Abstract
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.