News release

From: Murdoch University

An international team that includes researchers from Murdoch University's Centre for Crop and Food Innovation (CCFI) has built the most comprehensive genetic map of the peanut yet and used this new genomic resource to breed a higher-yielding dwarf peanut line.

Led by the Shandong Academy of Agricultural Sciences in China and in collaboration with Murdoch University’s Centre for Crop and Food Innovation, the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Guangxi Academy of Agricultural Sciences, the Chinese Academy of Agricultural Sciences and the Henan Academy of Agricultural Sciences, the research team developed a graph-based pan-genome for cultivated peanut and used it to resequence 2,320 accessions from 87 countries and regions, with their findings published in Nature Genetics.

Peanut feeds hundreds of millions of people and is a critical source of protein and cooking oil in South Asia and Africa. However, given the severe genetic bottlenecks during peanut’s evolution and domestication, it has narrow genetic diversity, meaning crop improvement through genetic diversity has been a long-standing barrier for breeders.

To resolve this challenge, the research team assembled 10 new reference-quality genomes and combined them with four published assemblies, covering all six botanical varieties of cultivated peanut. They then read the DNA of 2,320 peanut accessions collected from 87 countries and regions against the new reference. The panel covers most of ICRISAT's core germplasm collection and well over half of the USDA's, representing the genetic breadth of the world's two largest peanut germplasm holdings.

The researchers uncovered two important genes. The first controls where flowers are produced, which determines the shape of the plant and how its pods are set. The second sits inside a large segment of chromosome that had physically swapped position with another chromosome — the reason it had escaped detection in previous sequencing efforts. The researchers found that silencing this gene reduced plant height and internode length, opening up opportunities to develop dwarf varieties. Using the new map, the researchers crossed a naturally dwarf peanut with a high-yielding Chinese variety and selected offspring carrying the best combination of genes. The resulting line, LuAi-1, is roughly half the height of the parent variety but yielded around 20 per cent more in the team's field trials when planted densely.

In a statement, CCFI Director and co-corresponding author of the study, Professor Rajeev Varshney FRS FAA, explained:

"The development of semi-dwarf wheat and rice varieties drove the Green Revolution and saved the lives of millions of people across the world, because compact plants tend to be sturdier, can be grown closer together on smaller plots, and are easier to harvest by machine. However, Peanut has never had its equivalent. This research demonstrates that it’s not only possible to develop dwarf varieties, it's possible to dramatically enhance peanut yield."

Pro-Vice Chancellor and Director of the Food Futures Institute, Professor Peter Davies, added that:

"This research project has direct implications to millions of smallholder farmers in Africa and Asia, where every yield increase paves the way towards more food secure outcomes. The Centre for Crop and Food Innovation continues to be a global leader in the development of pangenome resources, and it is fantastic to see the Centre contribute to research at this scale and of this importance."

Murdoch University Deputy Vice Chancellor, Research and Innovation, Professor Peter Eastwood, said:

“This paper encapsulates Murdoch University’s approach to science, which is to deliver translational and collaborative research that benefits both people and planet. Peanut may have a relatively small market share in Australia, however, on a global level it is a critically important crop. My congratulations to all the authors for developing a new resource that will accelerate and improve peanut breeding.”

ENDS

Notes on the study:

The researchers assembled 10 new reference-quality genomes and combined them with four published assemblies, covering all six botanical varieties of cultivated peanut. Aligning 13 of these genomes to the Tifrunner reference identified 126,758 structural variations, condensed to a non-redundant set of 44,073 that were built into a graph-based pan-genome. Resequencing 2,320 accessions against that graph yielded 29,195,792 SNPs and short insertions/deletions. The accession panel covers 88.03% of the ICRISAT core germplasm collection and 59.21% of the USDA core collection.

Using the pan-genome, the team ran GWAS across 25 agronomic traits in 555 accessions, identifying 221 significant loci and 157 superior haplotypes, and then used marker-assisted selection to combine favourable haplotypes into a new line, LuAi-1. In field trials, LuAi-1 produced pod-yield increases of 17.28–20.79% over the control cultivar Dabaisha under high-density planting across two consecutive seasons, and 19.34–22.90% in larger-scale trials at Ningyang and Sanya.