Deciphering germination rate differences in quinoa genotypes via integrated phenotypic, structural, and transcriptomic approaches

Quinoa (Chenopodium quinoa Willd.) is a nutritionally valuable and stress-tolerant crop in which seed germination plays a critical role in seedling establishment and yield formation. However, the integrated regulatory mechanisms underlying genotypic variation in germination are not yet fully understood. Most existing studies have focused on phenotypic traits or single-omics approaches, leaving a knowledge gap in systematic analyses that combine seed coat architecture, hormone dynamics, transcriptomics, and gene co-expression networks. Phenotypic analysis showed that WT seeds achieved 100% germination at 12 h, while the moderately germination‑defective TF and the severely germination-defective TS mutants reached 92% and 29.33%, respectively. Seed coat characterization revealed that the palisade layer thickness was 13.31 μm in WT, increasing to 16.66 μm in TF and 20.07 μm in TS. Hormone dynamics monitoring indicated that GA₃ content in WT peaked at 1.859 ng·g⁻¹ at 8 h of imbibition, with a GA₃/ABA ratio of 0.53. In contrast, GA₃ levels in the TS mutant remained below 0.200 ng·g⁻¹ throughout, and the GA₃/ABA ratio stayed under 0.05. Transcriptomic and WGCNA analyses identified the Tan module, positively correlated with germination rate (r = 0.89), and the Black module, negatively correlated (r = − 0.60), and screened hub genes within the regulatory network. These results demonstrate that the coordinated actions of seed coat structure, hormone homeostasis, and transcriptional programming collectively determine the germination performance of different quinoa genotypes. This study provides multi-dimensional integrated data for deciphering the regulatory mechanisms of quinoa seed germination, and systematically clarifies how seed coat structure, hormone dynamics, and transcriptional networks synergistically regulate the germination process. These findings deepen our understanding of the biological basis of quinoa seed germination and establish a solid foundation for future functional studies and molecular improvement of germination-related traits in quinoa.