Location: National Peanut Research Laboratory
2019 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
Thanks to two international collaborations we were able to accelerate the discovery and characterization of peanut germplasm, both diploid and tetraploid, with resistance to smut disease, and made this information public by publishing in peer review journals. Also, as part of our RNA interference (RNAi) project, we are generating a Database of Aspergillus genomes that we use to mine for common sequences to target by RNAi; for this we have uploaded to NCBI a total of 17 genomes of Aspergillus from Ethiopia, that will be published soon. We sequenced several gene fragments from approximately 300 isolates of Aspergillus section Nigri (causal agent of peanut crown rot) and found widespread of mutations that confer resistance to fungicides; this indicates a need for immediate change in the management practices of this disease. We continue our effort to provide curators at Banks of Germplasm with a large number of molecular markers for tropical plants, we uploaded to NCBI (the National Center for Biotechnology Information) 9,567 sequences for Melicoccus bijugatus that will be released along with an already accepted paper.
For leaf spot resistance field study, several susceptible and resistant breeding lines were identified. Select lines were utilized to correlate specific R-gene expression. Three R-genes on chromosome #9, six on chromosome #8, and one on chromosome #5 were highly correlated with leaf spot resistance. These candidate genes will be evaluated further to determine if gene regulated be attributed to allelic variation, gene-copy number, or other factors. For drought research, a middle season drought application to 162 peanut genotypes for the last several years identified drought susceptible and tolerant peanut lines. A validation drought study is in progress with 36 peanut genotypes in 5 replicated environmental controlled plots (Dawson, Georgia) targeting middle season drought tolerance. Information will facilitate drought tolerant peanut varieties.
For the current crop year 2019, 1,600 breeding progeny lines arranged from F2 to F7 were planted at Headland, Alabama, and Dawson, Georgia by the USDA-National Peanut Research Laboratory (NPRL) personnel and students from Auburn University, for selection of high yield, leaf spot and tomato spotted wilt virus (TSWV) resistances, as well as drought tolerance. Fifty advanced lines have been tested at three locations in Georgia and Alabama for yield and disease trials. Advanced breeding line named ‘AU16-28’ with drought tolerance characteristics was identified as a new promising line for release. We have planted 2 acres as breeder seeds for release. It is derived from the cross of ‘C76-16’ X “AT-3085 RO”. Another advanced breeding line ‘AU17-7’ derived from the cross of ‘Exp31-1516’ x ‘G02C’ has high yield and high oleic fatty acid content. It has been promoted to further Uniform Peanut Performance Tests (UPPT) performed at the NPRL in Dawson, Georgia, and at the USDA-Market Quality and Handling Research Unit in Raleigh, North Carolina.
Accomplishments
1. Identified wild species of peanut. ARS researchers in Dawson, Georgia identified wild species of peanut that even under conditions highly conducive for Aspergillus infection, did not accumulate aflatoxin. These species will be incorporated into our pre-breeding program. We also reported in two published papers, two genetic sources of resistance to peanut smut, a disease that can have devastating effect.
2. Resistance Gene Analogs or R-genes, associated with plant disease resistance in many important crops, were identified in peanut based on conserved DNA motifs and homologous gene cloning. ARS researchers in Dawson, Georgia evaluated peanut genotypes, with a wide range of leaf spot disease responses, in the field and under controlled environmental shelters. Leaf spot susceptible and resistant select lines were utilized to identify peanut R-genes. From 381 R-gene targets in published literature, 214 produced PCR products which were cloned, sequenced, and verified to have functional open reading frames (ORF). From this, 89 R-genes were evaluated utilizing quantitative real time PCR (qRT-PCR) identifying 39 up-regulated, 38 down-regulated, and 12 with both up- and down-regulated genes comparing resistant to susceptible lines. This work was published and the information is being utilized to develop molecular markers for leaf spot resistance. For drought study, several tolerant breeding lines were identified utilizing environmental controlled rainfall shelters. Drought tolerant lines, along with susceptible and release peanut varieties, will facilitate the identification of more drought regulated genes that can be applied as potential molecular markers in peanut breeding programs.
