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United States Department of Agriculture

Agricultural Research Service


Location: Crop Genetics Research

2009 Annual Report

1a. Objectives (from AD-416)
Determine the inheritance and identify molecular markers linked to genes controlling resistance to Macrophomina phaseolina; identify differential sources of resistance/tolerance to Asian soybean rust and identify molecular markers associated with responsible genes; identify differential sources of resistance/tolerance and associated molecular markers for the Phomopsis/Diaporthe complex; and conserve available genetic diversity in genus Glycine; acquire and characterize new accessions to enhance the southern USDA Soybean Germplasm Collection.

1b. Approach (from AD-416)
Phenotype an F5 derived recombinant inbred (RIL) population segregating for resistance to Macrophomina phaseolina in replicated, multi-location, multi-year field tests, create a molecular map of the RIL population, determine the inheritance of resistance and identify molecular markers linked to resistance loci. Develop populations segregating for resistance to Phakopsora pachyrhizi. Phenotype selected populations in the field in Paraguay, determine whether resistance loci represent new genes, identify molecular markers linked to any new resistance loci, develop RIL populations as needed, and select for enhanced resistant germplasm. Evaluate lines identified and evaluated in Paraguay in the quarantine facility at Stoneville against US and Mississippi ASR isolates. Screen selected lines from the USDA-ARS germplasm collection for resistance to Phomopsis seed decay (PSD). Create molecular mapping populations, determine whether resistance loci represent new genes, identify linked molecular markers, and determine the inheritance of any new resistance genes. Incorporate novel resistance genes into germplasm readily suitable for use in the breeding industry. Characterize, pure-line, maintain purity, and increase seed of the approximately 6,500 MG V-VIII accessions of the USDA-ARS Soybean Germplasm Collection grown at Stoneville, MS. Submit pure-lined and detailed characterization of new accessions to the collection. Provide quality seed to the collection for use by soybean researchers worldwide and to maintain viable seed in the collection.

3. Progress Report
The research of this project is focused on reducing soybean yield losses from disease through genetic improvement. Three diseases (charcoal rot, soybean rust, and Phomopsis seed decay) are targeted in the research which is proceeding according to plan. The research involves major field studies both in the U.S. (charcoal rot and Phomopsis) and in Paraguay (soybean rust). Important soybean rust experiments were also conducted in the Quarantine Facility at Stoneville, MS. Extensive molecular marker assays, pathology assays, and seed quality assays were conducted in the laboratory facilities of the project. In addition to the research program, the project also maintains the southern portion of the USDA-ARS Soybean Germplasm Collection (MG V-VIII). Field experiments in two locations were established to measure charcoal rot resistance within a select group of about 26 cultivars and a 271 member recombinant inbred population segregating for resistance. Sampling and data collection are proceeding as expected. In addition, other resistant x susceptible crosses have been made. Last season in Paraguay (Dec 2008 to May 2009), genetic experiments examined the segregation of rust resistance in more than 10 different populations. Although analysis of the data is not complete, so far two new sources of Rpp1 and one new source of Rpp3 and Rpp4 have been identified. The new Rpp4 source likely has a new alternative allele. Also identified was an apparent new rust phenotype designated as “localized tan”. Additionally, several resistant breeding lines are near yield testing. In the Quarantine Facility at Stoneville, research also identified new sources of soybean rust resistance to specific Mississippi rust isolates. For the Phomopsis seed decay research, field trials are underway to identify potential resistant parental lines. Experiments are proceeding according to plan. Seed increase plots for the germplasm collection were established and are being maintained appropriately. Rust research is being done in cooperation with the Camara Paraguaya de Exportadores de Cereales y Oleaginosas (CAPECO) AGREEMENT NO.: 58-0206-5-F176. Other research is being conducted with scientists at other institutions including: 6402-21220-010-08R, Screening Germplasm and Breeding for Resistance to Phomopsis Seed Decay in Soybean (USB # 9261); 6402-21220-010-05R Identification and Utilization of Exotic Germplasm to Improve Soybean Productivity; 6402-21220-010-06R, Genetics and Mapping of Genetic Inheritance of Charcoal Rot Resistance; and 6402-21220-010-07R Coupling High Throughput Genetic and Phenotypic Information for Yield Enhancement. Separate reports present progress under these agreements.

4. Accomplishments
1. Genetics and Mapping of Adult Plant Rust Resistance in Soybean PI 587886 and PI 587880A. Soybean rust can be a devastating disease if environmental conditions are conducive. Development of naturally resistant soybean lines can be the most economical way of ameliorating the effects of the disease. In this research we determined the genes controlling rust resistance in two soybean genotypes. These genotypes are being used as the source of resistance in plant breeding programs designed to develop soybean rust resistant cultivars.

Review Publications
Li, S., Hartman, G.L., Chen, Y. 2009. Evaluation of Aggressiveness of Fusarium virguliforme Isolates That Cause Soybean Sudden Death Syndrome. Journal of Plant Pathology.91(1):77-86

Li, S., Hartman, G.L., Domier, L.L., Boykin, D.L. 2008. Quantification of Fusarium solani f. sp. glycines Isolates in Soybean Roots by Colony-forming Unit Assays and Real-time Quantitative PCR. Journal of Theoretical and Applied Genetics. 117:343-352.

De. Fraias Neto, A.L., Schmidt, M., Hartman, G.L., Li, S., Diers, B.W. 2008. Greenhouse Inoculation Methods for Evaluating Resistance of Soybean to Sudden Death Syndrome. Brazilian Journal of Agricultural Research. 43:1475-1482.

Smith, J.R., Mengistu, A., Nelson, R.L., Paris, R.L. 2008. Identification of Soybean Accessions with High Germinability in High-temperature Environments. Crop Science. 48:2279-2288

Li, S. 2009. Reaction of Soybean Rust Resistant Lines Identified in Paraguay to Mississippi Isolates of Phakopsora pachyrhizi, the Causal Agent of Soybean Rust. Crop Science. 49(3):887-894

Hyten, D.L., Smith, J.R., Frederick, R.D., Tucker, M.L., Song, Q., Cregan, P.B. 2009. Bulk Segregate Analysis using the GoldenGate Assay to Locate the Rpp3 Locus that Confers Resistance to Phakopsora pachyrhizi (Soybean Rust) in Soybean. Crop Science. 49:265-271.

Ray, J.D., Wilfriod, M., Smith, J.R., Frederick, R.D., Miles, M.R. 2009. Genetics and mapping of adult plant rust resistance in soybean PI 587886 and PI 587880A. Theoretical and Applied Genetics. 119:271-280.

Li, S., Young, L.D. 2009. Evaluation of Selected Genotypes of Soybean for Resistance to Phakopsora pachyrhizi. Plant Health Progress. doi:1094/PHP-2009-0615-01-RS

Charlson, D.V., Bhatnagar, S., King, C.A., Ray, J.D., Sneller, C.H., Carter Jr, T.E., Purcell, L.C. 2009. Polygenic Inheritance of Canopy Wilting in Soybean [Glycine max (L.) Merr.]. Theoretical and Applied Genetics. 119: 587-594.

Last Modified: 06/25/2017
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