An international team of researchers has produced complete, gap-free genome sequences for six peanut varieties, providing a comprehensive blueprint for future peanut breeding and improvement strategies.
In a new paper published today in Nature Genetics , researchers from Murdoch University's Centre for Crop and Food Innovation, Peking University Institute of Agricultural Sciences, Guangxi Provincial Academy of Agricultural Sciences, Shandong Academy of Agricultural Sciences, and Zhejiang University sequenced two wild ancestors of cultivated peanut, four cultivated varieties, and developed reference genomes for two peanut subspecies that had never been fully mapped.
The researchers then analysed DNA from 521 peanut accessions collected from around the world to identify genetic variants linked to seed size, oil content, and other key agronomic traits.
Peanut has been notoriously difficult to sequence due to its complex genetic structure that is littered with repetitive DNA. Given these challenges, previous sequencing efforts have left significant gaps and unmapped regions, restricting modern genomics-assisted breeding efforts.
However, this new telomere-to-telomere genome assembly has filled in the gaps and identified two candidate genes, one linked to oil content and one to seed size.
The first gene, named AhWRI1, is associated with a difference of roughly six percentage points (around 48 per cent versus 54 per cent) in seed oil content between peanut varieties carrying different versions of the gene.
The second gene, AhGSA1, is associated with substantially larger seeds, and peanut lines carrying one version of the gene averaged around 846 grams per thousand seeds, compared with 491 grams for lines carrying the alternative version — a difference of more than 70 per cent.
Both variants could be used as DNA markers in conventional peanut breeding programs to accelerate the development of higher-yielding, higher-oil varieties.
CCFI Director and co-corresponding author of the study, Professor Rajeev Varshney, explained:
"Peanut is a staple source of edible oil and protein for hundreds of millions of people, yet its genetics have remained harder to work with than most major crops. But with this new genomic resource, breeders and researchers finally have a gap-free reference genome they can rely on to develop higher-yielding, nutrient-rich peanut varieties."
The study also identified a large stretch of DNA that is present in all sampled plants of one peanut subspecies (var. hirsuta) but largely absent from another (var. hypogaea). The region contains genes linked to plant architecture and lipid metabolism, offering a concrete explanation for some of the visible differences between these peanut types.
The new genomes also reveal that the two halves of the peanut genome have been evolving at strikingly different rates, as evidenced by differences in the amount of repetitive DNA, the reshaping of their centromeres in opposite directions, and the frequency of structural changes.
"We knew that cultivated peanut carries two sets of chromosomes from two different ancestral species that were fused thousands of years ago," Prof Varshney said.
"But what we didn't realise was how asymmetrical the evolution of these two halves was, or why. Understanding how these two subgenomes have diverged helps explain why peanut behaves the way it does genetically, and where the useful diversity for breeding is likely to be found."
Speaking on the findings, Food Futures Institute Pro Vice Chancellor, Prof Peter Davies, said:
"Peanuts play a vital role in global food security and nutrition, and their nitrogen-fixing properties make them an excellent option for sustainable crop rotations. So while Australia's peanut industry may be modest by global standards, Murdoch's research footprint on this critically important crop continues to grow. My congratulations to Prof Varshney and the team, as it is through resources like this that we can take meaningful steps toward a more food-secure and sustainable agricultural system."
Murdoch University Deputy Vice Chancellor Research & Innovation, Prof Peter Eastwood, added:
"The first T2T assembly of a human genome was achieved only four years ago. Given that peanuts have four sets of chromosomes that come from two different species, this new T2T assembly of six varieties is a remarkable achievement. We're immensely proud to have researchers at Murdoch University at the frontier of genomics research, and look forward to seeing Prof Varshney and his team apply this approach to wheat and other key broadacre and horticultural crops."
