1a. Objectives (from AD-416):
(1) Identify and confirm resistance to soybean rust at multiple locations in the southern U.S.; (2) Characterize relationships among different rust resistance genes and breed soybean lines with various resistance genes singly and in pairs; (3) Assess genetic and virulence diversity within and among domestic populations of the soybean rust fungus.
1b. Approach (from AD-416):
(1) Coordinate field testing of exotic germplasm, improved breeding lines and sets of differentials for resistance to soybean rust (SBR) in the southern U.S., and in greenhouse evaluations in Griffin GA and Urbana IL. Plant Introductions from the USDA Soybean Germplasm Collection will be screened for resistance to SBR at field nurseries in Baton Rouge and Bossier City, LA; Fairhope, AL; and Quincy, FL, to determine which have resistance. Tests will also be conducted at greenhouses in Georgia and Illinois. (2) Use phenotypic, genetic mapping and genomic data to characterize relationships among Rpp genes from germplasm accessions with SBR resistance, and develop breeding and experimental lines that carry Rpp genes singly or in pairs. Experiments will be conducted to determine which resistance genes and pairs of genes are most effective, and these genes will be selected for in soybean breeding lines. (3) Assess genetic and virulence diversity within and among domestic P. pachyrhizi populations, and maintain a collection of representative isolates that will be necessary for identifying and verifying specific resistance. Samples of the soybean rust fungus will be collected in the field, purified, and tested to determine what reactions they provoke on a set of soybean lines with known resistance genes.
3. Progress Report:
Research for this project was conducted partly at the University of Illinois in Urbana, IL and partly at university research stations in Quincy, FL (Univ. of Florida); Athens, Griffin and Attapulgus, GA (Univ. of Georgia); and Fairhope, AL (Auburn Univ.) in collaboration with other scientists. A Specific Cooperative Agreement was established with the University of Georgia as a subcontractor in the soybean rust research proposal supported by the United Soybean Board. A Specific Cooperative Agreement established with the University of Florida using USDA-ARS funds also promoted better leverage of the support obtained from the United Soybean Board for research on resistance to soybean rust. Field, greenhouse and laboratory studies were conducted by ARS in Urbana and by the University of Georgia. In collaboration with Auburn University, a soybean rust nursery was planted at the Auburn research station in Fairhope, AL. Germplasm evaluation for resistance to soybean rust in Florida Soybean plots were planted at the North Florida Research and Education Center (NFREC) in June and in August, 2012, and were harvested after they matured. Due to a strong effect of environmental conditions on the annual soybean rust epidemics in the southeastern U.S., the level of disease pressure and the rate at which a rust epidemic develops can vary considerably in different years, but plots planted in August have a higher chance of getting soybean rust than plots planted in June. The earlier planting is necessary, however, for assessment of agronomic value and yield potential. The June-planted plots included an experiment to evaluate tolerance to soybean rust and more than 1,500 breeding lines segregating for rust resistance. Six cultivars developed by southeastern U.S. university breeding programs were evaluated for tolerance to rust, which means that the disease causes less yield loss than on most other susceptible cultivars. When this study was conducted in previous years, the University of Georgia line G00-3209 consistently had a lower percent yield loss than other entries tested, so the entries chosen for 2012 included G00-3209, its sister line G00-3213, the two cultivars that these lines were derived from, and two cultivars with a low tolerance to soybean rust. Fungicide protected and unprotected plots were grown side by side, with two border rows separating them to prevent fungicide from drifting onto plants in the unprotected treatment. To determine percent yield loss, the seed yields of the unprotected plots (which had been infected with rust) were compared to the yields of the fungicide-protected plots, which did not have the disease. Differences in loss percentages were compared statistically. The 2012 data and data from previous years that the study was conducted are being compiled into a manuscript. Other June-planted plots included 1,050 rows of breeding lines and F2 populations derived rust-resistant Asian soybean Plant Introductions (PIs). The F2 populations were grown in a single row, whereas later generations were grown in hill plots, 5’ rows, or 10’ rows. F2 and F3 plants from 22 other populations were grown in hand-planted hill plots and short rows. Plants were selected on the basis of agronomic appearance (lodging and shattering resistance, pod set, and seed appearance), as well as resistance to soybean rust and other foliar diseases. A soybean rust screening nursery was planted at the NFREC in Quincy in mid-August to evaluate soybean germplasm accessions and breeding lines for rust resistance. One experiment, which has been planted annually since 2006, was conducted to evaluate the resistance of 114 PIs from the USDA Soybean Germplasm Collection compared to 12 susceptible