Research Project: Genetic Improvement of Peanut for Production in the Southwest United States Region

Location: Peanut and Small Grains Research Unit

2022 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
Progress was made on all three objectives. For Objective 1, a second year of phenotyping for early leaf spot resistance was completed on the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) mini-core collection. An initial set of recombinant inbred line (RIL) validation population members was selected based on preliminary genotyping. These members will be phenotyped in the coming year. DNA was also taken from the entire mapping population, the selected validation population members, and their respective parental lines for whole genome sequencing and subsequent analysis. For Objective 2, field evaluation of all breeding lines was completed. Breeding lines were identified for all generations that will be moved forward for further testing and advanced line performance trials. Greenhouse testing of F1 and F2 hybrids was completed, and selections were made to advance to field testing. Progress was also made related to the effects of cover and rotation crops on peanut pod rot. The first year of summer rotation crops was harvested, a second year of winter cover crop treatments was planted, and a second year of summer rotation crops was planted. Progress was made for Objectives 3. Year 4 of phenotyping for resistance to peanut smut was completed. This year’s phenotyping trials included purified accessions from the ICRISAT germplasm, and sources of smut resistance were identified in that material. Work continued on the X-ray system for phenotyping peanut smut. Potential problems with the original design were identified and the system was redesigned.

Accomplishments
1. Identification of germplasm immune to peanut smut. Peanut smut, a devastating disease caused by the fungus Thecaphora frezzii, is currently found only in South America but threatens peanut production worldwide. ARS researchers at Stillwater, Oklahoma, with colleagues in Argentina, evaluated 208 peanut genotypes comprised of germplasm accessions, breeding lines, and cultivars for resistance to T. frezzii in highly infested Argentinean fields. Among the genotypes evaluated for three years, eight entries appeared immune to peanut smut, with 0% disease incidence. An additional eight genotypes that were tested for two years also exhibited no infection by T. frezzii. Because the germplasm used in this study was purified by single seed descent and increased before evaluation, the entries identified as immune are a valuable resource for peanut breeding programs. The resistant entries will be used by breeders to develop locally adapted, high-yielding, smut-resistant cultivars, thereby protecting the U.S peanut industry should this emerging pathogen arrive in the country.

Review Publications
Chamberlin, K.D., Grey, T.L., Puppala, N., Holbrook, C.C., Isleib, T.G., Dunne, J., Dean, L.O., Hurdle, N.L., Payton, M.E. 2021. Comparison of field emergence and thermal gradient table germination rates of seed from high oleic and low oleic near isogenic peanut lines. Peanut Science. 48:131-143.
Otyama, P.I., Chamberlin, K., Ozias-Akins, P., Graham, M.A., Cannon, E.K.S., Cannon, S.B., MacDonald, G.E., Anglin, N.L. 2022. Genome-wide approaches delineate the additive, epistatic, and pleiotropic nature of variants controlling fatty acid composition in peanut (Arachis hypogaea L.). Genes, Genomes, Genetics. 12(1). Article jkab382. https://doi.org/10.1093/g3journal/jkab382.
Chamberlin, K., Bennett, R.S., Isleib, T.G., Copeland, S., Dunne, J.C. 2022. Registration of 'Comrade' peanut. Journal of Plant Registrations. Article 20233. https://doi.org/10.1002/plr2.20233.
Sayantan, S., Oakes, J., Cazenave, A.-B., Burow, M.D., Bennett, R.S., Chamberlin, K.D., Wang, N., White, M., Payton, P., Mahan, J., Chagoya, J., Sung, C.-J., Mccall, D.S., Thomason, W.E., Balota, M. 2022. Evaluation of the U.S. peanut germplasm mini-core collection in the Virginia-Carolina region using traditional and new high-throughput methods. Agronomy Journal. 12(8). Article 1945. https://doi.org/10.3390/agronomy12081945.