Researchers take proactive measures to protect the U.S. peanut industry from this devastating fungal disease.
Peanut smut, a soilborne fungal disease caused by Thecaphora frezzii, was first described in 1962 infecting wild peanut in Brazil. The disease did not appear in commercial peanut fields until 1995, when it was reported in Argentina. Currently, smut can be found in every commercial peanut field in Argentina, and the possible spread of the disease is threatening global peanut production. In 2017, U.S. peanut stakeholders approached the U.S. Department of Agriculture’s Agricultural Research Service regarding the threat and urged the agency to take proactive action to protect U.S. peanut producers.
The Team And Project Goals
Researchers at ARS quickly responded to this need by assembling a team of researchers to tackle peanut smut. The team is led by Dr. Kelly Chamberlin, ARS supervisory research biologist of the peanut and small grains research unit (part of the Oklahoma and Central Plains Agricultural Research Center) in Stillwater, Oklahoma. Joining her are Dr. Rebecca Bennett, ARS research plant pathologist, also of the PSGRU; Dr. Josh Clevenger, faculty investigator at HudsonAlpha Institute for Biotechnology, Dr. Corley Holbrook, supervisory research geneticist of the ARS Crop Genetics and Breeding Research Unit in Tifton, Georgia; Dr. Peggy Ozias-Akins, distinguished research professor of the University of Georgia in Tifton; Dr. Phat Dang, research chemist of the ARS National Peanut Laboratory in Dawson, Georgia; Dr. Shyam Tallury, plant geneticist and curator of the USDA peanut germplasm collection of the Plant Genetic Resources Conservation Unit in Griffin, Georgia; Dr. Rachel Koch Bach, research plant pathologist with the ARS Foreign Disease-Weed Science Research Unit at Ft. Detrick, Maryland; and Dr. Jorge Baldessari, peanut breeder from the Instituto Nacional de Tecnología Agropecuaria, Argentina.
This team of experts quickly got to work to find resistance to peanut smut, identify the genomic region responsible for resistance, develop resistant peanut cultivars, characterize the pathogen’s diversity and develop diagnostic tools for detecting the pathogen.
Finding Resistance In The U.S. Germplasm Mini Core
Since 2017, the team has been evaluating germplasm in Argentina for resistance to peanut smut. Thus far, more than 300 genotypes comprised of purified U.S. peanut mini core accessions, U.S. cultivars and breeding lines and purified accessions from the International Crops Research Institute for the Semi-Arid Tropics, known as ICRISAT, peanut collection have been tested. The team was successful in identifying sources of smut resistance, including eight accessions from the U.S. germplasm collection that had no disease over a testing period of three years. These accessions are being used to develop smut-resistant cultivars of all market types suitable for production in all peanut-growing regions of the United States. New sources of resistance continue to be discovered through additional years of testing.
Markers For Selection
Included in their studies, the team characterized a recombinant inbred line population designed to map smut resistance. Genotyping was conducted using the Khufu platform developed in Dr. Clevenger’s lab at HudsonAlpha Institute. A strong quantitative trait locus, or QTL, which is a region of DNA associated with a particular phenotypic trait and in this case is associated with resistance to peanut smut, was identified on chromosome 12. Markers for genotypic selection of this locus were developed and validated in field studies. These markers are over 99% accurate in selecting smut-resistant germplasm without actual field testing.
The ability to select for resistance by genotyping rather than years of phenotyping is amazing to say the least. The team has been able to reduce the number of lines to be phenotyped by 93% while maintaining a probability of over 99% that selected lines will be resistant.
This marker is now being used to quickly select smut-resistant materials in breeding programs developing resistant cultivars of all peanut market types. Runner types are being developed by Drs. Holbrook and Chamberlin, with the latter also developing smut-resistant Spanish and Virginia types. Dr. Naveen Puppala, New Mexico State University peanut breeder, is developing resistant Valencia types.
Monitoring The Pathogen
Characterization of the pathogen population in Argentina is essential to ensure breeding efforts are inclusive of all pathogen strains. In cooperation with the Fundación para el Estudio de Especies Invasivas in Argentina, the team was able to collect spores of the pathogen from different regions in the country. Characterization of these pathogen isolates indicated that the pathogen is uniform in Argentina, and no significant variants have been observed. However, these studies were limited in number, and the team continues to collect spores from fields in Argentina to ensure new variants of the pathogen do not emerge as resistant cultivars are produced. The team has generated a complete high-quality genomic sequence of the pathogen that will be published soon, which will allow the development of specific diagnostic assays for the pathogen as well as phylogenetic studies.
Molecular Diagnostics
Currently no diagnostic tools have been deployed to detect smut in peanut seed lots or soil. Dr. Dang has been working to solve this problem, but the task has proven difficult since the pathogen has not been reported in the United States. Dang has developed diagnostic assays to detect other fungal pathogens of peanut, and now that the team has generated a sequence of the pathogen genome, a diagnostic assay to detect smut is not far away.
Future Outlooks
Whether smut will eventually be detected in the United States is uncertain, but the possibility exists since the pathogen spores are easily spread by wind, weather events and trade. This team is dedicated to protecting U.S. peanut production and help eliminate the threat of smut, should it appear. They are also developing smut-resistant cultivars that are stacked with additional traits, such as the high-oleic trait and resistance to leaf spot, white mold, tomato spotted wilt virus, nematode and Sclerotinia blight.
This project has been funded by USDA-ARS and INTA projects, the USDA-ARS Plant Disease Recovery System and by Mars, Incorporated. USDA is an equal opportunity employer and provider. PG