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ARS Home » Southeast Area » Tifton, Georgia » Crop Protection and Management Research » Research » Research Project #425281

Research Project: Developing Genomic Approaches to Improve Resistance to Diseases and Aflatoxin Contamination in Peanut and Corn

Location: Crop Protection and Management Research

2018 Annual Report


Objectives
1. Evaluate molecular markers and saturated genetic maps that can be used to identify quantitative trait loci (QTLs) associated with important agronomic traits of peanut and develop effective marker-assisted selection methods for peanut breeders. 1.A. Construction and use of saturated genetic map for identification of quantitative trait loci (QTLs) associated with disease resistance and oil quality. 1.B. Application of marker-assisted selection method for breeding to combine two traits into one genotype. 2. Evaluate corn germplasm for drought tolerance, understand the underlying molecular mechanisms, and develop molecular markers for identifying drought tolerant corn germplasm. 2.A. Identification and re-sequencing of genes in response to drought stress and development of polymorphic markers associated with drought tolerance in corn. 2.B. Corn germplasm and breeding lines re-evaluation for preharvest aflatoxin resistance and drought tolerance and genotyping with the polymorphic markers for association study.


Approach
1. Genotype and phenotype data for a genetic segregation population can be associated with QTLs and markers for trait of study and a genetic linkage map could be constructed. Peanut germplasm accessions have variable levels of disease resistance. The mapping population(s) will be genotyped using primarily SSRs, and ultimately the sequence-based markers will be added into this collection when Peanut Genome Sequence Project will be completed soon, in which the four parental line, Tifrunner, GT-C20, SunOleic 97R and NC94022, and their RILs will be sequenced. Field phenotyping for TSWV, leaf spots and other agronomic traits will be conducted for at least two years and at least two different locations with at least three replications. 2. Marker-assisted breeding will be employed as an example to combine two different traits with known linked marker(s) for faster and accurate transfer of trait from donor to elite lines through a back cross program or pedigree selection. Two traits can be combined into one productive peanut cultivar. Available markers for nematode, rust, and high oleic traits and new markers identified for TSWV and leaf spots will be compiled. The outcome of these efforts will enable more precise and effective molecular breeding for peanut improvement. 3. Drought stress during the late kernel development enhances aflatoxin contamination before harvest. The differences in drought-tolerance or -sensitivity of different corn accessions will display different profiles of expressed genes in developing kernels in response to A. flavus infection and the drought stress. It is possible to identify different genes responding to drought stress, and characterize the genes that may be associated with drought tolerance in different corn lines. Genes/markers associated with drought tolerance will be identified as “candidate” genes for association studies of resistance to Aspergillus flavus and preharvest aflatoxin contamination (PAC) and used in germplasm screening for drought tolerance. 4. Drought tolerance is a characteristic that has the potential to serve as an indirect selection tool for resistance to preharvest aflatoxin contamination (PAC). The outcome of these efforts will enable effective method to screen germplasm for drought tolerance and resistance to PAC in breeding program using marker-assisted selection.


Progress Report
This is the final report for the project, which terminated February 27, 2018 and has been replaced by the new project 6048-21000-028-00D "Improvement of Genetic Resistance to Multiple Biotic and Abiotic Stresses in Peanut." The primary focus of this research was to develop and employ genomic tools and resources to identify genetically diverse corn and peanut germplasm that harbor resistance genes/markers and to elucidate resistant mechanisms. Development of the molecular tools and resources for construction of genetic linkage maps and quantitative trait loci (QTL): Genetic linkage maps are critical for genetic study as a road-map to visualize genetic variation and to identify the QTL underlining targeted traits. During the life of this project, two intra-specific recombined inbred line (RIL) populations have been developed and used for genetic studies by the International Peanut Genome Consortium and the U.S. Peanut Genome Sequencing Project. The mapped QTLs associated with resistance to TSWV (Tomato spotted wilt virus), early leaf spot, late leaf spot, and oil quality traits such as high or low oil content, as well as high oleic acid have been used to develop a new MARS (marker-assisted recurrent selection) population in order to pyramid all or most favorable alleles for breeding peanut cultivars with high oleic acid of low or high oil contents and resistance to TSWV and leaf spots (early and late). Furthermore, 141 and 118 RILs from the “S” and the “T” population, respectively, have been re-sequenced under the international peanut genome sequencing project. Ultra-high density SNP-based maps have been developed and used for tetraploid genome assembly, which was released on December 25, 2017. The first high-density genetic map and the first recombination bin map for peanut have been constructed with 8,869 and 11,106 (5816 bins) markers, respectively, and the major markers/genes have been identified for peanut resistance to early leaf spot, late leaf spot and TSWV, which could be used for molecular-assisted breeding selection.


