Location: National Peanut Research Laboratory
2020 Annual Report
Objectives
Objective 1. Characterize peanut pathogens, host responses, and host-plant interactions, including diversity of plant invasion and plant health genes, and use genomic and transcriptomic knowledge for discovery and development of novel methods or technologies to control diseases.
Objective 2. Identify, characterize, and evaluate peanut genes involved in disease resistance and drought tolerance, including discovery and elucidation of agriculturally-relevant candidate genes, and work with breeders to facilitate implementation into breeding programs.
Objective 3. In collaboration with Auburn University partners, develop and release superior peanut cultivars and improved germplasm with disease resistance and input-use efficiency.
Approach
Double strand RNA (dsRNA) that targets aflatoxin synthesis can be used as a therapeutic control of mycotoxins in peanut without genetic transformation. Knowing the genetic makeup of peanut pathogens (Cercospora arachidicola, Cercosporidium personatum, Thecaphora frezzi, Aspergillus (A.) niger, A. flavus and A. parasiticus) allows for a better disease management and longer effectiveness of control. Identification and validation of molecular markers associated with biotic (early and late leaf spot, peanut smut, crown rot disease, mycotoxin producing fungi), and abiotic (drought) stress resistance in wild peanuts and land races will accelerate breeding programs.
Progress Report
Fifteen molecular duplexes and various combinations of them were applied by ARS researchers at Dawson, Georgia, to peanut plants in the field with the goal that the plants will activate their silencing machinery, accumulate small molecules in their seeds that could prevent the fungus Aspergillus from making aflatoxins. Seeds were challenged with Aspergillus flavus in the laboratory for evaluation of aflatoxin accumulation, and their nucleic acids were sequenced. For one combination of molecular duplexes we observed a reduction in aflatoxin of 40 % (p = 0.02) and 30 %. In 2020, working with an engineer, ARS researchers at Dawson, Georgia, are testing a more efficient delivery system with the goal of increasing effectiveness. ARS researchers at Dawson, Georgia, also studied the generation of silencing signals at the application site by sequencing nucleic acid libraries, a manuscript is under review.
ARS researchers at Dawson, Georgia, sequenced the genomes of five isolates of the fungus Thecaphora frezii that causes peanut smut. So far, ARS researchers at Dawson, Georgia, have been able to assemble the mitochondrial genome and several genes that are target of fungicides used on peanut crops. In this fungus, ARS researchers at Dawson, Georgia, identified mutations known to confer resistance to strobilurin and carboxamide fungicides.
ARS researchers at Dawson, Georgia, are currently surveying hundreds of isolates of Aspergillus niger from Georgia peanuts, the fungus causes crown-rot in peanut, the goal is to determine if there is broad resistance to six common fungicides used in the peanut crop.
For leaf-spot studies, the newly identified 24 differentially regulated resistance (R)-genes were further evaluated by ARS researchers at Dawson, Georgia, for genomic sequence differences between leaf spot resistant and susceptible lines. Amplification and sequencing of target coding regions of the 24 R-genes candidates of selected lines (4 susceptible, 4 resistant and 3 checks) was performed. The results identified 4 R-genes with differences at the nucleotide level between susceptible and resistant lines. These R-gene sequence differences will be validated through utilization of single nucleotide polymorphism (SNP) genotyping methods.
For a drought study, a sub-set of 18 peanut lines from the 36 previously evaluated lines are currently being evaluated by ARS researchers at Dawson, Georgia, for middle season drought tolerance utilizing environmentally controlled rainout shelters. Physiological measurements will be conducted, and leaves will be collected during drought treatment. Yield will be evaluated at harvest to correlate it with drought tolerance. Identification of resistant lines will be valuable as novel sources of genetic materials for future crosses.
In year 2020, 1,400 breeding progeny lines from F2 to F7 were planted at two locations, Headland, Alabama and Dawson, Gerogia, with the participation of the USDA-National Peanut Research Laboratory (NPRL) personnel and students from Auburn University, Alabama. The goal is to select for high yield, leaf spot and TSWV resistance, as well as drought tolerance. Forty-eight advanced lines have been tested at three locations in Georgia and Alabama for yield and disease trials. Advanced breeding line named ‘AU14-34’, a Virginia type peanut with high yield, high oleic and strong resistance to leaf spot will be released in 2021. Another two advanced breeding lines ‘AU18-35’ and ‘AU18-53’ have been tested under Uniform Peanut Performance Tests (UPPT) in 2020.
Accomplishments
1. Progress in non-transgenic delivery of molecular duplexes to prevent aflatoxin in peanut, and characterization of predominant Aspergillus in Ethiopia. ARS scientists in Dawson, Georgia, identified at least one group of molecular duplexes that applied to peanut plants in the field, resulted in a 40 % and 30 % reduction of aflatoxin when the seeds of those plants were challenged with Aspergillus on separate experiments. In a survey of aflatoxigenic Aspergillus fungi that invade peanuts in Ethiopia, ARS scientists in Dawson, Georgia, in collaboration with scientists from Dire Dawa, Ethiopia were able to identify, sequence and publish 16 genomes of representative isolates, this information could be used to design technology (molecular duplexes) targeting those isolates in Ethiopia.
