Location: Crop Genetics Research
2019 Annual Report
Objectives
Objective 1: Identify sources of resistance to newly emerging soybean cyst nematode populations, develop new soybean germplasm with resistance, and develop methods for managing soybean cyst nematodes in soybeans using traditional and marker assisted breeding methods.
Subobjective 1a. Phenotype Glycine max accessions available in USDA soybean germplasm collection for reaction to SCN populations. Identify new/additional sources of resistance, characterize for unique resistance genes and develop molecular markers associated with resistance.
Subobjective 1b. Pyramid nematode resistance genes into elite backgrounds of maturity groups IV and V in combination with resistance to charcoal rot and Frogeye leaf spot to develop new germplasm/cultivars.
Subobjective 1c. Determine the effect of soybean cyst nematode in combination with other plant-parasitic nematodes on crop damage in Mid South soybean production fields.
Subobjetive 1d. Evaluate entries in USDA Uniform Soybean Tests for Southern States and ARS breeding lines for reaction to SCN.
Objective 2: Determine mechanisms underlying host-pathogen interactions in soybean for the fungal diseases charcoal rot and frogeye leaf spot, identify new sources of resistance in soybean to these diseases using improved screening methods, and develop methods for managing these fungal diseases using traditional and marker assisted breeding methods.
Subobjective 2a. Evaluate and identify new sources of germplasms, breeding lines, and cultivars for charcoal rot and frogeye leaf spot resistance in stress and non-stress environments for use in breeding programs.
Subobjective 2b. Evaluate the effects of cultural practices on charcoal rot and frogeye leaf spot severity and yield and develop alternate management practices for control of these diseases in soybean.
Approach
Identify new sources of resistance to nematode populations in soybean that will potentially broaden diversity among resistance genes in soybean cultivars and may provide more durable resistance. New soybean germplasm line or lines will be developed in two different maturity groups IV and V with resistance to soybean cyst nematode, frogeye leaf spot, and charcoal rot, as well as other fungal pathogens, nematodes and insect pests. Nematodes will be found in soybean fields, especially those with corn and/or cotton in the rotation. Valuable data for the reaction of breeding lines to nematode populations will be available to be utilized by the breeders for potential release to public and private sectors. New accessions and germplasm lines with resistance to charcoal rot and
frogeye leaf spot will be identified and released.
Progress Report
Progress was made on both objectives of this project. We are working to find new sources of resistance to soybean cyst nematode and the fungi that cause the diseases frogeye leaf spot and charcoal rot, and to incorporate the resistance into new varieties of soybean. We also are evaluating the impact of cultural practices such as tillage and planting date on disease severity and yield loss and will use that information to improve crop management recommendations to better manage these diseases.
ARS scientists at Jackson, Tennessee, are making progress related to developing soybean with resistance to one or more diseases, which is related to Sub-objective 1B. We previously developed and released soybean JTN-5203 for its broad resistance to soybean cyst nematode, reniform nematode and major fungal diseases combined with high yield potential. In 2019, JTN-5203 continued to be a standard resistant check in USDA Soybean Uniform Tests Southern States. Due to the high cost of commercially available herbicide tolerant soybean seed for planting, some of the growers in Arkansas, Missouri, North Carolina and Kentucky continue to plant JTN-5203 in their fields. This progress is related to Sub-objective 1A.
We evaluated progenies from 10 different specific soybean crosses that were planted in progeny-rows for developing improved soybeans with broad resistance to soybean cyst nematode populations. Approximately 290 unique breeding lines that were planted, and 503 single plants were individually selected and harvested for further evaluations. These selections were made based on visual appearance, primarily for their desirable agronomic traits under field conditions.
Over the winter, 89 selected breeding lines were evaluated using live soybean cyst nematodes in the greenhouse for resistance to multiple populations. Additionally, 142 selected single rows and 119 single plant progenies were also greenhouse tested for soybean cyst nematode resistance based on their desirable field performance. These selected soybean lines are considered unique because they have new sources of resistance from China and Japan, which were not used previously. Concurrently, the DNA (genetic material) from leaves of these greenhouse grown seedlings was collected and laboratory tests were conducted using known DNA markers linked to nematode resistance. This methodology is called marker assisted selection (MAS) and is intended for further confirmation of resistance.
An additional 1,639 single plants were evaluated for charcoal rot resistance, and seeds from 60 of these plants were planted in the field for further selection and advancement. Their value will be determined based on the field performance.
