1a. Objectives (from AD-416):
The overall objective of the project “Identification and Utilization of Resistance to Soybean Rust” is to identify and develop soybean germplasm with broad resistance to Phakopsora pachyrhizi, the cause of soybean rust (SBR). Characterization of virulence diversity among P. pachyrhizi populations and the reactions of resistant lines are important to guide breeding for effective and durable resistance. Specific objectives will be to (1) identify resistant plant introductions (PIs) from the USDA Soybean Germplasm Collection; and (2) map and transfer resistance genes to germplasm adapted to the U.S.
1b. Approach (from AD-416):
Objective 1 will be addressed by testing soybean germplasm accessions from the USDA-ARS Soybean Germplasm Collection and breeding lines developed from crosses made with those accessons for resistance to soybean rust (Phakopsora pachryhizi) in the field and greenhouse. Due to demonstrated ability of the rust pathogen to evolve and to evidence that multiple pathotypes and virulence groups already exist in the southern U.S., it will be important to confirm the resistance of historically resistant accessions as well as identifying additional sources of novel resistance genes. This will be done annually in locations in the southern U.S. through the assistance of collaborators. The Rpp (Resistance to Phakopsora pachyrhizi) genes responsible for the resistance in these accessions would then need to be characterized by developing lines and populations that can be used to map their locations in the genome and study their effects both singly and in combination with other Rpp genes. This information will be important to allow breeders to decide which genes to combine to achieve broader and more durable resistance. Assessments of genetic and pathogenic diversity within and among populations of the rust fungus are important to develop effective breeding and management strategies, so the third objective of this project will be to collect and characterize isolates of the rust fungus that have been collected in different years and locations. The germplasm screening nurseries established to meet Objective 1 would provide sources of contemporary isolates, and colleagues in areas that experience soybean rust epidemics are likely to submit local samples of SBR as well. Isolates from field populations will be pathotyped using a set of differential lines and will also be characterized genetically using DNA markers.
3. Progress Report:
This cooperative project between the USDA-ARS and the soybean breeding program at the University of Georgia was initiated in June, 2012. The project involved research conducted in the field, greenhouse and laboratory. The field and greenhouse studies were conducted primarily to evaluate germplasm for rust resistance, and the laboratory research involved the use of DNA markers to map Rpp (Resistance to Phakopsora pachyrhizi) genes in soybean germplasm accessions. Field tests A field test to evaluate the reactions of 114 Plant Introductions (PIs) from the USDA Soybean Germplasm Collection to soybean rust infection was planted in mid-August at the Attapulgus Research and Education Center in southwestern Georgia. Eleven cultivars were included as susceptible checks and indicators of the amount of rust present at the site, and the PIs that were tested were chosen because they either carry a known resistance gene or had shown resistant in previous assays. These were rated in November for rust lesion severity in the field, lesion severity using a pictorial scale, and sporulation. At least 72 of the PIs were resistant to rust at Attapulgus. Accessions that showed immunity or near-immunity were PI423958, PI547875 (a Williams 82 isoline with the Rpp1 gene), PI567020A, PI567025A, PI567046A, PI567054C, PI567061, PI567068A, PI567090, PI567102B (Rpp6), PI567104B, and PI635999. We were unable to obtain rating data for PI200492, the original source of Rpp1, but that accession has historically and consistently been one of the most resistant. Up-to-date information about which accessions are most resistant to soybean rust in the southern USA is crucial for soybean breeders who are trying to develop cultivars and lines with rust resistance for producers operating in the Mid-South and Southeast. Twenty lines developed in the USDA-ARS soybean rust breeding program were evaluated for agronomic performance in Athens, GA in 2012. These had been selected for rust resistance and promising agronomic appearance in Quincy, FL, but we wanted to evaluate their seed yields farther north in an area where some soybean production occurs. The yields of 12 lines were not significantly lower than the check cultivars, and the yields of some lines were similar to that of the highest-yielding check in each of two tests. Although these yields are only from a