BEIJING, China — A single linear reference genome cannot represent the full range of insertions, deletions, and complex sequence differences found across maize. A research team led by scientists at China Agricultural University and collaborating institutions has developed MaizeGP 1.0, a graph-based maize pangenome built from 48 representative genomes. The publicly accessible platform brings structural variation, functional annotations, and interactive visualization together for exploration from individual loci to gene families and trait associations.
Unlike a conventional reference genome, a graph-based pangenome represents alternative DNA sequences from multiple genomes, providing a broader view of genetic diversity.
Building a Broader Map of Maize Diversity
The team began with 38 high-quality inbred genomes, including 12 founder lines and 26 nested association mapping (NAM) lines. An additional 10 genetically diverse inbreds representing European flint, sweet maize, and quality protein maize were then incorporated. The resulting graph contained 8.739 Gb of nonredundant sequence. The added lines contributed 10,858 low-frequency structural variants (SVs) absent from the original panel and 493.3 Mb of globally private graph sequence, highlighting the additional genomic diversity captured through broader maize representation.
Graph-Resolved Structural Variation and Regulatory Landscape
The researchers identified alternative DNA paths within the graph, allowing them to examine insertions, deletions, and more complex structural differences. Integration with published ATAC-seq data, which identify regions of DNA accessible to proteins involved in gene regulation, showed that many structural-variant breakpoints overlapped accessible chromatin, highlighting regions where genomic variation may intersect with gene regulation.
From Candidate Variants to Gene Families
The team revisited known functional loci, demonstrating how MaizeGP can resolve and visualize structural variation, and further examined flowering-related variation. A 175-bp insertion upstream of a maize gene contains a predicted regulatory protein-binding site and was associated with lower expression of the nearby gene and variation in silking time. Another larger insertion was also associated with flowering-related traits and gene-expression differences. Together, these examples highlight candidate regulatory variants for further investigation.
At the gene family level, the study also identified 6,286 NLR immune-receptor genes involved in plant defense across the 48 genomes. The analysis revealed differences in gene presence, copy number, and genomic organization.
An Open Portal for Exploration and Reuse
MaizeGP 1.0 includes a Locus Explorer and a Data Downloads module. The browser allows researchers to compare genomic regions and view structural variation alongside gene, transposable-element, and accessible-chromatin tracks. Downloads include versioned graph-derived structural variation, chromatin-accessibility, gene presence–absence variation, and trait-association data. Graph files, annotations, and analysis scripts are also available for reuse. The platform can be accessed at https://www.maizepan.cn.
A Resource for Maize Research
The platform provides researchers with an accessible resource for examining known loci, exploring gene-family diversity, and investigating trait-associated variation. These capabilities support further investigation of maize genome diversity and its biological implications, with potential longer-term relevance to crop improvement.
Orginal Source:
Jia, N., Kuang, X., Wang, Y., Song, W., Du, Y., Guo, Y., Guo, Y., Yi, C., Ma, Z., Chen, S., Fu, J., & Liu, W. (2026). MaizeGP: An open graph-based maize pangenome platform for integrative multi-scale exploration of structural variation. J. Integr. Plant Biol. https://doi.org/10.1111/jipb.70439 | Code: https://github.com/Jia-nianhua/Maize-Graph-Pangenome
Keywords: maize; graph-based pangenome; structural variation; genome visualization; genetic diversity; functional genomics
About the Journal:
The Journal of Integrative Plant Biology (JIPB) is a peer-reviewed monthly journal publishing research across plant biology. It was established in 1952 as Acta Botanica Sinica, and is sponsored by the Institute of Botany, Chinese Academy of Sciences and the Botanical Society of China. JIPB ranks among the top plant science journals globally, with a 2025 Journal Impact Factor of 12.5 and a ranking of 9th out of 285 journals in Plant Sciences (Top 3%, JCR Q1). More information about JIPB can be found at https://www.jipb.net.
