Location: Insect Control and Cotton Disease Research
2025 Annual Report
Objectives
Objective 1. Develop molecular tools to rapidly identify and detect presence of cotton boll rot pathogens in plants and insects. (NP303, C1, PS1A, PS1B)
Objective 2. Improve the understanding of insect vector/pathogen interactions and pathogen reservoirs to reduce the spread of cotton diseases. (NP303, C2, PS2C, PS2D)
Objective 3. Identify fungal and host genes that can be targeted for disease suppression, and develop cotton germplasm resistant to FOV and nematodes. (NP303, C2, PS2A, PS2B; C3, PS3A, PS3B)
Objective 4. Evaluate national and international sorghum germplasm resources, and determine the inheritance and allelic relationships of host plant resistance to anthracnose, grain mold, head smut, and downy mildew diseases. (NP303, C3, PS3A; C2, PS2A)
Objective 5. Determine the population structure of diverse anthracnose (Colletotrichum sublineolum) and head smut (Sporisorium reilianum) isolates and phenotypic expression patterns of virulence on host differentials. (NP303, C2, PS2A)
Approach
Boll rots, nematodes, and fungal pathogens continue to pose the greatest threat to U.S. cotton production. To address boll rots, we previously sequenced the genome of several bacterial boll rot pathogens vectored by cotton fleahoppers, stink bugs, and verde plant bugs to identify pathogenicity genes involved in boll rot disease. In this project, we will confirm whether Lygus spp. and stink bugs vector boll rot and Fusarium wilt pathogens, respectively, and identify pathogenicity genes common to all bacterial boll rot pathogens with the long-term goal of developing a PCR-based kit that can be used in the field to rapidly detect insects harboring pathogens. The ability to rapidly detect boll rot pathogens within insects and plants, along with an improved understanding of insect vector and pathogen interactions, are both critically needed to develop sound management strategies for cotton diseases and respective insect vectors. A strain of Fusarium oxysporum f. sp. vasinfectum, known as race 4 (FOV4), was recently detected in several cotton fields in West Texas and New Mexico. This strain was initially detected and confined to cotton fields in California. Unlike other FOVs, race 4 does not require the presence of nematodes to cause severe disease of plants; however, the interaction between root knot nematodes and FOV4 pathogenicity remains unclear. Spread of FOV4 in the United States could be catastrophic because there are currently no feasible control options once this pathogen is established in a field. The development of resistant germplasms is widely deemed the most practical and long-term solution for managing this disease. To this end, we will identify and test sources of resistance to FOV4 and develop respective markers which will be incorporated into previously developed nematode-resistant germplasm to facilitate our breeding efforts to produce cotton lines that are resistant to both FOV4 and nematodes.
Progress Report
Work by this project in FY 2025 provided a clearer understanding of the dynamics of a major cotton disease in the United States, Fusarium wilt caused by Fusarium oxysporum f. sp. vasinfectum (FOV), and several fungal diseases that affect sorghum production world-wide. Work under Objective 3 led to the development of several genetically near-identical (isogenic) cotton lines that vary in their resistance/susceptibility to FOV caused by race 4 (FOV4). The development of these isogenic lines is critical for establishing the underlying mechanism(s) of FOV4 resistance in cotton and may also provide potential sources of FOV4 resistance that can be incorporated into cotton breeding programs. In related research, several cotton germplasm lines that showed resistance to FOV4 under controlled environmental conditions were identified; the most promising candidates were propagated to increase seed production for field evaluations. In work addressing Objective 4, research with academic cooperators evaluated more than 350 sorghum lines and commercial hybrids for resistance to anthracnose, grain mold, and downy mildew; 40 sorghum lines are currently being evaluated in the greenhouse for head smut resistance. Some of the lines showed significant resistance to one or more of the diseases; these lines will likely be useful in breeding more disease-resistant sorghum varieties for use by U.S. farmers. In research addressing Objective 5, greenhouse evaluations were conducted to establish the virulence patterns of a number of isolates of the anthracnose and head smut pathogens. Field studies are currently underway to compare the efficacy of two commercial fungicides and an experimental biocontrol agent, Bacillus velezensis LP16S, against the anthracnose and grain mold diseases in sorghum.