single year and location, the results are promising and the 12 best lines are being evaluated again in the 2013 growing season. Greenhouse experiments An experiment was conducted in a greenhouse at the Griffin, GA Experiment Station to compare soybean seedling reactions to a 2012 isolate collected from infected soybean leaves in Attapulgus, GA with reactions to a pooled Georgia isolate derived from infected kudzu and soybean leaves in 2008. Several researchers have reported temporal and geographical variation in the virulence of P. pachyrhizi populations, so the objective of this experiment was to determine whether any shifts had occurred in populations from Georgia. The experiment included susceptible and resistant checks, and 24 plants of each entry were inoculated with each of the isolates. After two weeks the reactions of the plants were classified as susceptible, red-brown (RB; indicating incomplete resistance); or immune. The reactions of the 16 entries were identical or nearly the same for both isolates, suggesting that the virulence of the two Georgia isolates has not changed much, if at all, between 2008 and 2012. The Rpp1 gene in PI200492 and the Rpp6 gene in PI 567102B conditioned immunity, indicating that these two genes would be excellent candidates for combining in a resistance gene pyramid. Although the line L85-2378 also carries the Rpp1 gene, and is typically as resistant as PI200492 in the field, variable reactions of plants to both of the isolates suggest that an accidental seed mixture may have occurred at some point. Gene mapping studies in laboratory Data from the Griffin greenhouse screening experiments indicated that there were seven F2:3 populations of an elite line (susceptible) x plant introduction (PI) (resistant) cross (Boggs x PI605885B, G00-3880 x PI416826A, Prichard x PI197182, Prichard x PI417116, Prichard x PI567123A, G00-3880 x PI423960A, and Prichard x PI423972) that contained a putative, unique source of resistance based on bulked segregant analysis (BSA) data using a 1,536 SNP marker assay. However, with the exception of PI567031B, after further investigation through isolate studies and the use of a 50,000 SNP marker assay versus the original 1536 marker assay, we found that these were likely false positives. Populations derived from PI567031B and six other accessions (PI606397B, PI567123A, PI605791A, PI417089A, PI417129B, PI423966) have not yet been evaluated with the 50,000 SNP panel, but will be in the near future to further assess if they have a unique source of resistance (i.e., different from the known sources Rpp1 through Rpp6). Novel genes will be mapped using F2:3 lines. F1 seed of 11 new SBR-susceptible x SBR-resistant populations (resistant PI’s include: PI200466, PI203398, PI224270, PI379621, PI416935, PI417125, PI417126, PI417208, PI423960B, PI423963, PI567189A) were grown in Puerto Rico to create F2 populations. These 11 new F2 populations were planted in the Griffin greenhouse this summer and will be phenotyped to create resistant and susceptible bulks for BSA in order to identify the genomic locations of SBR resistant genes. F2 seed of these 11 populations were also planted at the Plant Sciences farm near Athens, GA to create F2:3 families. Resistant and susceptible bulks of these populations will be sent to Michigan State University to narrow down the region of the putative unique gene further. Novel genes will be mapped using F2:3 lines. Crossing and variety development BC6F2:3 seed to G00-3213 of the Rpp1, Rpp2, Rpp3, and Rpp4 resistance genes were obtained in order to create the near-isogenic lines (NILs) each containing a single SBR resistance gene in a common MG VII genetic background (G00-3213). We will phenotype and genotype these families to select homozygous lines. Additional backcrosses to G00-3213 of the Rpp5 and the new Rpp6 resistance genes will be made this summer. The resulting NILs can then be used as a set of differentials to determine which resistance genes are effective in different environments. In addition, three new PIs (PI567191, PI567188, and PI605823) that show red-brown, non-sporulating rust resistance (based on the Griffin greenhouse and Attapulgus screening data), will be crossed in the summer crossing block to a SBR-susceptible cultivar in order to create three new mapping populations with potential putative unique sources of resistance. Elite F6, MG VII breeding lines with pyramided Rpp1 and Rpp3 genes are being developed by the University of Georgia soybean breeding program for the Southeast, and are being evaluated in the 2013 season. Additionally, cooperators have developed three elite lines containing the Rpp3 gene which are in Maturity Group VI, VII, or VIII and are currently in the second year of advanced yield testing. They have been planted in multiple locations across the southeastern USA.