Citrus leaves exhibit remarkable morphological diversity, yet the genetic underpinnings of this variation remain poorly understood. In this study, we investigated the genetic architecture controlling citrus leaf shape by performing genome-wide association studies (GWAS) on over 3,000 digitized leaves collected from 150 citrus varieties across two years (2021 and 2022). Using a 50K SNP Axiom array, we identified consistent genomic regions on chromosomes 2, 3, 5, and 7 that were significantly associated with leaf length, width, and area. Linkage disequilibrium patterns within these regions revealed variability, and gene ontology enrichment indicated that genes involved in cell division, photosynthesis, and transcriptional regulation are overrepresented. Our results highlight the strong and heritable basis of leaf morphology in citrus and suggest that regulatory mechanisms play a major role in shaping these traits. This work provides key insights into the genetic control of leaf form and has potential implications for citrus breeding and functional genomics.
