A Tale of Taste: Comparative Transcriptome Associated with Grain Quality in Brazilian Rice Cultivars

Rice (Oryza sativa L.) is a major crop and a strategic component of global food security. Brazil is the largest rice producer outside Asia, with production ranging from 10 to 12.7 million tons between 2020 and 2024. Grain quality is a key trait in rice breeding and cultivar adoption. It is determined by physical, chemical and cooking properties, particularly amylose content. Its genetic control involves major genes, QTLs, regulatory networks and environmental interactions. Transcription factors (TFs) are components of these networks. This study aimed to identify expressed TFs during grain formation in BR-IRGA 409 (high-quality) and BR-IRGA 410 (low-quality) cultivars. Transcriptome sequencing was performed on grains collected at 0, 8, and 16 days post anthesis. A total of 52 DEGs-TFs from 19 families were identified, with ERF, MYB and bHLH being the most represented. Eleven TFs were detected at 0 DPA, 37 at 8 DPA and 16 at 16 DPA. Expression patterns shifted temporally, with higher expression predominating in BR-IRGA 409 at 0 DPA and in BR-IRGA 410 at later stages. The Os03g0188400 (OsbHLH044/OsbHLH96) gene locus was particularly notable due to its association with grain chalkiness. These results reveal dynamic transcriptional regulation during grain formation and identify candidate TFs for molecular-marker development in rice breeding.