Traversing the effects of ploidy changes in different Eragrostis curvula genotypes through high‐throughput RNA sequencing

Polyploidization has played a key role in plant genome evolution. Eragrostis curvula (Schrad.) Ness, a perennial forage grass species of the Poaceae family, is an excellent model for investigating genome duplication due to its natural variation in ploidy levels. To explore the transcriptomic consequences of polyploidy, we performed high-throughput RNA-Seq on leaf tissue from 10 E. curvula genotypes ranging from diploid to octoploid. Differential expression analyses revealed that the number of differentially expressed genes increased with increasing ploidy, suggesting a rewiring of the gene regulatory network. Several putative genes associated with stress tolerance and epigenetic regulation were modulated at higher ploidy levels. Forage digestibility and saccharification efficiency were likely altered at higher ploidy levels, mainly due to the upregulation of putative genes involved in lignin biosynthesis, cell wall remodeling, and polysaccharide metabolism. Our results may reveal a fine-tuning regulation favoring stress tolerance over forage digestibility. The analysis of the core set of 433 Ploidy_vs_2x DEGs, consistently expressed in a polyploidy-sensitive manner, revealed upregulation of genes involved in the ubiquitination pathway, stress response, cell wall remodeling, hormonal regulation, and terpenoid biosynthesis. Ploidy-dependent transcriptional responses were also observed in the patterns of transcription factor families, underlining a different reprogramming of the transcriptional network at each ploidy level. An integrated network-based approach combining WGCNA and SWIM (SWItchMiner) identified a predicted master regulator target gene putatively associated with increased forage digestibility. Our findings provide valuable insights into the molecular mechanisms underlying polyploidization in E. curvula, with implications for breeding strategies to balance stress tolerance and biomass digestibility.