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Male sterility (MS) caused by aborted pollen is a vital germplasm resource. In this study, metabolomic, transcriptomic, and proteomic analyses were performed to investigate the molecular regulatory mechanism of cytoplasmic male sterility (CMS) in the flower buds of the male sterile line 09-05A and its maintainer line, 09-05B, of Brassica juncea. Our metabolomic analysis revealed that 41 metabolites involved in pollen development and male fertility formation were differentially accumulated between 09-05A and 09-05B at the bi-nucleate stage of B. juncea. Integrated omics indicated that the expression of key genes and proteins in the amino acid and phenylpropanoid metabolic pathways was remarkably downregulated in the flower buds of 09-05A. Furthermore, the abnormal expression of key transcription factor (TF) genes related to tapetum development and pollen wall formation may affect pollen development in the 09-05A CMS line. The results indicated that the downregulated expression level of critical genes and proteins in amino acid metabolism; phenylpropanoid synthesis; and TF genes, such as shikimate kinase, phenylalanine ammonia-lyase, and MYB103, may have led to impaired tapetum and pollen wall development, thereby causing pollen abortion in 09-05A. This study provides new insights into the metabolic and molecular regulatory mechanisms underlying the formation of CMS in B. juncea and lays a foundation for detailed studies on the identity and characteristics of MS-related genes.
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