Massive Peanut Pan-Genome Uncovers Hidden DNA Variation to Accelerate Breeding

Cultivated peanut, one of the world’s most important oilseed and food legumes, has long frustrated plant geneticists. Despite its enormous agricultural value, the crop carries remarkably little DNA-level diversity, a legacy of its origin as a recent polyploid hybrid and centuries of selection. That bottleneck has slowed the search for genes controlling yield, plant architecture and adaptation. Now, an international team has shattered part of that barrier by constructing a graph-based pan-genome for peanut and using it to resequence 2,320 germplasm accessions, producing one of the most comprehensive genomic resources ever assembled for the crop and delivering immediately actionable tools for breeders.

The study, led by researchers at the Shandong Academy of Agricultural Sciences in collaboration with the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Murdoch University and other partners, began with a de novo sequencing effort that produced ten new high-quality genome assemblies. These were combined with previously published references to create a pan-genome of fourteen genomes representing all six botanical varieties of cultivated peanut. Long-read sequencing platforms, including PacBio HiFi and Oxford Nanopore technologies, together with Hi-C scaffolding, allowed the team to resolve the peanut’s complicated tetraploid genome, which harbors two distinct subgenomes derived from the wild ancestors Arachis duranensis and Arachis ipaensis.

The resulting pan-genome cataloged a striking wealth of variation invisible to earlier single-reference analyses. The team identified tens of thousands of structural variants across the fourteen assemblies, including more than 21,000 deletions, over 21,500 insertions, hundreds of copy number variations, inversions and translocations. Presence-absence variants, large chunks of DNA found in some accessions but not others, proved especially common in intergenic regions, where they can alter gene regulation. Gene counts fluctuated widely among the genomes: the analysis distinguished a core set of roughly 48,948 genes shared by all accessions, alongside thousands of softcore, dispensable and private genes whose presence or absence correlated with measurable differences in gene expression and with pathways tied to adaptation and agronomic performance.

Armed with this graph-based reference, the researchers genotyped an unprecedented collection of 2,320 accessions drawn from global genebanks, material covering 88.03 percent of the ICRISAT core collection and 59.21 percent of the USDA core germplasm. Because reads were mapped to a pan-genome graph rather than a single reference sequence, the team could call variants with far greater accuracy, particularly in the duplicated, highly similar regions that pervade the peanut genome. Phylogenetic and population-structure analyses of the resequenced accessions recovered the major cultivar groups and traced patterns of geographic spread and gene flow, offering a detailed picture of how this crop diversified after its domestication in South America.

One of the study’s central technical achievements involved homoeologous exchanges, the swapping of chromosome segments between the A and B subgenomes of this young allopolyploid. Such exchanges create a genotyping nightmare, because sequence reads from one subgenome can be misassigned to its counterpart, distorting both variant calls and association signals. By explicitly characterizing homoeologous exchange events across the pan-genome and modeling them during genotyping, the researchers showed that these exchanges have contributed meaningfully to population divergence among peanut groups and even to the differentiation of subspecies, influencing genes such as a phytochrome A ortholog involved in photoperiod response and a DAG1-like gene tied to seed biology.

The pan-genome framework immediately paid off in gene discovery. A structural-variant genome-wide association study pinpointed a major locus for flowering pattern on chromosome 12. The team identified AhTFL1, a homolog of the TERMINAL FLOWER 1 gene family that represses flowering, as a key regulator. In an alternate allele carried by the accession Shitouqi, a 1,489-base-pair deletion disrupts the gene. Transgenic experiments in Arabidopsis confirmed that the intact peanut TFL1-like allele delays flowering and alters inflorescence architecture, while the deleted version loses that capacity, explaining differences between sequential and alternate flowering patterns that shape peanut plant habit and harvest timing.

Dwarfism, a trait of intense breeding interest because compact plants resist lodging and tolerate denser sowing, yielded a second discovery. Fine mapping in a cross between the reference cultivar Tifrunner and a dwarf accession revealed an abnormal recombination region on chromosome 02, caused in part by a balanced reciprocal translocation between chromosomes 02 and 12 present in several accessions. Within the critical interval, the researchers identified a 47.31-kilobase deletion in dwarf lines that removes a gene, Ah12g032500, implicated in gibberellin-related growth regulation. Virus-induced gene silencing of this gene in normal plants reproduced the dwarf phenotype, and biochemical assays showed altered gibberellin content, with dwarf seedlings resuming elongated growth after treatment with exogenous gibberellic acid, cementing the gene’s role in a pathway reminiscent of the Green Revolution dwarfing genes of rice and wheat.

Beyond single genes, the pan-genome enabled association mapping across a broad spectrum of agronomic traits, linking structural variation to characteristics ranging from pod architecture to plant height. The team then translated this knowledge directly into breeding practice. By integrating superior haplotypes identified through the pan-genome with elite germplasm resources, they developed high-yield dwarf peanut lines, demonstrating that the resource is not merely a catalog but a working platform for cultivar improvement. For a crop central to food security and nutrition across Asia and Africa, where peanuts supply protein and oil to hundreds of millions of people, the ability to combine dwarfing architecture with high pod yield could reshape on-farm performance.

The study aligns with a broader movement in plant science away from single reference genomes and toward pan-genomes that capture the full spectrum of diversity within a species. Comparable efforts in barley, wheat, rapeseed and soybean have repeatedly revealed that structural variation, not just single-letter DNA changes, drives trait differences of agricultural importance. Peanut’s pan-genome now places this orphaned-genome crop in that company, and the scale of the resequencing panel ensures that breeders worldwide can find genetic material close to their own local varieties and mine it for favorable alleles.

All of the underlying data have been released to the community. The ten new assemblies and their sequencing reads are deposited in public archives at the National Genomics Data Center and NCBI, along with the resequencing data for the 2,320 accessions, and the complete analysis code is available on GitHub and Zenodo. That openness matters: genomics-assisted breeding in peanut has historically lagged behind maize, rice and wheat, partly because resource-rich and resource-poor breeding programs diverged in their access to data. By publishing a graph pan-genome, thousands of genotyped accessions, cloned genes for flowering and dwarfism, and ready-made high-yield dwarf lines, the consortium has effectively handed the global peanut community a new starting point for the next generation of cultivars, one in which hidden structural variation becomes a resource rather than a blind spot.

Subject of Research: A graph-based pan-genome and large-scale resequencing of cultivated peanut revealing structural variation and breeding-relevant genes

Article Title: Pan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut

Article References: Pan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut. (n.d.). https://doi.org/10.1038/s41588-026-02765-x

Image Credits: AI Generated

DOI: 10.1038/s41588-026-02765-x

Keywords: peanut, pan-genome, structural variation, homoeologous exchange, Arachis hypogaea, genomics, plant breeding, dwarfism, flowering, AhTFL1, gibberellin, germplasm