Transcriptomic Analysis of Space-Induced Compound Leaf Variants in Medicago sativa: Unveiling Molecular Mechanisms Behind 5- to 13-Leaflet Number Variation in Alfalfa Mutants

(1) Background: Compound leaf morphogenesis in alfalfa (Medicago sativa), a key trait determining yield and agronomic value, is governed by complex molecular mechanisms. (2) Methods: This study systematically investigates the transcriptomic profiles of space-induced alfalfa mutants exhibiting diverse compound leaf numbers through RNA sequencing and Short Time-series Expression Miner (STEM)-based data analysis. (3) Results: Our findings reveal that transcriptional regulators, phosphorylation-related protein kinases, and glycoside hydrolases collectively modulate this trait. Specifically, GRAS and WRKY transcription factors show positive correlations with increased leaflet numbers, highlighting their roles in promoting leaflet initiation. Conversely, transcript levels of serine-threonine/tyrosine-protein kinases are inversely related to leaflet number, suggesting their involvement in suppressing excessive leaflet formation via post-translational modifications. Notably, glycoside hydrolases exhibit suppressed expression in mutants with higher leaflet numbers compared to wild-type plants, implying a regulatory role in balancing cell wall plasticity during morphogenesis. (4) Conclusions: These results provide critical insights into the interplay between transcriptional control, phosphorylation dynamics, and cell wall remodeling in shaping compound leaf architecture. Furthermore, the identified genes and pathways offer novel molecular targets for breeding strategies aimed at optimizing multi-leaflet alfalfa varieties, with potential applications in agricultural productivity and functional genomics.