Comparative Effects of Radiation Mutagenesis and Somaclonal Variation Breeding on the Genetics and Transcriptomic Defense Response to Fusarium Wilt of Banana

Banana Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), poses a severe threat to global banana production, and breeding resistant cultivars remains the most effective control strategy. Mutation breeding, including radiation mutagenesis and somaclonal variation, has become a primary approach for developing resistant germplasm in triploid Cavendish bananas. However, whether secondary bud-sport selection from resistant somaclonal lines inadvertently compromises original resistance mechanisms at the molecular level remains poorly understood. In this study, we generated 44 mutants from Baxi jiao via 60Co γ-irradiation and selected five lines with distinct phenotypic variations. We also collected somaclonal variant lines GCTCV-218, GCTCV-119, GCTCV-105, their bud-sport derivatives (NK_No.1, NTH, RK_No.1), and the radiation-induced resistant mutant ‘Zhongre No.1’. Using whole-genome resequencing and transcriptome analysis, we systematically compared the genetic and transcriptomic outcomes of these breeding strategies. Radiation mutagenesis induced substantial genomic structural variations and generated novel expression patterns of defense-related genes. In contrast, while bud-sport derivatives of GCTCV-218 remained genetically similar to their parent, they exhibited significant downregulation or loss of key resistance gene expression, particularly PR-1 family members. Our findings reveal that phenotype-driven somaclonal selection can inadvertently erode original resistance mechanisms, and we recommend prioritizing radiation mutagenesis for developing banana cultivars with stable and durable resistance to Foc TR4.