Integrative nuclear and total proteomics of compound leaves in semi-leafless and leafed pea cultivars reveal regulatory cues in leaf development

Leaf architecture is a critical determinant of crop productivity, influencing light interception, canopy organization, and lodging tolerance. In pea (Pisum sativum L.), the semi-leafless phenotypes with well-developed tendrils improved the standability of the crop which resulted in better photosynthetic ability of the canopy and yield, reduced losses to diseases, and improvement in seed quality. These traits associated with semi-leafless cultivars have transformed modern breeding programs. The underlying molecular networks governing compound leaf development, however, remain poorly understood. Here, we present an integrative proteomic atlas of pea leaf tissues, generated by profiling both nuclear and total proteomes of semi-leafless (Cooper) and leafed (Trapper) cultivars. Quantitative analyses identified more than 8,500 nuclear and 7,700 total proteins across tendrils, stipules, leaflets, rachis, and petioles. Comparative profiling revealed stronger conservation in nuclear proteomes (~ 37% differentially abundant proteins) than in total proteomes (~ 78%), with young tissues contributing disproportionately to proteomic variation. Tissue-and cultivar-specific differences were pronounced. The genetic variation at the afila locus strongly influenced tendril proteomes, with Cooper displaying widespread proteome reprogramming consistent with its highly branched phenotype, whereas Trapper’s residual tendril development was heavily shaped by nuclear regulation. Proteins associated with transcription factor families, including WDR, C2H2, bZIP, PHD, TF-B3, redox-homeostasis regulators, phytohormone signaling, chromatin modulators, and proteins regulating cell structure emerged as important contributors to different leaf developmental pathways. Additionally, clusters of uncharacterized proteins with unique abundance patterns across tissues and cultivars point to potential roles in organ identity and regulatory complexity yet to be uncovered. Together, these results provide unparalleled resolution of the proteomic landscape underlying pea leaf development. The resource offers novel insights into the regulatory complexity of compound leaf formation and establishes a foundation for systems-level approaches for molecular understanding.