Work to combine resistance to multiple diseases into a single soybean line continued in 2019 (Sub-objective 1B). A total of 61 pooled lines and 366 individually selected plant progenies are being planted. Among them, 196 soybean lines have new sources of nematode resistance in their background and expected to provide more durable and broad resistance. The remaining 69 lines were derived from the soybean crosses where the parents chosen were either with charcoal rot resistance, or with resistance to soybean cyst nematodes and with/without frogeye leaf spot resistance. The traditional breeding methods of selection used in the field and the standard greenhouse techniques adopted for testing together with MAS have allowed us to produce unique progenies. Presumably, most of these unique progenies have combined resistance to these three major diseases. The strategy of combining resistance to soybean cyst nematode, charcoal rot, and frogeye leaf spot together in a single plant is called gene pyramiding and is usually difficult to achieve. This is a time-consuming process.
A Research Plant Pathologist (Nematologist) position has been a critical vacancy since the inception of the project. The critical germplasm screening work for cyst nematode resistance for the Uniform Soybean Tests – Southern States under Sub-objective 1D proceeded on schedule under the direction of the project’s Lead Scientist.
Soybean lines were evaluated for resistance to charcoal rot and frogeye leaf spot in stress and non-stress environments to identify new sources of resistance that can be used in breeding programs. In 2018, a total of 75 Roundup Ready cultivars and 105 conventional breeding lines were screened for charcoal rot resistance. Compared to the reactions of susceptible and resistant checks, 30 lines showed moderate resistance. An additional four soybean breeding lines with resistance to both drought and charcoal rot were identified. That same growing season, a total of 114 soybean breeding lines and conventional varieties were planted in a field in Milan, Tennessee, with a history of known natural infection. The field was irrigated at flowering using central pivot system to encourage infection and disease development. Evaluation for resistance was based on percent leaf area covered by frogeye leaf spot. About 60 lines had significantly lower levels of disease severity with less than 10% infection. It is essential to identify alternative sources of resistance to frogeye leaf spot than currently derived resistance from the cultivar ‘Davis’, and also to ensure that these lines are resistant to many of the field isolates.
In addition, approximately 800 F6 populations representing six specific crosses that were recently developed by collaborators were evaluated. The genetic information from a total of 400 of them was characterized using a method called marker-trait association analysis. Selections under field conditions for charcoal rot resistance within each line from four specific crosses (215) were made and advanced for future public release. In combination, the observed resistance and the genetic data can be used to determine the location of resistance genes in a process known as fine-mapping, and to develop breeder friendly DNA markers for MAS. This progress is related to Sub-objective 2A.
Evaluations for the impact of planting date on charcoal rot and variety type were completed in 2018. Data are being analyzed for manuscript preparation and publication in a refereed journal. Based on available data, there is a significant difference in disease severity and yield for the three planting dates.
A field study examining the response of frogeye leaf spot to six fungicides applied in tilled and not tilled fields was completed. The results from the showed that tillage did not affect severity of the disease or soybean yield. However, there were significant effects from fungicides. Among the six fungicides, Topsin, Topguard, Quadris TOP SBX, and Priaxor significantly reduced disease severity. All fungicide applications improved yield relative to the untreated check cultivar. Topsin and Quadris TOP SBX, however, consistently had the highest percent yield increases. These results suggest that not all fungicides that reduced frogeye leaf spot severity equally protected yield, indicating that yield and environmental conditions need to be considered when making appropriate fungicide recommendations in tilled and no-till systems. This progress is related to Sub-objective 2B.
Accomplishments
1. First report of soybean lines PI 437655 and PI 494182 are potentially new sources for broad resistance to predominant nematode populations. Soybean cyst nematodes cause yield loss, are genetically variable and can adapt to currently grown resistant cultivars over time, so new sources of resistance area needed. Two plant introductions, PI 437655 from China and PI 494812 from Japan, were crossed to elite lines by ARS researchers in Jackson, Tennessee, and progeny with desirable seed traits and resistance to multiple populations of soybean cyst nematode were selected. Yield potential for these progeny range from 52-54 bushels per acre, which are comparable to commercially available cultivars. These lines are excellent source materials to breed new cultivars for broad nematode resistance in all maturity groups with higher yields for wider adaptation. Ultimately, soybean growers will be the beneficiaries.
2. Genetic makeup of resistance to charcoal rot disease in soybean. Progress in breeding efforts has been slow due to the insufficient information available on the genetic mechanisms related to resistance. A technique known as genome-wide association enables unraveling the genetic architecture of resistance and identification of causal genes. ARS researchers in Jackson, Tennessee, identified new sources of charcoal resistance from field screening from soybean in maturity groups I, II, and III. Five potential genes were found to be related to abiotic (drought, etc.) and biotic (diseases) stress responses. These findings provide useful information to plant breeders for advancing breeding for charcoal rot resistance as well as understanding the genetic mechanism of resistance itself.
