Genome-wide association study identifies candidate genes associated with leaf morphological traits in grape (Vitis...

Grape leaf serration morphology is a key physiological trait that influences photosynthetic efficiency, leaf boundary layer dynamics, and stress adaptability, thereby affecting yield and quality. In this study, we phenotyped 10 mature leaf morphological traits in 153 grape accessions over two consecutive years. Among these traits, five showed high interannual stability (|r| ≥ 0.8). GWAS of these five stable traits using three models (GLM, MLM, and FarmCPU) identified seven high-confidence SNP loci reproducibly associated with mature leaf serration morphology. Ten candidate genes were screened within ±15 kb of these SNPs, including genes related to ubiquitin-mediated protein degradation (Cullin-4), ubiquitin ligase activity (SP-RING-type protein), and two-component signaling (histidine kinase). Based on their predicted roles in leaf development and cell differentiation, we selected four genes for qRT-PCR validation. We observed differential expression patterns associated with serration morphological variation: Cullin-4 and SP-RING-type protein were upregulated in straight-sided serrations, whereas histidine kinase was upregulated in convex-sided serrations. These expression patterns provide preliminary evidence that ubiquitin-proteasome pathway activity and phosphorylation signaling may be associated with serration variation, although direct functional validation is required. This study characterizes the genetic architecture of grape leaf serration morphology and suggests possible differential regulatory mechanisms involving protein degradation and signaling pathways, providing a foundation for future functional studies.