Polyploidization-Driven Functional Innovation of AGPase Small Subunit Gene APS1 Regulates Starch Biosynthesis in Banana (Musa acuminata)

Starch biosynthesis is a fundamental process influencing yield and fruit quality in banana, with ADP-glucose pyrophosphorylase (AGPase) serving as the rate-limiting enzyme catalyzing sucrose conversion into starch. However, the mechanisms underlying functional differentiation of <i>AGPase</i> family genes following polyploidization remain largely unexplored. In this study, eight <i>AGPase</i> genes, including large (<i>MaAPL</i>) and small subunit (<i>MaAPS</i>) members, were identified from the banana <i>(Musa acuminata</i>) genome, all harboring the conserved ADP-glucose pyrophosphorylase domain. Phylogenetic analysis traced their evolutionary origin to the ancient moss <i>Physcomitrella patens</i>, with polyploidization identified as the primary driver of gene family expansion. These genes exhibit conserved codon usage bias and have undergone strong purifying selection. Among them, <i>MaAPS1</i> displayed distinct functional differentiation, increased intron number, enriched promoter <i>cis</i>-elements, and significantly elevated expression-features likely contributing to its adaptation for enhanced starch accumulation in fruit. Furthermore, the MaAPS1 protein was predominately localized in the chloroplast. Functional validation supported its regulatory involvement: transient silencing in banana fruit reduced starch content, while transient overexpression in banana fruit increased starch levels. Co-expression and molecular docking analyses revealed that transcription factors ERF1, C3H1, bZIP1, and bZIP3 may interact with the <i>MaAPS1</i> promoter, indicating a multifactorial regulatory network. Overall, this study provides insights into polyploidy-driven functional innovation and transcriptional regulation of <i>MaAPS1</i> in banana starch biosynthesis, providing valuable molecular targets for genetic improvement of yield and fruit quality.