PJB-2023-411
Identification of seed germination process Co-expression Modules and Hub Genes in Brassica napus L by WGCNA
TIANYUAN XUE
Abstract
Abstract
To investigate the genes involved in the seed germination process in Brassica napus L, We chose the top 25 000 genes with high expression variation among three independent samples after filtering out the low-expression genes (c032, c033, c129). Using transcriptome data from Brassica napus L seeds at various stages of germination, a weighted gene co-expression network analysis was performed (WGCNA). The findings revealed that a total of 23 gene co-expression modules were created, five of which were significantly connected to seed germination in Brassica napus L. The darkoliveveen4 and pink modules, in particular, were favorably connected with seed germination for 72 hours, whereas the coral1 module was positively correlated with seed germination for 12 hours. Seed germination 36 hours was inversely linked with the indianared4 and cyan modules. The researchers looked on three distinct modules that were positively linked with seed germination. The results of the functional enrichment analysis revealed that the three specific modules positively related to seed germination were significantly enriched in several seed germination-related entries, including transmembrane transport, regulation of cellular catabolic processes, secondary metabolic processes, and tetrapyrrole biosynthetic processes. The core genes in the specificity module were chosen using Cytoscape software, and their roles were predicted using online blast. The core genes in the coral1 module might be engaged in processes including lipid transfer proteins, auxin response proteins, and indole-3-acetic acid amino synthase. The core genes of the darkolivegreen4 module may be involved in biological processes like purine permease and mitogen-activated protein kinase; the core genes of the pink module may be involved in biological processes like aquaporins, chlorophyll biosynthesis, chloroplast photosystem I reaction center subunit III, and other biological processes; and finally, 30 potential hub genes related to Brassica napus L germination were discovered, but their specific functions are still unknown.
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