Tomato breeding depends on finding useful natural variants behind complex traits, but conventional linear reference genomes represent only a limited slice of the species’ diversity. Graph-based pangenomes can capture broader variation, including single-nucleotide polymorphisms, insertions and deletions, and structural variants, yet large graphs can be computationally demanding and may emphasize structural changes while missing smaller variants. Complex traits such as fruit weight, metabolite composition, and disease resistance are also controlled by interacting loci, making causal genes difficult to pinpoint. Integrating a purpose-built genetic population with genomic, transcriptomic, and metabolomic data can sharpen that search. Because of these challenges, deeper research is needed to develop efficient pangenomic strategies that connect comprehensive genetic variation with measurable tomato traits.
Researchers from China Agricultural University, the Agricultural Genomics Institute at Shenzhen of the Chinese Academy of Agricultural Sciences, Henan University, and Huazhong Agricultural University published (DOI: 10.1093/hr/uhag147) the study in Horticulture Research on April 16, 2026. The team built MiniTG1.0, a graph-based pangenome derived from cultivated Solanum lycopersicum TS-RS1 and wild Solanum pimpinellifolium TS-RS2, then analyzed 230 seventh-generation recombinant inbred lines. By combining genome-wide association studies with expression, metabolite, and functional experiments, they mapped genes controlling fruit development, chemical composition, and fungal resistance.
MiniTG1.0 integrated single-nucleotide polymorphisms (SNPs), insertions and deletions (INDELs), and structural variants (SVs), capturing 5.76 million variants across the recombinant inbred line (RIL) population. Joint analysis of these variants explained 18.18% more average trait heritability than the linear reference genome and improved mapping of established loci controlling trichomes and growth habit. The graph also placed the H and SELF-PRUNING (SP) genes closer to their expected trait signals than the linear reference. For fruit weight, the researchers recovered the known fw2.2 region and discovered a new locus, fw6.4. Within it, SlILL6 emerged as a strong candidate: plants overexpressing SlILL6 produced fruits weighing about 62–63 grams, compared with roughly 101 grams in wild-type plants, supporting a role in limiting fruit growth through cell expansion. Metabolite profiling detected 1,258 compounds and identified 128 that accumulated differently between parental backgrounds. A metabolome-based genome-wide association study (mGWAS) then connected chlorogenic acid (CQA) variation to SlCGT. Clustered regularly interspaced short palindromic repeats-associated nuclease 9 (CRISPR-Cas9) knockout lines accumulated more CQA and developed smaller lesions after Botrytis cinerea infection, while overexpression lines showed the opposite pattern. CQA also directly suppressed fungal growth, linking the gene to a measurable fruit-defense pathway.
The authors said the study shows that a smaller, strategically designed genome graph can deliver both computational efficiency and biological precision. They said combining a wild parent, a cultivated parent, and a segregating population made it possible to follow inherited variation directly into fruit traits rather than searching through diversity alone. The discovery of SlILL6 and SlCGT, they added, demonstrates how the same framework can move from statistical association to experimentally tested function. In their view, this creates a clearer route from pangenomic data to breeding decisions involving fruit size, quality-related metabolites, and resistance to postharvest disease.
The work offers a practical blueprint for molecular design breeding in tomato. SlILL6 could be evaluated as a target for adjusting fruit size, while SlCGT may provide a route to raise chlorogenic acid and strengthen resistance to gray mold without reducing soluble solids in the tested lines. MiniTG1.0 also supplies a compact analytical resource for tracking small and large variants together, which may help breeders recover useful alleles from wild germplasm more efficiently. However, the findings were generated from two parental genomes, greenhouse-grown recombinant lines, and targeted functional tests. Field trials across diverse environments and genetic backgrounds will be needed to confirm agronomic performance, disease protection, and any trade-offs before these targets enter commercial breeding programs.
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References
DOI
10.1093/hr/uhag147
Original Source URL
https://doi.org/10.1093/hr/uhag147
Funding information
This research was supported by the National Key Research and Development Program of China (2023YFF1000100 to T.L.), the National Natural Science Foundation of China (32422078 to T.L.), the 111 Project (B17043 to T.L.), the Construction of Beijing Science and Technology Innovation and Service Capacity in Top Subjects (CEFF-PXM2019_014207_000032 to T.L.), and the Chinese Universities Scientific Fund.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.