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United States Department of Agriculture

Agricultural Research Service


Location: Crop Genetics Research

2012 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. Primarily, three diseases (charcoal rot, soybean rust, and Phomopsis seed decay) are targeted. 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, pathological, and seed quality assays were conducted. In addition to the research program, the project also maintains the southern portion of the USDA-ARS Soybean Germplasm Collection (MG V-VIII). For the rust research program, almost 2,000 plots were planted and screened for rust resistance in Capitan Miranda, Paraguay. Experiments included spray/no spray fungicide trials using a recombinant inbred population developed in Stoneville, MS, that is segregating for rust tolerance, evaluation of plant introductions and cultivars for resistance and the evaluation and selection of breeding lines with rust resistance. Breeding lines developed with rust resistance were also grown at Stoneville, MS, and selections for agronomic characteristics made. Populations segregating for rust resistance were evaluated at the quarantine facility at Stoneville, MS, and Ft. Detrick, MD. Analysis and molecular mapping led to the identification of a new rust resistance gene. Experiments conducted at Stoneville, MS, for charcoal rot research included a trial designed to evaluate the relationship between seed yield and charcoal rot in irrigated conditions. Preliminary analysis indicated soybean genotypes may vary in yield response to charcoal rot. This field experiment will be repeated. Breeding lines were also evaluated and advanced based on charcoal rot resistance ratings. Molecular marker assays of approximately 300 charcoal rot isolates were also completed in this reporting period. The assays are currently being analyzed but preliminary results indicate that isolates can be differentiated by the molecular markers developed at Stoneville, MS. Analysis of field data collected in previous reporting periods for two sets of maturity isolines on two soil types, indicated that there was little relationship between maturity and the incidence of charcoal rot but that environmental parameters may affect charcoal rot incidence. Past screening of over 500 soybean lines identified at least eight with varying levels of Phomopsis resistance. Using this information, genetic populations were constructed for the purpose of identifying and mapping Phomopsis resistance genes. These populations are currently being phenotyped for resistance and genotyped with molecular markers. Additionally, breeding lines with resistance are being developed. Seed quality has a significant relationship to disease incidence and can impact farm profits. Data collected and analyzed over the last year led to the identification and mapping of a new gene involved in seed wrinkling. Overall, experiments are proceeding according to plan. For the Germplasm Collection work, seed increase plots were established and are being maintained appropriately.

4. Accomplishments
1. Identification of a new soybean rust resistance gene. Soybean rust (SBR) is one of the most economically important diseases of soybean. Durable resistance to SBR is the most effective long-term strategy to control SBR. A new resistance gene was identified in PI 567102B by pathological and molecular evaluation. Incorporating the new gene into improved soybean cultivars may have wide benefits as it has been shown to have resistance to SBR in Paraguay and the U.S.

2. Release of a new soybean line with exotic genetic background. Soybean yield is thought to be restricted by the limited genetic diversity among progenitors of current cultivars. LG01-5087-5, a high-yielding breeding line derived from PIs 427099, 438151, and 445830, was officially released. This was the first release with a pedigree including PI 438151. Development of new high yielding experimental lines from exotic germplasm and distribution of these lines to U.S. soybean breeders can enhance the yield of new soybean cultivars.

Review Publications
Ray, J.D., Smith, J.R., Taliercio, E.W., Fritschi, F.B. 2011. Genomic location of a gene conditioning a miniature phenotype in soybean. Plant Biology. 55:26-32.

Wei, W., Xu, Y., Li, S., Lui, J., Han, X., Li, W., Ji, P. 2012. Analysis of Fusarium populations in a soybean field under different fertilization management by real-time quantitative PCR and denaturing gradient gel electrophoresis. Journal of Plant Pathology. 94(1):119-126.

Arias, R.S., Molin, W.T., Ray, J.D., Peel, M., Scheffler, B.E. 2011. Isolation and characterisation of the first microsatellite markers for Cyperus rotundus. Weed Research. 51:451-460.

Allen Jr, L.H., Vu, J.C., Anderson, J.C., Ray, J.D. 2011. Impact of elevated carbon dioxide and temperature on growth and sugar yield of the C4 sugarcane. Current Topics in Plant Biology. 12:171-178.

Kebede, H.A., Fisher, D.K., Young, L.D. 2011. Determination of moisture deficit and heat stress tolerance in corn using physiological measurements and a low-cost microcontroller-based monitoring system. Journal of Agronomy and Crop Science. 198:118-129.

Li, S., Smith, J.R., Nelson, R.L. 2011. Resistance to phomopsis seed decay identified in maturity group V soybean plant introductions. Crop Science. 51:2681-2688.

Arias, R.S., Ray, J.D., Mengistu, A., Scheffler, B.E. 2011. Discriminating microsatellites from Macrophomina phaseolina and their potential association to biological functions. Plant Pathology. 60(4):709-718 DOI:10.1111/j.1365-3059.2010.02421.x.

Porch Clay, T.G., Urrea, C., Beaver, J., Valentin, S., Peña, P.A., Smith, J.R. 2011. Registration of TARS-MST1 and SB-DT1 multiple-stress tolerant black bean germplasm. Journal of Plant Registrations. 6(1):75-80.

Ray, J.D., Smith, J.R., Morel, W., Bogado, N., Walker, D.R. 2011. Genetic resistance to soybean rust in PI 567099A is at or near the Rpp3 locus. Journal of Crop Improvement. 25(3):219-231.

Li, S., Sciumbato, G. 2011. Evaluation of maturity group IV soybean lines for resistance to purple seed stains in Mississippi 2010. Plant Disease Management Reports. 5:FC123.

Li, S., Sciumbato, G. 2011. Reaction of maturity group V soybean lines to purple seed stains in Mississippi 2010. Plant Disease Management Reports. doi:10.1094/PDMR05:FC122.

Li, S., Sciumbato, G. 2012. Evaluation of maturity group III soybean lines for resistance to purple seed stain in Mississippi, 2010. Plant Disease. doi:10.1094/PDMR06: ST004.

Li, S., Smith, J.R., Ray, J.D., Frederick, R.D. 2012. Identification of a new soybean rust resistance gene in PI 567102B. Theoretical and Applied Genetics. 125:133-142.

Gao, X., Lu, X., Wu, M., Pan, R.Q., Tian, J., Li, S., Liao, H. 2012. Co-inoculation with rhizobia and arbuscular mycorrhizal fungi inhibited soybean red crown rot: from field study to plant defense-related gene expression analysis. PLoS One. 7(3):e33977.

Last Modified: 2/23/2016
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