Transcriptome and Gene Co-Expression Network Analysis Identifying Differentially Expressed Genes and Signal Pathways Involved in the Height Development of Banana (Musa spp.)

Plant height is an important and valuable agronomic trait associated with yield and resistance to abiotic and biotic stresses. Dwarfism has positive effects on plant development and field management, especially for tall monocotyledon banana (Musa spp.). However, several key genes and their regulation mechanism of controlling plant height during banana development are unclear. In the present study, the popular cultivar ‘Brazilian banana’ (‘BX’) and its dwarf mutant (‘RK’) were selected to identify plant height-related genes by comparing the phenotypic and transcriptomic data. Banana seedlings with 3–4 leaves were planted in the greenhouse and field. We found that the third and fourth weeks are the key period of plant height development of the selected cultivars. A total of 4563 and 10507 differentially expressed genes (DEGs) were identified in the third and fourth weeks, respectively. Twenty modules were produced by the weighted gene co-expression network analysis (WGCNA). Eight modules were positively correlated with the plant height, and twelve other modules were negatively correlated. Combining with the analysis of DEGs and WGCNA, 13 genes in the signaling pathway of gibberellic acid (GA) and 7 genes in the signaling pathway of indole acetic acid (IAA) were identified. Hub genes related to plant height development were obtained in light of the significantly different expression levels (|log2FC| ≥ 1) at the critical stages. Moreover, GA3 treatment significantly induced the transcription expressions of the selected candidate genes, suggesting that GA signaling could play a key role in plant height development of banana. It provides an important gene resource for the regulation mechanism of banana plant development and assisted breeding of ideal plant architecture.