Genome-Wide Identification and Expression Profiling of the SPL Gene Family in Musa acuminata: Insights into Their Response to Drought Stress and Serendipita indica Inoculation

Banana productivity is severely limited by drought, yet the molecular basis of drought adaptation and endophyte-mediated stress alleviation remains poorly understood. Here, we performed a genome-wide analysis of the SQUAMOSA promoter-binding protein-like (SPL) transcription factor family in Musa acuminata and examined their transcriptional responses to drought stress and Serendipita indica inoculation. We identified 38 MaSPL genes, all encoding proteins with the conserved SBP domain and predicted nuclear localization. Phylogenetic, motif, gene structure, and collinearity analyses indicated that MaSPL genes are evolutionarily conserved, unevenly distributed across chromosomes, and expanded primarily through segmental duplication under purifying selection. Promoter analysis showed several cis-acting elements and transcription factor binding sites related to light, phytohormone, and stress signaling. Ten MaSPL genes were predicted as putative targets of miR156. qRT-PCR analysis showed that drought stress markedly downregulated the tested MaSPL genes, whereas miR156a expression increased, supporting an inverse regulatory relationship. Under drought, S. indica inoculation enhanced expression of most tested MaSPLs, restoring transcript accumulation while reducing miR156a to near-basal levels. Notable responses were observed in members of the MaSPL2, MaSPL9, and MaSPL13, respectively. S. indica improves drought tolerance by enhancing antioxidant defenses, reducing oxidative stress, and preserving photosynthetic and osmotic stability. Taken together, our results demonstrate that S. indica confers drought resilience in banana by counteracting drought-induced repression of MaSPL genes via the miR156–SPL module and by strengthening key physiological defense mechanisms.