Sweet Potato Gene Clusters Control Anthocyanin Biosynthesis and Leaf Morphology

Authors

• Dong An, Shanghai Chenshan Botanical Garden
• Tiechen Shen, Shanghai Chenshan Botanical Garden
• Shiyu Wu, Zhejiang Agriculture and Forestry University
• Yanshen Li, Shanghai Chenshan Botanical Garden
• Weijuan Fan, Shanghai Chenshan Botanical Garden
• Mengxiao Yan, Shanghai Chenshan Botanical Garden
• Yinghui Meng, Shanghai Chenshan Botanical Garden
• Xinyi Wang, Shanghai Chenshan Botanical Garden
• Ximing Xu, Zhejiang Agriculture and Forestry University
• Zunfu Lv, Zhejiang Agriculture and Forestry University
• Ling Yuan, University of KentuckyFollow
• Jun Yang, Shanghai Chenshan Botanical GardenFollow
• Guoquan Lu, Zhejiang Agriculture and Forestry UniversityFollow
• Hongxia Wang, Shanghai Chenshan Botanical GardenFollow

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 potato.

Document Type

Article

Publication Date

7-1-2026

Notes/Citation Information

Publisher Copyright: © 2026 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Digital Object Identifier (DOI)

10.1111/pbi.70636

Archival?

Archival

Repository Citation

An, Dong; Shen, Tiechen; Wu, Shiyu; Li, Yanshen; Fan, Weijuan; Yan, Mengxiao; Meng, Yinghui; Wang, Xinyi; Xu, Ximing; Lv, Zunfu; Yuan, Ling; Yang, Jun; Lu, Guoquan; and Wang, Hongxia, "Sweet Potato Gene Clusters Control Anthocyanin Biosynthesis and Leaf Morphology" (2026). Plant and Soil Sciences Faculty Publications. 194.
https://uknowledge.uky.edu/pss_facpub/194