Pangenomic characterization and grain-development expression analysis of the OVATE gene family in sorghum

The OVATE family proteins (OFPs) are plant-specific regulators that modulate organ morphogenesis and grain development. To elucidate their roles in sorghum (Sorghum bicolor L.) grain development, we performed a pan-genome-informed comparative analysis of the OFP family using 17 published sorghum genomes and identified 498 SbOFP genes. These 498 genes were classified into 35 SbOFP orthologous gene families, which were grouped into 5 Core, 9 Softcore, and 21 Shell families based on presence/absence variation (PAV). Collinearity and Ka/Ks analyses showed that 2 Softcore (OFP7, OFP13) and 3 Shell (OFP25, OFP26, OFP30) members exhibited elevated pairwise Ka/Ks ratios in subsets of inter-accession comparisons, whereas the majority of SbOFPs evolved under purifying selection during sorghum evolution. Core OFP genes were consistently retained in all 17 accessions (at least one copy per genome) and exhibited higher sequence stability than Shell members. SbOFP genes were predominantly expressed during seed and inflorescence development. In addition, SbOFP promoters contain abundant hormone-responsive and grain development-related cis-acting elements. Exogenous hormone treatment further showed that SbOFP genes exhibited expression changes in response to ABA, BR, MeJA, and IAA, and that the response patterns were broadly consistent with the presence of corresponding hormone-responsive cis-elements in their promoters. Grain transcriptome analysis identified SbOFP14 and SbOFP15 as dominantly expressed members throughout grain development. Weighted gene co-expression network analysis revealed hub SbOFP genes co-expressed with NAC, MYB, MADS, and bHLH transcription factors, among which SbOFP32 and SbOFP13 showed the highest connectivity. These transcription factors are candidate partners whose expression covaries with that of SbOFP hub genes during grain development. These findings provide the theoretical basis for further elucidating the molecular mechanism of SbOFP genes in sorghum grain development and hormone signal regulation, and lay the foundation for genetic improvement of sorghum grain traits.