3. A genome-wide association study. ARS researcher in Dawson, Georgia conducted a genome-wide association study (GWAS) using Affymetrix SNP chip (version 2.0) to associate resistance to tomato spotted wilt (TSW), early leaf spot (ELS), and late leaf spot (LLS) evaluating 120 different peanut genotypes mainly from the U.S. peanut mini-core collection. A total of 158 quantitative trait loci (QTLs) were identified with phenotypic variation explained (PVE) from 10.2% to 24.1%, in which 112 QTLs are for resistance to TSW, 18 QTLs for ELS, and 28 QTLs for LLS. Among the 158 QTLs, there were six, four, and two major QTLs with PVE higher than 14% for resistance to TSW, ELS, and LLS, respectively. A number of candidate genes have been identified and will be evaluated further to validate functionality in peanut breeding program.
Review Publications
Arias De Ares, R.S., Sobolev, V., Massa, A.N., Orner, V.A., Walk, T., Simpson, S.A., Ballard, L.L., Puppala, N., Scheffler, B.E., De Blass, F., Tallury, S.P., Guillermo, S. 2018. New tools to screen wild peanut species for aflatoxin accumulation and genetic fingerprinting. Biomed Central (BMC) Plant Biology. https://doi.org/10.1186/s12870-018-1355-9.
Bressano, M., Massa, A.N., Arias De Ares, R.S., Oddino, C., De Blas, F., Faustinelli, P.C., Soave, S., Soave, J., Perez, M., Sobolev, V., Balzarini, M., Buteler, M.I., Seijo, G.J. 2019. Introgression of peanut smut resistance from landraces to elite peanut cultivars (Arachis hypogaea L.). PLoS One. https://doi.org/10.1371/journal.pone.0211920.
De Blas, F., Bressano, M., Teich, I., Balzarini, M., Arias De Ares, R.S., Manifesto, M., Costero, B., Oddino, C., Soave, S., Soave, J., Buteler, M., Massa, A.N., Seijo, G. 2019. Identification of smut resistance in wild Arachis species and its introgression into peanut elite lines. Crop Science. https://www.doi.org/10.2135/cropsci2018.10.0656.
Martinez-Castillo, J., Blancarte-Jasso, N.H., Chepe-Cruz, G., Nah-Chan, N., Ortiz-Garcia, M., Arias De Ares, R.S. 2019. Structure and genetic diversity in wild and cultivated populations of Zapote mamey (Pouteria sapota, Sapotaceae) from southeastern Mexico: its putative domestication center. Tree Genetics and Genomes. https://doi.org/10.1007/s11295-019-1368-z.
Mohammed, A., Chala, A., Ojieawo, C., Dejene, M., Fininsa, C., Ayalew, A., Hoisington, D., Sobolev, V., Arias De Ares, R.S. 2019. Integrated management of Aspergillus species and aflatoxin production in groundnut (Arachis hypogaea L.) through application of farm yard manure and seed treatments with fungicides and Trichoderma species. African Journal of Plant Science. https://doi.org/10.5897/AJPS2018.1688.
Sobolev, V., Walk, T., Arias De Ares, R.S., Massa, A.N., Lamb, M.C. 2019. Inhibition of aflatoxin formation in aspergillus species by peanut (Arachis hypogaea) seed stilbenoids in the course of peanut-fungus interaction. Journal of Agricultural and Food Chemistry. 67(22):6212-6221. https://doi.org/10.1021/acs.jafc.9b01969.
Reznikov, L.S., Vellicce, G.R., Mengistu, A., Arias De Ares, R.S., Gonzalez, V., De Lisi, V., Garcia, M.G., Rocha, C., Pardo, M., Castagnaro, A.P., Ploper, D. 2018. Disease incidence of charcoal rot (Macrophomina phaseolina) on soybean in north-western Argentina and genetic characteristics of the pathogen. Canadian Journal of Plant Pathology. 40(3):423-433. https://doi.org/10.1080/07060661.2018.1484390.
Dang, P.M., Lamb, M.C., Chen, C. 2018. Identification of expressed R-genes associated with leaf spot diseases in cultivated peanut. Molecular Biology Reports. 48:225-239. https://doi.org/10.1007/s11033-018-4464-5.