Accomplishments
1. New sources of downy mildew resistance in sorghum. Several new genetic variations (pathotypes) of the downy mildew pathogen have emerged and could cause significant economic losses in sorghum yield and seed quality. The development of new disease-resistant sorghum varieties is considered to be the most practical solution for managing these new pathotypes. ARS researchers at College Station, Texas, in collaboration with academic colleagues, evaluated hundreds of sorghum lines from Niger and Senegal, and identified several lines that are highly resistant to downy mildew. Genetic studies of a subset of the lines from these two countries identified several genetic anomalies, known as single nucleotide polymorphisms, that appear to play a role in sorghum’s response to disease and environmental stress. This accomplishment provides several new sources of downy mildew resistance that may be incorporated into breeding programs to develop improved, more disease-resistant sorghums for productive use by American farmers.
2. Interrelationships among agronomic traits and fungal diseases. Anthracnose and grain mold are two of the most significant diseases of sorghum world-wide, causing economic losses of hundreds of millions of dollars annually. Prior work has indicated that relationships exist between sorghum agronomic traits (e.g., growth, productivity, grain quality) and the severity of disease caused by these two pathogens; however, these relationships have not been extensively investigated and defined. ARS researchers at College Station, Texas, in collaboration with academic colleagues, defined and quantified the influence of certain agronomic traits on the occurrence of these two diseases. The work uncovered positive and negative relationships between the severity of these diseases and key sorghum characteristics, including seed weight, germination rate, plant height, and panicle morphology. This accomplishment is significant because it defines important aspects of the complex relationship between agronomic traits and disease resistance. The results of this work will be utilized by breeders to develop improved sorghums that are disease resistant while maintaining important growth and quality traits that are critical to farmer success in growing productive and high-quality sorghum crops
Review Publications
Prom, L.K., Ahn, E.J.S., Cuevas, H.E., Liu, J., Isakeit, T.S., Magill, C.W. 2024. Association and interrelationship among agronomic traits and fungal diseases of sorghum, anthracnose and grain mold. Crops. 4(4):651-666. https://doi.org/10.3390/crops4040045.
Prom, L.K., Fall, C., Isakeit, T.S., Ahn, E.J.S., Liu, J., Magill, C.W. 2024. Genome-wide association study of Nigerien and Senegalese sorghum genotypes for their response to downy mildew. Journal of Plant Studies. 14(1):1-9. https://doi.org/10.5539/jps.v14n1p1.
Prom, L.K., Esquivel, J.F., Liu, J. 2025. Agronomic traits and fungal diversity between commercial and non-commercial sorghum fields. Journal of Plant Studies. 14(1):10-16. https://doi.org/10.5539/jps.v14n1p10.
Ahn, E.J., Prom, L.K., Park, S., Hu, Z., Magil, C. 2024. Genome-wide association analysis uncovers genes associated with resistance to head smut pathotype 5 in senegalese sorghum accessions. Plants. 13(7). Article 977. https://doi.org/10.3390/plants13070977.
Cuevas, H.E., Prom, L.K. 2024. The NPGS Sudanese sorghum core collection encloses novel grain mold resistant germplasm. Genetic Resources and Crop Evolution. https://doi.org/10.1007/s10722-024-02039-7.
Baek, I., Lim, S., Jang, J., Hong, S., Prom, L.K., Kirubakaran, S.J., Cohen, S.P., Lakshman, D.K., Kim, M.S., Meinhardt, L.W., Park, S., Ahn, E.J. 2025. Pathogen-specific stomatal responses in cacao leaves to Phytophthora megakarya and Rhizoctonia solani. Scientific Reports. https://doi.org/10.1038/s41598-025-94859-5.
Fall, C., Lim, S., Ahn, E.J., Park, S., Prom, L.K., Magill, C. 2025. Unveiling the potential role of dhurrin in sorghum during infection by the head smut pathogen sporisorium reilianum f. sp. reilianum. Plants. https://doi.org/10.3390/plants14050740.
Ahn, E.J., Park, S., Hu, Z., Ellur, V., Cha, M., Yoonjung, L., Prom, L.K., Magill, C. 2024. Genome-wide association study of seed morphology-related traits in sorghum mini core and Senegalese lines. Crops. 4:156–171. https://doi.org/10.3390/crops4020012.
Botkin, J.R., Medina, C.A., Park, S., Poudel, K., Cha, M., Lee, Y., Prom, L.K., Curtin, S.J., Xu, Z., Ahn, E.J. 2024. Analyzing Medicago spp. seed morphology using GWAS and machine learning. Scientific Reports. https://doi.org/10.1038/s41598-024-67790-4.