3. Population structure of fungicide resistance to frogeye leaf spot from Tennessee. Frogeye leaf spot causes significant damage to soybean in the U.S. One control strategy is the use of fungicide known as quinone outside inhibitor. The introduction of site-specific fungicides has revolutionized chemical plant protection, providing highly efficient, low toxicity compounds for control of most fungal diseases. However, it was soon discovered that plant pathogenic fungi can adapt to fungicide treatments by mutations leading to resistance and loss of disease control by these fungicides. From an in-house collection of 437 Tennessee isolates of the fungus that causes frogeye leaf spot, ARS researchers in Jackson, Tennessee, characterized a subset of 186 of these isolates for their genetic makeup and their resistance to the fungicide. The genetic structure clustered into three groups with two groups containing only sensitive isolates and the remaining group containing all resistant isolates. Two mating types were found in isolates from Jackson and Milan, Tennessee, and may be playing a role in disease epidemics in the field. Analysis of these isolates using genetic markers proved useful to investigate population diversity and management of fungicide resistance.
4. Release of soybean germplasm line LG03-4561-14 with high yield and improved resistance to southern stem canker and frogeye leaf spot. Genetic diversity is limited in the U.S. soybean breeding pool. Incorporating new genetic diversity from exotic sources into soybean breeding lines may provide the resources needed to meet current and future problems that reduce soybean yield and increase profitability. ARS researchers in Stoneville, Mississippi, Jackson, Tennessee, and Urbana, Illinois, developed and released the new germplasm lines LG03-4561-14. This release is a high-yielding, conventional, late maturity group III germplasm line that brings in new genetic diversity for potentially increasing seed yield. In addition to high yield, the line has resistance to southern stem canker and frogeye leaf spot. LG03-4561-14 is available to breeders in both the public and private sectors.
Review Publications
Mengistu, A., Kelly, H., Bellaloui, N., Arelli, P.R., Lin, B. 2018. Quantifying the effects of fungicides and tillage on Cercospora sojina severity and yield of soybean. Plant Health Progress. 19:226-232. https://doi.org/10.1094/PHP-04-18-0017-RS.
Gillen, A.M., Mengistu, A., Arelli, P.R., Stetina, S.R., Bellaloui, N. 2018. Registration of soybean germplasm line DB0638-70 with high yield potential and diverse genetic background. Journal of Plant Registrations. 13:96-102. https://doi.org/10.3198/jpr2018.03.0016crg.
Shrestha, S., Cochran, A., Mengistu, A., Lamour, K., Castro-Rocha, A., Young-Kelly, H. 2017. Population structure and the rapid increase of QoI fungicide resistance in frogeye leaf spot (Cercospora sojina) from Tennessee. PLoS One. 12(5):e0177220. https://doi.org/10.1371/journal.pone.0177220.
Smith, J.R., Ray, J.D., Mengistu, A. 2018. Genotypic differences in yield loss of irrigated soybean attributable to charcoal rot. Journal of Crop Improvement. 32(6):781-800. https://doi.org/10.1080/15427528.2018.1516262.
Coser, S., Reddy, C., Zhang, J., Mueller, D., Mengistu, A., Wise, A., Allen, T., Singh, A., Singh, A. 2017. Genetic architecture of charcoal rot (Macrophomina phaseolina) resistance in soybean revealed using a diverse panel. Frontiers in Plant Science. 8:1-12. https://doi.org/10.3389/fpls.2017.01626.
Nouri, A., Lee, J., Yin, X., Tyler, D.D., Jagadamma, S., Arelli, P. 2018. Soil physical properties and soybean yield as influenced by long-term tillage systems and cover cropping in the midsouth USA. Sustainability. 10(12):4696. https://doi.org/10.3390/su10124696.
Reznikov, L.S., Vellicce, G.R., Mengistu, A., Arias De Ares, R.S., Gonzalez, V., De Lisi, V., Garcia, M.G., Rocha, C., Pardo, M., Castagnaro, A.P., Ploper, D. 2018. Disease incidence of charcoal rot (Macrophomina phaseolina) on soybean in north-western Argentina and genetic characteristics of the pathogen. Canadian Journal of Plant Pathology. 40(3):423-433. https://doi.org/10.1080/07060661.2018.1484390.
