Peanut genome sequenced
The International Peanut Genome Initiative (IPGI)—a multinational group of crop geneticists who have been workingwith The Peanut Foundation —announced on April 2, 2014, that they have successfully sequenced the peanut (groundnut) genome. The new sequence is now available to researchers and plant breeders around the world for use in breeding more productive and more resilient peanut varieties.
Richard Wilson—former president of AOCS, retired US Department of Agriculture National Program Leader for oilseed research and now a consultant dealing in oilseeds and biosciences—said that the genomic sequences now available at the Peanutbase.org website are “extremely high-quality roadmaps to gene locations on each peanut chromosome.” He indicated that this resource will enable and expedite efforts to develop enhanced peanut cultivars in the United States, China, India, South America, and Africa. At least four future outcomes from this work should be of interest to AOCS members:
- Early efforts will be directed toward increasing the supply of peanuts with higher oleic acid content. This trait will help extend the shelf life of peanut products, particularly in the United States where about 80% of the peanuts grown are eaten whole, in confections, or in peanut butter products.
- The time required to develop new varieties will be cut considerably, from a typical six years to perhaps as low as two years.
- Farmer costs per acre to grow peanuts should fall. At present peanut plants are susceptible to a number of fungal infections, requiring farmers to treat their crops with fungicides many times during the growing season. With a blueprint of the peanut genome in hand, researchers will be able to identify genes in strains known to have some resistance to fungal infection and develop new crosses that enhance disease resistance.
- Greater availability of high-quality peanuts will help ensure food security in nations that suffer from chronic hunger.
According to FAO statistics, in 2012 farmers in a total of 113 countries raised peanuts on 24.7 million hectares and harvested about 41 million metric tons.
Although peanuts (Arachis hypogaea) have been bred for intensive cultivation for thousands of years, relatively little had been known about the legume’s genetic structure because of its complexity, according to Peggy Ozias-Akins, a plant geneticist with the University of Georgia (UGA)-Tifton (USA) who also works with the IPGI and directs the UGA Institute of Plant Breeding, Genetics, and Genomics.
The peanut in fields today is the result of a natural cross between two wild species, Arachis duranensis and Arachis ipaensi, which occurred in northern Argentina 4000–6000 years ago. Because its ancestors were two different species, today’s peanut is a polyploid, meaning the species can carry two separate genomes, designated A and B subgenomes.
To map the peanut’s structure, researchers sequenced the genomes of the two ancestral parents, because together they represent the cultivated peanut. The sequences provided researchers access to 96% of all peanut genes in their genomic context, providing the molecular map needed to more quickly breed drought- and disease-resistant, lower-input and higher-yielding varieties of peanuts.
The two ancestor wild species had been collected in nature decades ago. Arachis duranensis is widespread in nature today, but A. ipaensis has only ever been collected from one location and may now be extinct in the wild. Long-sighted efforts toward germplasm collection and conservation of these species provided IPGI with the materials to understand the peanut genome better.
Knowing the genome sequences of the two parent species will allow researchers to recognize the cultivated peanuts’ genomic structure by differentiating between the two subgenomes present in the plants. Being able to see the two separate structure elements also will aid future gene marker development—the determination of links between a gene’s presence and a physical characteristic of the plants.
In addition, these genome sequences will serve as a guide for the assembly of the cultivated peanut genome that will help to decipher genomic changes that led to peanut domestication, which was marked by increases in seed size and plant growth habit.
Scientists from all around the world worked together through the IPGI to delineate peanut genome sequences, characterize the genetic and phenotypic variation in cultivated and wild peanuts, and develop genomic tools for peanut breeding. Research was carried out in US universities (California-Davis, Georgia, Texas A&M, North Carolina), the USDA Agricultural Research Service (USDA-ARS; Georgia, Mississippi, Iowa), the National Center for Genome Resources (New Mexico, USA), Brazil (University Brasilia, Embrapa Recursos Genéticos e Biotecnologia), China (Academy of Agricultural Sciences, Beijing Genome Institute, Shandong Academy of Agricultural Sciences, Henan Academy of Agricultural Sciences), ICRISAT (International Crops Research Institute for the Semi-Arid Tropics), Japan, Israel, and Australia. A complete list of the institutions involved with the project and funding sources.
The initial sequencing was performed by the Beijing Genomic Institute (BGI). Assembly was carried out at the BGI, USDA-ARS (Ames, Iowa), and the University of California-Davis.