Genome-wide association studies reveal genetic diversity and regulatory loci underlying dwarfing traits in banana.

Bananas (Musa ssp.) are globally important staple crops increasingly constrained by biotic stressors, climatic instability, and the high labor demands of cultivation. The genetic improvement of dwarf phenotypes offers a strategic pathway to enhance mechanization and reduce production costs. In this study, we have carried out whole-genome resequencing of 300 Musa accessions to analyze genome-wide allelic diversity and identify loci associated with shoot architecture. Our analysis uncovered extensive genetic variation within the A subgenome, pivotal for environmental adaptability, and detected introgression from Musa itinerans (subgroup A) into cultivated varieties (subgroup F), suggesting a broadened genetic base amenable to breeding. A genome-wide association study (GWAS) pinpointed MabHLH30 as a crucial gene associated plant stature. Functional validation confirmed MabHLH30 as a critical regulator of plant stature and leaf morphology. Leveraging this finding, we developed molecular markers for MabHLH30, enabling marker-assisted selection (MAS) to accelerate the breeding of compact, high-yielding cultivars. Collectively, these results provide a genomic framework for the targeted improvement of banana architecture and represent a valuable resource for cultivar development under diverse agroecological conditions.