Multi-Level Characterization Reveals Divergent Heat Response Strategies Across Wheat Genotypes of Different Ploidy

Understanding heat stress (HS) responses across wheat species with different ploidy is crucial for breeding climate-resilient varieties. We combined field experiments with RNA sequencing to compare diploid (T. monococcum), tetraploid (T. turgidum), and hexaploid (T. aestivum) wheat during early grain filling. Under severe HS, grain yield declined most drastically in the diploid (74%) and substantially in the hexaploid (37.8%), while the tetraploid showed the greatest resilience limiting loss to only 19%. Transcriptome profiling revealed ploidy-associated reprogramming, with the hexaploid exhibiting the largest set of differentially expressed genes (2,227 vs. 859 and 757 in diploid and tetraploid, respectively). Alternative splicing patterns also diverged; notably, we detected species-specific, heat-induced exon skipping of the NF-YB transcription factor exclusively in hexaploid wheat, potentially compromising the transcription factor complex stability. Gene co-expression analysis identified 12 modules linked to grain traits, underscoring the relationship between transcriptional control and phenotype. Together, these results reveal contrasting heat response strategies among the examined genotypes. While the tetraploid genotype displayed the greatest yield resilience coupled with a streamlined transcriptional response, the hexaploid genotype engaged more extensive regulatory networks. These patterns are consistent with ploidy-associated regulatory differences, though genotype-specific factors may also contribute. These insights provide candidates for breeding heat-tolerant wheat varieties and a framework for future multi-genotype studies.