Drought is one of the leading factors that negatively affects the peanut crop. Researchers from New Mexico and Texas had identified single-nucleotide polymorphism (SNP) markers associated with drought resistance in peanut C76-16; scientists from ARS in Dawson, Georgia, validated 25 of those markers and together they published the work. These markers will be essential in breeding efforts toward drought tolerance in peanut.
Fragmentation and loss of habitat can trigger extinction of tropical species before they can be identified or preserved in banks of germplasm, and those that are preserved, require molecular tools for their proper identification. Though the genomes of many plant species are being sequenced, knowledge of tropical plants is lagging. ARS scientists at Dawson, Georgia, supported USDA-Germplasm Conservation efforts by publishing 1,900 molecular markers for 7 species of tropical plants that produce edible fruits or shoots, the markers can be used for species identification and conservation in banks of germplasm, as well as for studies in population genetics.
2. Peanut breeding lines for drought tolerance and leaf-spot resistance. Leaf-spot disease and drought are among the top factors causing loses in the peanut crop. Leaf-spot field evaluations by ARS scientists in Dawson, Georgia, have identified 4 peanut breeding lines that have significantly higher resistance compared to others, and they will be incorporated into the peanut breeding program. Twenty-four R-genes were identified to be highly correlated to leaf spot resistance and will be further evaluated for application in molecular breeding strategy. In addition, 2 lines were identified to be drought tolerant and will be incorporated into the breeding program.
3. Advanced breeding line to be released in 2021. Leaf-spot disease and drought are among the top factors causing loses in the peanut crop. Forty-eight advanced lines have been tested at three locations in Georgia and Alabama by ARS scientists from Auburn, Alabama, and Dawson, Georgia, working performing yield and disease trials. Advanced breeding line named ‘AU14-34’, a Virginia type peanut with high yield, high oleic and strong resistance to leaf spot will be released in 2021.
Review Publications
Bhogireddy, S., Xavier, A., Garg, V., Leyland, N., Arias De Ares, R.S., Payton, P.R. 2020. Genome-wide transcriptome and physiological analyses provide new insights into peanut drought response mechanisms. Scientific Reports. 10:4071. https://doi.org/10.1038/s41598-020-60187-z.
Zhang, H., Chu, Y., Dang, P.M., Tang, Y., Jiang, T., Clevenger, J.P., Ozias-Akins, P., Holbrook Jr, C.C., Wang, M.L., Campbell, H., Hagan, A., Chen, C. 2020. Identification of QTLs for resistance to leaf spots in cultivated peanut (Arachis hypogaea L.) through GWAS analysis. Theoretical and Applied Genetics. 133:2051-2061. https://doi.org/10.1007/s00122-020-03576-2.
Arias De Ares, R.S., Ballard, L.L., Duke, M.V., Simpson, S.A., Liu, X.F., Orner, V.A., Sobolev, V., Scheffler, B.E., Martinez-Castillo, J. 2020. Development of nuclear microsatellite markers to facilitate germplasm conservation and population genetics studies of five groups of tropical perennial plants with edible fruits and shoots: ranbutan (Nephelium lappaceumt). Genetic Resources and Crop Evolution. https://doi.org/10.1007/s10722-020-00965-w.
Arias De Ares, R.S., Cazon, I., Massa, A.N., Scheffler, B.E., Sobolev, V., Lamb, M.C., Duke, M.V., Simpson, S.A., Conforto, C., Paredes, J., Soave, J., Buteler, M., Rago, A.M. 2019. Mitogenome and nuclear-encoded fungicide-target genes of Thecaphora frezii- causal agent of peanut smut. Fungal Genomics and Biology. (9)1:160. https://doi.org/10.35248/2165-8056.19.9.160.
Martinez-Castillo, J., Arias De Ares, R.S., Andueza-Noh, R.H., Ortiz-Garcia, M.M., Irish, B.M., Scheffler, B.E. 2019. Microsatellite markers in Spanish lime (Melicoccus bijugatus Jacq., Sapindaceae), a neglected Neotropical fruit crop. Genetic Resources and Crop Evolution. 66(7):1371-1377. https://doi.org/10.1007/s10722-019-00815-4.
Portilla, M., Blanco, C.A., Arias De Ares, R.S., Zhu, Y. 2020. Effect of two Bacillus thuringiensis proteins on the development of the fall armyworm after a seven-day exposure. Southwestern Entomologist. https://doi.org/10.3958/059.045.0208.
Zhang, H., Wang, M.L., Schaefer, R., Dang, P.M., Jiang, T., Chen, C. 2019. GWAS and co-expression network reveal ionomic variation in cultivated peanut. Journal of Agricultural and Food Chemistry. 63(43)12026-12036. https://doi.org/10.1021/acs.jafc.9b04939.
Arias De Ares, R.S., Mohammed, A., Orner, V.A., Faustinelli, P.C., Lamb, M.C., Sobolev, V. 2020. Sixteen draft genomes sequences representing the genetic diversity of Aspergillus flavus and Aspergillus parasiticus colonizing peanut seeds in Ethiopia. Microbiology Resource Announcements. 9(30):e00591-20. https://doi.org/10.1128/MRA.00591-20.