cultivars. The plants in these plots were not rated for agronomic traits, since they flowered and matured early due to the late planting date. Through collaboration with university colleagues, the same 114 accessions were also planted in rust nurseries at Attapulgus, GA and Fairhope, AL. The germplasm accessions were rated for soybean rust severity and the relative amount of sporulation from rust lesions. Useful rating data were collected in Attapulgus and Quincy, but data from Fairhope were less useful due to a combination of severe bacterial pustule and a frost that killed the plants before a second rating could be made. The 2012 data from Quincy and Attapulgus have been combined with rust reaction data from 2009 and 2011 in a manuscript which was recently submitted to Crop Science. In addition, 340 breeding lines from several sources were also planted at Quincy in August to be screened for soybean rust resistance. These included 83 backcross lines that had been developed by ARS researchers from crosses between Glycine max and an Australian accession of the perennial soybean species G. tomentella. These interspecific backcross lines are unique in the world, due to the difficulty of obtaining viable progeny from such crosses. Ten lines were screened by an ARS Research Geneticist in Stoneville, MS, in addition to 214 additional lines from the ARS Urbana breeding program. Selected lines are being re-evaluated in 2013 to confirm their resistance to the local soybean rust population. In addition to soybean rust, there was a high incidence of downy mildew in the 2012 field plots at Quincy, FL, so there was a high probability that plants lacking symptoms of that disease were resistant to it. Data were collected on the presence of the disease to allow selection against susceptible plants. Frogeye leaf spot and damping off caused by soil pathogen infections were not as common in 2012 as they have been in some previous years. Breeding line development in Urbana A total of 2,024 plots were grown in Urbana, of which the majority were breeding lines derived from crosses with rust-resistant PIs from the USDA Soybean Germplasm Collection. The remaining plots were maturity checks, F2 populations, rows of F1 hill plots, and the crossing parents that were planted in the crossing block. Soybean rust is very rare in central Illinois, but the lines were evaluated for seed yield (in later generations), pod set (in earlier generations), lodging, shattering, maturity, and the presence and severity of other diseases like virus stunting and Phomopsis seed decay. Greenhouse and laboratory studies of P. pachyrhizi isolates Isolates of P. pachyrhizi were collected from the field in Quincy in 2012 and purified in the laboratory in Urbana. The 2012 field population of the fungus had induced higher levels of disease and sporulation on many historically resistant PIs than the 2009 or 2011 populations had caused, although the 2011 population had been more virulent or aggressive than previous populations at that research station. We were therefore curious to know whether 2012 isolates from Quincy would exhibit a similarly high virulence on detached leaves and seedlings from historically resistant PIs. The isolates were cultured and maintained on leaflets from plants carrying either the Rpp1 or the Rpp6 resistance genes to prevent them from losing their virulence towards hosts with those genes. Soybean rust resistance experiments were conducted in a biosafety level 2 greenhouse in Urbana during the winter of 2012-2013. The objective of one was to compare the reactions of inoculated seedlings inoculated with a 2012 isolate from Quincy, FL to the reactions of adult plants challenged with the local 2012 field population in Quincy. The entries consisted of six soybean PIs with the Rpp1 to Rpp6 genes, 22 PIs with unknown resistance genes, and two control cultivars known to be susceptible to rust. These lines were inoculated with six different domestic P. pachyrhizi isolates in a factorial design. The isolates had been collected from locations in the southern U.S. between 2008 and 2012. Variation was observed both among entries inoculated with the same isolate, and in the reactions of entries to different isolates for disease severity, sporulation, numbers of uredinia per lesion, and other measures of disease. In the second greenhouse experiment, 45 different PIs from the USDA Soybean Germplasm Collection were inoculated with the same six P. pachyrhizi isolates used in the first experiment. The collection of evaluation data preserved leaf tissue is nearing completion. In the meantime, our observations confirming that 2011 and 2012 isolates from Quincy, FL had adapted to the Rpp1 and Rpp6 resistance genes were reported in a short manuscript by Paul et al. entitled ‘First report of Phakopsora pachyrhizi adapting to soybean genotypes with Rpp1 or Rpp6 rust resistance genes in field plots in the United States’. This was accepted by Plant Disease, and should be published online during the summer of 2013. Another experiment was conducted to examine the rate of growth of the rust fungus in detached leaves from seven different germplasm accessions up to 16 days after they were inoculated. An analysis of the increase of P. pachyrhizi DNA over this period indicated that two of the accessions may have rate-limiting type of resistance that delayed fungal growth temporarily, whereas the resistance of other five was more stable over time.