2012 Annual Report
1a.Objectives (from AD-416):
(1) Develop peanut genomic tools and strategies to elucidate the molecular mechanisms that define crop defense pathways and regulation of resistance to diseases such as tomato spotted wilt virus (TSWV), leaf spots and aflatoxin contamination in peanut. (2) Evaluate corn germplasm that harbors resistance genes that reduce aflatoxin contamination and understand the responding genes and pathways in corn.
1b.Approach (from AD-416):
(1) Replicated laboratory and field screening and evaluation of peanut accessions for disease resistance will be conducted in order to identify the “resistant” germplasm for further genomic studies. The resistant germplasm will be utilized in molecular marker development for marker-assisted breeding. (2) ESTs (expressed sequence tags) will be generated from cDNA libraries constructed from seed and leaf tissues of two genotypes, Tifrunner and GT-C20. EST-derived SSR markers will be developed and peanut oligo-microarray will be produced for gene expression study. (3) Genetic mapping populations (RILs, recombinant inbred lines) will be produced from crosses of Tifrunner and GT-C20, and SunOleic 97R x NC94022. QTL mapping will be conducted for resistance to tomato spotted-wilt virus (TSWV) and leaf spots, and aflatoxin contamination. (4) Microarray experiments will be used to identify candidate genes in corn-Aspergillus flavus and drought stress interactions that are turned on or off during corn kernel development. The candidate genes identified from microarray will be verified or confirmed through real time PCR or other well established methods. Another goal is to develop a macroarray tool (membranes) using these candidate genes from microarray to assess resistance or drought tolerance in corn germplasm for their stability of expression in native crops under environmental conditions (e.g., drought) known to be conducive to aflatoxin contamination. The genes identified in corn kernels also will be applied in searching possible ‘orthologs’ in peanut genome and peanut germplasm.
Peanut production and consumer acceptability are adversely affected by several biotic/abiotic stresses and poor oil quality. In order to deal with these concerns, the developed genetic map from one peanut population derived from SunOleic 97R × NC94022 by Qin et al. (2012) using 190 subset with 172 markers was further advanced with additional 77 polymorphic marker loci on all 353 lines. The saturated genetic map possesses 249 loci distributed on 23 linkage groups with total map distance of 3,433.5 cM. Multiple phenotyping data of all lines on several economically important traits was used for quantitative trait loci (QTL) analysis, resulting in identification of a total of 155 QTLs with phenotypic variance (PVE) that ranged from 1.48 to 65.2% and the log-of-odds (LOD) ranged from 2.51 to 83.68. One major Quantitative Trait Loci (QTL) (16.7% PVE) for Tomato spotted wilt virus (TSWV) resistance, three major QTLs for late leaf spot (12.42 -20.59%), two major QTLs for growth habit (11.90 - 14.05% PVE) while one major QTL each for leaf color (10.43% PVE), pod shape (11.55% PVE) and pod reticulation (14.01% PVE), and four QTLs for seed color (10.12-18.45% PVE) were identified. QTL analysis also revealed that FAD2B gene contributes up to 74.03% PVE while FAD2A gene could contribute only 11.13% PVE for high oleic/linoleic (O/L) ratio. Interestingly, the A- and B-genome mutations of FAD2 were also found to contribute to other fatty acids, such as palmitic acid (PVE 21.26 and 27.77%) and gadoleic acid (PVE 13.73 and 10.32%), respectively. The markers linked to major QTLs could be utilized for peanut genetic improvement through molecular marker-assisted selection in breeding.
Identification of peanut expressed resistance genes. Peanut expressed sequence tag public database offers a possibility to identify expressed disease resistance genes for genetic study. ARS researchers at Tifton, Georgia, conducted data mining from the public database for potential plant disease resistance genes. As a result, a total of 1,053 R-gene-like expressed genes targeting different classes of known R genes were recovered. After further analysis, 385 expressed resistance-like genes were identified, and 28 molecular markers and two gene-specific markers were also developed. Interestingly, three markers with possible links to resistance to tomato spotted wilt virus (TSWV) have been mapped on the same map region. The expressed resistance-like genes provide large sequence dataset for expressed gene-tagged marker development and will be useful in future isolation of resistance genes from peanut.
Construction saturated genetic map for marker identification in peanut. A saturated genetic linkage map has potential to help the peanut breeder to visualize peanut genome and to apply biotechnology for improving peanut cultivar selection, but there is none available. A further saturated map using all 353 peanut inbred lines from one population has been developed by ARS scientists at Tifton, Georgia. The saturated genetic map possesses 249 loci distributed on 23 linkage groups with total map distance of 3,433.5 cM. This research showed the application of this map by identification of quantitative trait loci (QTLs) with multiple phenotype data such as one major QTL (16.7%) for tomato spotted wilt virus (TSWV) resistance and three major QTLs for late leaf spot (12.42 - 20.59%) resistance. This study also revealed that FAD2B gene contributes up to 74.03% while FAD2A gene could contribute only 11.13% for high oleic/linoleic (O/L) ratio. The markers linked to major QTLs could be utilized for peanut genetic improvement through molecular marker-assisted selection in breeding.
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Guo, B., Fedorova, N.D., Chen, X., Wan, C., Wang, W., Nierman, W., Bhatnagar, D., Yu, J. 2011. Gene expression profiling and identification of resistance genes to aspergillus flavus infection in peanut through EST and microarray strategies. Toxins. 3:737-753.
Pandey, M.K., Monyo, E., Ozias-Akins, P., Liang, X., Guimaraes, P., Nigam, S.N., Upadhyaya, H.D., Janila, P., Zhang, X., Guo, B., Cook, D.R., Bertioli, D.J., Michelmore, R., Varshney, R.K. 2012. Advances in Arachis genomics for peanut improvement. Biotechnology Advances. 30:639-651.
Wang, H., Penmetsa, R.V., Yuan, M., Gong, L., Zhao, Y., Guo, B., Farmer, A.D., Rosen, B.D., Gao, J., Isobe, S., Bertioli, D.J., Varshney, R.K., Cook, D.R., He, G. 2012. Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.). Biomed Central (BMC) Plant Biology. 12:10.
Guo, B., Yu, J., Ni, X., Lee, R.D., Kemerait, R.C., Scully, B.T. 2012. Crop stress and aflatoxin contamination: Perspectives and prevention strategies. In: Venkateswarlu, B., Shanker, A.K., Shanker, C., Maheswari, M., editors. Crop Stress and its Management: Perspectives and Strategies. London, NY: Dordrecht Heidelberg Springer. p. 399-427.
Holbrook Jr, C.C., Ozias-Akins, P., Chu, Y., Guo, B. 2012. Impact of molecular genetic research on peanut cultivar development. Agronomy. 1:3-17.