Abstract

Sweet potato ( Ipomoea batatas ) exhibits diversity in pigmentation and leaf morphology, yet the genetic architecture and regulatory organisation underlying these traits remain poorly resolved, particularly with respect to organ-specific control. We hypothesised that phenotypic variation is governed by clustered genetic modules comprising regulatory and structural genes operating in an organ-specific manner. To test this, we conducted genome-wide association studies (GWAS) using 4.6 million SNPs across 260 diverse accessions, integrated with transcriptomic, haplotype and functional analyses. GWAS identified two tandem clusters of MYB transcription factors on chromosome 5 as the primary regulators of leaf anthocyanin accumulation. Expression profiling, heterologous expression and transcriptional activation assays demonstrated that IbMYB2 and IbMYB3 function as key transcriptional activators and form a mutually reinforcing regulatory module. In contrast, pigmentation in storage roots was associated with a spatially distinct genomic region enriched in anthocyanin biosynthetic genes, including IbAOMT , Ib3GGT and IbLDOX , indicating different regulations between aerial and underground organs. Comparative genomic analysis further revealed expansion and conservation of MYB clusters in sweet potato, suggesting evolutionary selection for enhanced transcriptional control. In addition, GWAS uncovered a major locus on chromosome 7 controlling leaf shape variation. Functional analyses demonstrated that conserved developmental regulators, including BEL1-like ( g29974 ), WD40 ( g26165 ) and LMI1-like ( g29859 ) genes, play causal roles in leaf margin development. CRISPR/Cas9-mediated knockout of g26165 directly reduced leaf lobing, confirming its functional importance. These findings reveal clustered regulatory and structural gene modules underlying key agronomic traits and provide insights into the genetic and evolutionary mechanisms driving phenotypic diversification in sweet