Location: Peanut and Small Grains Research Unit
2023 Annual Report
Objectives
The long-term objective of this research is to develop and release high oleic peanut cultivars with superior oil chemistry, disease resistance, and agronomic performance. Over the next 5 years this research proposal will address the following objectives:
OBJECTIVE 1: Identify new sources of resistance to industry-relevant peanut pathogens, and use improved marker assisted selection (MAS) methods and QTL analyses to incorporate those genes into existing and new peanut cultivars.
Subobjective 1A: Phenotype existing recombinant-inbred line (RIL) populations and the minicore collection from the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) for Sclerotinia blight and/or early leaf spot resistance and the U.S. mini-core germplasm collection for southern blight resistance in field trials.
Subobjective 1B: Genotype existing RIL populations and the U.S. and ICRISAT mini-core germplasm collections using a 48K SNP micro-array chip for tetraploid peanut; genotype existing RIL populations with SSR markers associated with Sclerotinia blight resistance. Analyze phenotypic and genotypic data collected in Subobjectives 1A and 1B to identify possible QTL for disease resistance and design molecular markers to be used in MAS breeding.
OBJECTIVE 2: Develop improved peanut varieties with superior genetic improvements and agronomic and plant health traits, including disease resistance, early maturity, elevated yield, oil, drought tolerance, and seed quality.
Subobjective 2A: Develop and release elite high-oleic, high-yielding, and/or early maturing runner, virginia, and spanish peanut cultivars with superior resistance to Sclerotinia blight, southern blight, drought and/or pod rot that are adapted for production in the SW United States.
Subobjective 2B: Phenotype U.S. peanut mini-core for drought tolerance and plant canopy architecture.
Subobjective 2C: Determine effects of cover crop mixtures and rotation crops on Pythium pod rot in susceptible commercial cultivars.
OBJECTIVE 3: Discover and characterize new genes from cultivated and wild Arachis species in the U.S. National Peanut Germplasm Collection for resistance to existing and emerging diseases, such as peanut smut.
Subobjective 3A: Phenotype the U.S. mini-core collection and other germplasm for resistance to peanut smut and develop new methodologies for high-throughput screening of peanut pods for the presence of peanut smut.
Subobjective 3B: Conduct crossing experiments between smut resistant germplasm and U.S. peanut cultivars to develop and release new smut resistant peanut varieties suitable for production in the Southwestern U.S.
Subobjective 3C: Phenotype wild Arachis species for resistance to Sclerotium rolfsii.
Approach
Objective 1: Two RIL populations (CAP and Sclerotinia marker) and germplasm collections will be evaluated for Sclerotinia blight and/or early leaf spot resistance in separate field experiments for three years. The U.S. mini core collection will also be evaluated for Sc. rolfsii resistance for three years. Genotyping of RIL populations will also be conducted using the Axiom Arachis Custom Array for tetraploid peanut, covering 48K SNPs as well as SSR markers identified as flanking the region reported as a possible QTL for Sclerotinia blight resistance. Phenotype and genotypic data will be combined for quantitative trait loci (QTL) mapping. Multiple methods for QTL detection will be implemented including interval mapping, and composite interval mapping. Phenotypic coefficients of variation and heritabilities also will be estimated. Genetic maps will be constructed.
Objective 2: Parental lines being used in such crosses include Arachis hypogaea L. cultivars, advanced breeding lines, and plant introductions (PIs) with demonstrated disease resistance and/or drought tolerance. For each cross performed, a modified bulk selection breeding method will be used. Breeding lines will be advanced annually, screening for disease resistance, oil composition, and agronomic performance. F7 generation ines will be entered into advance performance trials such as the Oklahoma Peanut Variety Tests, advanced line disease resistance tests and the national Uniform Peanut Performance tests and tested by the USDA ARS Peanut Market Qualtiy lab before release. The U.S. mini-core collection will be evaulated for drough tolerance and canopy architecture by monitoring performance under water deficit irrigation and collecting data on leaf wilting, paraheliotropism, normalized difference vegetation index, upper canopy temperature, flower abundance, SPAD chlorophyll stability, and descriptive canopy traits. The canopy traits will be collected using a LiDAR camera. A four-year experiment to determine the effect of cover crops on pod rot persistence will be conducted. Experimental treatments will include combinations of three winter cover crops and two rotation crop sequences.
Objective 3: The U.S. mini-core collection and other selected genotypes will be evaluated for at least 3 years in T. frezzii-infested fields in Manfredi, Argentina. To incorporate newly found smut resistance into adapted peanut lines, crossing and early generation breeding line and cultivar development will be conducted. Prototypes of a new smut screening technology will be developed and shipped to Argentina and test. Seeds will be removed from pods and replaced with talcum powder to simulate T. frezzii spores. Acoustic measurements will be taken from twenty pods of each treatment. To discover new southern blight resistance among wild Arachis species, experimental treatments will include a total of 62 accessions representing 26 species of Arachis, in addition to the susceptible cultivar Florunner.
