Unlocking The Genetic Code

In reporting on their success, the International Peanut Genome Initiative has released the first peanut genome sequences.

The International Peanut Genome Initiative (IPGI) – a multinational group of crop geneticists working in cooperation for several years – has successfully sequenced the genome of the peanut. The new peanut genome sequence will be available to researchers and plant breeders across the globe to aid in the breeding of more productive, more resilient peanut varieties.

Nearly ten years ago, The Peanut Foundation embarked on an industry-supported effort to organize and coordinate peanut genomic research with the goal of reducing the costs of production and improving yield and quality.

Project Start
Genomics is the identification and study of gene sequences in the DNA of organisms, and this was determined as the best way to improve the competitiveness of peanut by enhancing varieties for disease resistance and yield potential. After researching different approaches, the Peanut Foundation selected Marker Assisted Selection (MAS) as the best means to deliver new varieties. Market Assisted Selection is a breeding method that relies on the use of DNA-markers found in plants to identify hybrids from a cross that have a desired trait before the hybrids are grown in the field, which gives breeders a time advantage in variety development.

The selection of the that approach was in 2010, and at the time peanut breeders had only about 6,000 DNA-markers identified and few of those were associated with selectable or measurable traits. For comparison, soybean and corn scientists had more than 100,000 useful DNAmarkers and the reason those researchers had so many markers is because DNAmarkers were easier to discover after the DNA sequence of the soybean and corn genome was known.

To find the useful DNA-markers in peanuts to be able to move forward with MAS breeding, it would be necessary to sequence the peanut genome, which is where the project is today.

Both Simple And Complex
The effort to sequence the genome of the peanut has been underway for several years. According to plant geneticist, Peggy Ozias-Akins, University of Georgia, while peanuts have been successfully bred for intensive cultivation, relatively little was known about the legume’s genetic structure because of its complexity. Two markers or traits peanut breeders have had for a several years are nematode resistance and high oleic oil chemistry.

“Those are two relatively simple traits, but other traits, particularly disease resistance, are much more complex,” says Ozias-Akins. “Knowing the sequence of the peanut genome will allow for the comparison of a lot of different genotypes of peanut from the germplasm collection to modern cultivars and really hone in on what variation is there and it will allow us to develop more molecular markers.”

Good For All
Scott Jackson, director of the University of Georgia (UGA) Institute of Plant Breeding, Genetics and Genomics at theCollege of Agricultural and Environmental Sciences, serves as chair of the International Peanut Genome Initiative. “The peanut crop is important in the United States, but it’s very important for developing nations as well,” Jackson said. “In many areas, it is a primary calorie source for families and a cash crop for farmers.”

According to plant geneticist Rajeev Varshney of India, “Improving peanut varieties to be more drought, insect and disease resistant, using the genome sequence, can help farmers in developed nations produce more peanuts with fewer pesticides and other chemicals and help farmers in developing nations feed their families and build more-secure livelihoods.” Plant geneticists David and Soraya Bertioli of Brazil expressed their enthusiasm for the new possibilities offered by the genome sequence, “Until now, we’ve bred peanuts relatively blindly compared to other crops. These new advances are allowing us to understand breeding in ways that could only be dreamt of before.”

Looking To Peanut Ancestors
The peanut grown in fields today is the result of a natural cross between two wild species, Arachis duranensis and Arachis ipaensis that occurred in the north of Argentina between 4,000 and 6,000 years ago. Because its ancestors were two different species, today’s peanut is a tetraploid, meaning the species carries two separate genomes which are designated A and B sub-genomes.

To map the peanut’s genome structure, IPGI researchers sequenced the two ancestral parents, because together they represent the cultivated peanut. The sequences provide researchers access to 96 percent of all peanut genes in their genomic context, providing the molecular map needed to more quickly breed drought-resistant, disease-resistant, lowerinput and higher-yielding varieties. The two ancestor wild species were collected from nature decades ago. One of the ancestral species, A. duranensis, is widespread but the other, A. ipaensis, has only ever been collected from one location, and indeed may now be extinct in the wild.

When grappling with the thorny problem of how to understand peanut’s complex genome, it was clear that the genomes of the two ancestor species would provide excellent models for the genome of the cultivated peanut: A. duranenis serving as a model for the A subgenome of the cultivated peanut and A. ipaensis serving as a model for the B subgenome. Fortunately because of the longsighted efforts of germplasm collection and conservation, both species were available for study and use by the IPGI.

Progress Made Toward Goal
Knowing the genome sequences of the two parent species will allow researchers to recognize the cultivated peanut’s genomic structure by differentiating between the two subgenomes present in this crop. Being able to see the two separate structural elements will also aid future gene marker development: the determination of links between a gene’s presence and a physical characteristic of the plant. Understanding the structure of the peanut’s genome will lay the groundwork for new varieties with traits like added disease resistance and drought tolerance.

The International Peanut Genome Initiative brings together scientists from the United States, China, Brazil, India and Israel to delineate peanut genome sequences, characterize the genetic and phenotypic variation in cultivated and wild peanuts and develop genomic tools for peanut breeding. The initial sequencing was carried out by the BGI, Shenzen, China. Assembly was done at BGI, USDA-ARS, Ames, Iowa, and UC Davis, Davis, Calif.

The project was made possible by funding provided by the peanut industry through the Peanut Foundation, by MARS Inc., and three Chinese Academies (Henan Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Shandong Academy of Agricultural Sciences). A complete list of the institutions involved with the project and the other funding sources is available at www.peanutbioscience.com.