The parallel mutation of tea stems and leaves is a new type of mutation, which is a high-quality material for developing bud tea, special tea products and edible and ornamental tea. Therefore, studying the causes of parallel variation in tea plants and mining its key control genes can provide new targets for the current diversified needs of tea breeding. In this study, the mutant stems and leaves were used as the research materials, and the normal stems and leaves were used as the control. The paraffin section method was used to observe the tissue structure, and the transcriptome sequencing technology and WGCNA analysis technology were used to excavate the key genes of the parallel phenomenon of stems and leaves in tea plants. The observation results of tissue structure show that parallel variation could not only increase the number of tea buds and yield, but also effectively increase the area and number of vessels in stems and leaves of tea plants, and improve the photosynthetic capacity and stress resistance of tea plants. The transcriptome sequencing study shows that the differential genes were mainly enriched in the two pathways: ABC transporters and plant-pathogen interaction, and 9 key genes were analyzed and mined. A total of 26 co-expression modules were identified by WGCNA, two trait-related specific modules were mined, and 8 core genes were screened. These 17 key genes are regulated in three forms: ABCB (ATP binding cassette subfamily B) and ABCC (ATP binding cassette subfamily C) families, RAC3 (RAC family small GTPase3), and FKBP (FK506-binding proteins). These genes are mainly involved in auxin and cell division. Genes such as ABCG34 (ATP binding cassette subfamily G34), CDPK2 (Calcium-dependent protein kina2), KCS2 (β-ketoacyl-CoA synthase2), LAC11 (Laccase11), EP1 (Epidermis-specific secreted glycoprotein1) and LTP (Lipid transfer protein) are involved in the biosynthesis of cellulose, lignin and pectin in the cell wall of tea plants, and regulate cell morphogenesis by regulating the synthesis and extension direction of cell wall, so as to realize the parallel differentiation of tea stems and leaf veins. Dimethylmenaquinone methyltransferase and histone-lysine N-methyltransferase regulate gene expression through DNA methylation, which eventually leads to the occurrence of the apparent morphology of parallel connection between tea stems and leaves.
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