Progress Report
This is the final report for project number 3070-21220-008-000D, entitled “Development of Improved Peanut Cultivars and Germplasm for the Southwest Peanut Region of the United States”, which terminated in January 2023 and continues as new project, "High Oleic Peanut Cultivars and Germplasm with Improved Disease Resistance for the Southwestern United States." Progress was made toward the completion of all three objectives. For Subobjective 1A, we completed a four-year evaluation of recombinant inbred line (RIL) populations for Sclerotinia blight resistance. The U.S. peanut mini-core collection was screened for southern blight in the field for three years, and accessions with high resistance to web blotch were also identified in the study. Accessions from the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) mini-core collection were purified through single seed descent and evaluated for field resistance to early leaf spot over three years. For Subobjective 1B, the U.S. and ICRISAT mini-core collections and two Sclerotinia blight RIL populations were genotyped using the single nucleotide polymorphism (SNP) array for tetraploid peanut and the Khufu analysis platform. The genotypic data collected for the germplasm collections will be correlated with phenotypic data to identify candidate quantitative trait loci (QTL) associated with disease resistance. Analyses of the genotypic and phenotypic data collected from the Sclerotinia RIL populations identified two QTL associated with resistance, and these QTL are being validated in the field in 2023. For Subobjective 2A, a new high-oleic Virginia-type cultivar, ‘Comrade’, was released for production in 2021. ‘Comrade’ has a high percentage of super jumbo pods, a characteristic necessary for the export markets. For Subobjective 2B, the U.S. mini-core was evaluated in tri-state study (Oklahoma, Texas, and Virginia) over three years for drought resistance using manual and high-throughput phenotyping methods. Experiments identified drought-associated traits that were consistent across diverse environments, as well as vegetation indices measured by unmanned aerial vehicles that showed promise for high-throughput phenotyping of drought resistance and agronomic traits. For Subobjective 2C, three winter cover crop treatments (no cover crop, cereal rye, and cereal-brassica mixture) and two rotation crop sequences (peanut-cotton-cotton-peanut and peanut-corn-corn-peanut) were planted over four years to assess effects on Pythium peanut pod rot. 2023 is the last year of the experiment; the treatments will be evaluated this autumn using a susceptible cultivar. For Subobjective 3A, over 250 accessions from germplasm collections were screened for peanut smut resistance in Argentina over five years. We identified at least 12 highly resistant accessions in the U.S. mini-core that exhibited zero peanut smut infection over three years of testing. Additional resistant accessions were identified in the ICRISAT mini-core. An X-ray system for phenotyping peanut smut was designed and constructed, and the system is currently being tested using faux-infected pods. Machine learning algorithms for automatic classification of infected and healthy pods are also in development. For Subobjective 3B, a total of 40 crossing combinations were made to incorporate smut resistance into cultivated runner, Spanish, and Virginia market types. Six resistant sources identified in Subobjective 3A were crossed with high-oleic cultivars currently in production. Over 700 F1 seed are being genotyped to confirm hybridity and will be used in back-crossing experiments to develop smut-resistant cultivars over the next several years. For Subobjective 3C, experiments evaluating 18 accessions of 15 wild Arachis species for resistance to Athelia (Sclerotium) rolfsii were completed. These experiments identified an accession of Arachis microsperma with resistance comparable to the most resistant cultivated peanuts.
Accomplishments
1. Discovery of a major QTL associated with peanut smut resistance. Peanut smut is currently present only in South America but is a devastating emerging disease that threatens peanut production worldwide. ARS researchers in Stillwater, Oklahoma, and Tifton, Georgia, with colleagues in Argentina, Alabama, and Georgia, identified a major quantitative trait locus (QTL) on chromosome 12 that is associated with strong resistance to peanut smut. DNA markers for this QTL were developed and are being used to select resistant lines within U.S. peanut breeding programs. The value of the U.S. peanut crop is greater than $1 billion annually. Discovery of this QTL preemptively protects the nation’s peanut industry by enabling rapid development of smut-resistant cultivars in case the smut pathogen arrives in the U.S.
Review Publications
Qiu, G., Liu, Y., Wang, N., Bennett, R., Weckler, P.R. 2023. Non-destructive method for measuring kernel weights from intact peanut pods using soft X-ray imaging. Agronomy. 13(4). Article 1127. https://doi.org/10.3390/agronomy13041127.
Ospina-Maldonado, S., Castlebury, L.A., Bennett, R.S., Salgado-Salazar, C. 2022. Peanut smut: a diagnostic guide. Plant Health Progress. 23:492-496. https://doi.org/10.1094/PHP-10-21-0131-DG.
Chamberlin, K.D., Baldessari, J., Bennett, R., Clevenger, J.P., Holbrook Jr, C.C., Tallury, S.P., Chu, Y., Ozias-Akins, P., Conde, M.B., Payton, M.E. 2022. Identification of germplasm resistant to peanut smut. Peanut Science. 49(1):1-16. https://doi.org/10.3146/0095-3679-491-PS21-10.
Bennett, R., Burow, M.D., Balota, M., Chagoya, J., Sarkar, S., Sung, C., Payton, M.E., Wang, N., Payton, P.R., Chamberlin, K.D., Mornhinweg, D.W. 2022. Response to drought stress in a subset of the U.S. peanut mini-core evaluated in Oklahoma, Texas, and Virginia. Peanut Science. 49(1):71-87. https://doi.org/10.3146/0095-3679-491-PS21-14.