Accomplishments
1. Deciphered the relationship of corn drought stress responses and aflatoxin production. In the field, the production of aflatoxin is exacerbated by drought stress, which also exposes the fungus to elevated temperatures and drought stress. Drought also reduces the ability of corn and peanut to resist the growth of the toxin producing fungi. In order to understand how the corn crop interacts with drought stress and the fungal pathogen resulting in aflatoxin production in the field, ARS researchers at Tifton, Georgia, investigated corn responses to drought stress to identify factors contributing to aflatoxin resistance and drought tolerance. This was done by using biotechnology such as transcriptomics, proteomics, metabolomics, and genome-editing, and studying the oxidative stress related chemical compounds, carbohydrate, and lipid metabolism related to corn drought responses and aflatoxin resistance. They also identified secondary metabolites including aflatoxin, aflatrem, cyclopiazonic acid, and kojic acid with potential antioxidant benefit in the fungus. The potential link between aflatoxin producing fungus Aspergillus flavus, drought stress, reactive oxygen species, and aflatoxin contamination in the field was also revealed. The environmental stress response mechanisms in corn and the fungus provide a direction for understanding the interactions and enhancement of host crop resistance through manipulation of host antioxidant capacity using genome-editing technology in order to mitigate aflatoxin contamination in agriculture commodities and improve food safety and security.


Review Publications
Fountain, J.C., Koh, J., Yang, L., Pandey, M.K., Nayak, S.N., Bajaj, P., Zhuang, W., Chen, Z., Kemerait, R.C., Lee, R.D., Chen, S., Varshney, R.K., Guo, B. 2018. Proteome analysis of Aspergillus flavus isolate-specific responses to oxidative stress in relationship to aflatoxin production capability. Scientific Reports. 8:3430. https://doi.org/10.1038/s41598-018-21653-x.
Yang, L., Fountain, J.C., Ji, P., Ni, X., Chen, S., Lee, R.D., Kemerait, R.C., Guo, B. 2018. Deciphering drought-induced metabolic responses and regulation in developing maize kernels. Plant Biotechnology Journal. p. 1-13. https://doi.org/10.1111/pbi.12899.
Shasidhar, Y., Vishwakarma, M.K., Pandey, M.K., Janila, P., Variath, M.T., Manohar, S., Guo, B., Varshney, R.K. 2017. Molecular mapping of oil content and fatty acids using dense genetic maps in groundnut (Arachis hypogaea L.). Frontiers in Plant Science. 8:794. https://doi.org/10.3389/fpls.2017.00794.
Zhao, C., Qiu, J., Agarwal, G., Wang, J., Ren, X., Xia, H., Guo, B., Ma, C., Bertioli, D.J., Varshney, R.K., Pandey, M.K., Wang, X. 2017. Genome-wide discovery of microsatellite markers from diploid progenitor species, Arachis duranensis and A. ipaensis, and their application in cultivated peanut (A. hypogaea). Frontiers in Plant Science. 8:1209. https://doi.org/10.3389/fpls.2017.01209.
Agarwal, G., Clevenger, J., Pandey, M.K., Wang, H., Shasidhar, Y., Chu, Y., Fountain, J.C., Choudhary, D., Culbreath, A.K., Liu, X., Huang, G., Wang, X., Deshmukh, R., Holbrook Jr, C.C., Bertioli, D.J., Ozias-Akins, P., Jackson, S.A., Varshney, R.K., Guo, B. 2018. High-density genetic map using whole-genome re-sequencing for fine mapping and candidate gene discovery for disease resistance in peanut. Plant Biotechnology Journal. 16:1954-1967. https://doi.org/10.1111/pbi.12930.
Wang, H., Guo, X., Pandey, M., Ji, X., Varshney, R.K., Nwosu, V., Guo, B. 2017. History and impact of the International Peanut Genome Initiative: the exciting journey toward peanut whole-genome sequencing. In: Varshney, R.K., Pandey, M.K., Puppala, N., editors. The Peanut Genome, Compendium of Plant Genomes. Cham, Switzerland: Springer International Publishing. p. 117-134. https://doi.org/10.1007/978-3-319-63935-2_8.