain level. A morphological correction factor ($\tilde{K}=0.4113$) enabled statistical conversion to volume equivalent measurements, and the method showed a significant positive correlation with the Coulter counter reference method (R² = 0.55) across 20 wheat varieties. SSDSG characterized the temporal dynamics during grain filling and intra-spike spatial heterogeneity, providing technical support for dissecting grain development and analyzing superior and inferior grains. High-throughput screening of 1667 EMS-mutagenized lines revealed broad variation in B-type starch proportion in total starch (84.01–98.69%), which is significant for further genetics and phenotypic analysis. Moreover, the non-destructive workflow allows a single grain being used for both phenotyping and propagation. The top 10% of the 204 F₂ breeding lines, with highest B-type starch proportion, were selected and propagated for further genetic analysis. Finally, characterization of barley and 24 diverse-ploidy wheat accessions revealed that tetraploid wheat had relatively lower B-type starch proportions. This is significant for understanding starch traits evolution during wheat polyploidization. Overall, SSDSG provides a practical high-throughput platform for single-grain starch phenotyping and quality-oriented wheat breeding.