Decoding the Peanut

Over the past couple years, an archaeological dig—of the genetic kind—has been in the works to uncover the complex beginnings of the beloved peanut, Arachis hypogaea.

Major headway was made in 2014, when an international team of scientists from the Agricultural Research Service (ARS), University of Georgia, and other organizations announced the completion of a first-draft sequence of the peanut’s book of life—or “genome.”

The team accomplished the feat using cutting-edge tools to decode the order of the DNA bases that make up the genomes of the modern peanut’s wild ancestors, which merged long ago to form the cultivated species grown today as a source of high-quality cooking oil and nutritious food.

A research paper published in the February 2016 issue of Nature Genetics describes the results of the team’s draft genome-sequencing efforts. The advance should speed efforts to breed new peanut varieties that have desirable traits like higher yield; longer shelf life; and greater resilience to pests, diseases, and drought.

According to Steven Cannon, one of four ARS participants on the Peanut Genome Project, the effort uncovers most of the genes and regulatory elements necessary for making a peanut plant. That’s no small task, considering that the modern-day peanut’s genome totals about 2.7 billion base pairs—a size approaching that of the human genome (3 billion base pairs).

The Nature Genetics paper clarifies humankind’s domestication of these ancestral peanuts, says Cannon, a plant geneticist at the ARS Corn Insects and Crop Genetics Research Unit in Ames, Iowa. “It is a bit of living genetic archaeology in the sense that the genome sequences tell us about how, where, and when the ancestor species came together to become the peanut that is grown by farmers now.”

Scientists believe the merger happened 9,000 to 10,000 years ago—quite possibly from wild peanut plants cross-pollinating in the hardscrabble plots of prehistoric farmers in what is today southeastern Bolivia.

One application of the latest sequencing effort will be the use of “molecular markers”—specific genomic regions that can flag the presence of nearby genes of interest, such as those for resistance to pests like the root-knot nematode. Using technology to detect the markers, for example, peanut breeders can check and select for the resistance trait in seedlings instead of growing the plants to maturity, infecting them with nematodes, and waiting for symptoms to appear.

Ultimately, such “marker-assisted selection” should help speed commercialization of sturdy new varieties with nematode resistance that will cut the need for chemical controls—an expense that costs U.S. peanut growers $25-30 million annually.

Scientists from nine countries participated in this phase of the Peanut Genome Project. Contributions by the ARS members Cannon, Brian Scheffler, and Baozhu Guo, as well as Noelle Barkley (formerly with ARS), included providing bioinformatics support, peanut germplasm resources, and data to help describe and analyze genomic points of interest.—By Jan Suszkiw, ARS Office of Communications.

“Decoding the Peanut” was published in the September 2016 issue of AgResearch Magazine.