An Integrated Analysis of the Heat Response in Wheat Reveals Ploidy-Dependent Effects on Transcriptomic Reprogramming.

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 moderately in the hexaploid (37.8%), while the tetraploid showed the greatest resilience (19% reduction). Transcriptome profiling revealed ploidy-dependent 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. Gene co-expression analysis identified 12 modules linked to grain traits, underscoring the relationship between transcriptional control and phenotype. Together, these results indicate that genome complexity shapes HS responses, with polyploid species exhibiting greater resilience supported by more intricate regulatory networks. These insights provide valuable information for breeding heat-tolerant wheat varieties and understanding the role of polyploidy in stress adaptation. Overall design: Expression profiling by high throughput sequencing