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Background: The pod shattering (PS) trait negatively affects the crop yield in rapeseed especially under dry conditions. To better understand the trait and cultivate higher resistance varieties, it's necessary to identify key genes and unravel the PS mechanism thoroughly. Results: In this study, we conducted a comparative transcriptome analysis between two materials significantly different in silique shatter resistance lignin deposition and polygalacturonase (PG) activity. Here, we identified 10,973 differentially expressed genes at six pod developmental stages. We found that the late pod development stages might be crucial in preparing the pods for upcoming shattering events. GO enrichment results from K-means clustering and weighed gene correlation network analysis (WGCNA) both revealed senescence-associated genes play an important role in PS. Two hub genes Bna.A05ABI5 and Bna.C03ERF/AP2-3 were selected from the MEyellow module, which possibly regulate the PS through senescence-related mechanisms. Further investigation found that senescence-associated transcription factor Bna.A05ABI5 upregulated the expression of SAG2 and ERF/AP2 to control the shattering process. In addition, the upregulation of Bna.C03ERF/AP2-3 is possibly involved in the transcription of downstream SHP1/2 and LEA proteins to trigger the shattering mechanism. We also analyzed the PS marker genes and found Bna.C07SHP1/2 and Bna.PG1/2 were significantly upregulated in susceptible accession. Furthermore, the role of auxin transport by Bna.WAG2 was also observed, which could reduce the PG activity to enhance the PS resistance through the cell wall loosening process. Conclusion: Based on comparative transcriptome evaluation, this study delivers insights into the regulatory mechanism primarily underlying the variation of PS in rapeseed. Taken together, these results provide a better understanding to increase the yield of rapeseed by reducing the PS through better engineered crops. [ABSTRACT FROM AUTHOR]