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 for 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."
