Abstract Introduction: Quality of bread baking is affected by gluten genes and balance between their expressions. Hence, it is necessary for a comprehensive research to study and compare all gluten genes and their regulating elements simultaneously. Objectives: The aim of this study was to evaluate the molecular mechanism of bread quality in the level of coding genes and regulating elements via comparative transcriptome analysis for two extreme wheat cultivars. Materials and methods: RNAs were extracted from grain of two wheat cultivars with high (Pishtaz) and low (Navid) bread making qualities, collected during endosperm development at five stages. mRNAs were sequenced and gluten transcripts were assessed to find differentially expressed genes. Then, transcription factors interacting gluten genes were detected and evaluated for expression. Results: Results showed that Ɣ-gliadin and LMW-GS genes had higher expression in Pishtaz and Navid, respectively. Most identified transcription factors were active at the early stage of growth and it seemed that NAC and ERF transcription factors had significant roles in regulating genes with different expressions. There was no significant difference in expression of NACs between two cultivars. It is proposed that ERF transcription factor which classified as BREB2C transcription factor could control the expression of LMW-GS genes in two cultivars and functionally act as a repressor for their target genes. Conclusion: The priority of Pishtaz in bread quality originated from high level expression of Ɣ-gliadin gene and ERF transcription factor.

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