Leaf transcriptome differences between diploid and tetraploid bahiagrass

Polyploid individuals of the subtropical forage grass Paspalum notatum Flüggé (bahiagrass) exhibit distinct phenotypes, including apomixis, enhanced vigor, gigas effects, and increased stress tolerance. While apomixis-based breeding programs supported by molecular tools have improved agronomic traits such as growth habit, forage dry matter, and lipid profile, a genome-wide understanding of ploidy-induced transcriptomic changes is still lacking. In this study, we aimed to generate a comprehensive reference catalog of transcripts differentially expressed in the leaves of diploid and tetraploid individuals, characterize genome responses to polyploidy, and identify candidate genes for breeding. Our results reveal distinct transcriptomic profiles in polyploids, with significant impacts on development, redox homeostasis, and photosynthesis-patterns consistent with those observed in other species. Gene ontology enrichment analyses highlighted key categories related to stress responses and signaling pathways. We also identified critical breeding targets, including transcription factors and hormone-related genes. Co-expression network analysis uncovered 532 master regulators affected by genome doubling, with non-random distribution across the genome and hotspot clustering in specific chromosomes. Overall, our findings provide novel insights into the molecular consequences of polyploidy in P. notatum, offering a valuable resource for molecular breeding programs aimed at improving stress tolerance, vigor, and other desirable traits.