Location: Corn, Soybean and Wheat Quality Research
2024 Annual Report
Objectives
Objective 1: Identify and characterize endemic and emergent viruses in corn and soybean, and develop sequence and detection resources.
Sub-objective 1: Identify, diagnose, and characterize insect-transmitted pathogens of maize and soybean.
Objective 2: Develop genetic markers and germplasm associated with corn virus resistance genes, and transfer information for practical management solutions.
Sub-objective 2.A: Confirm the identity of HPWMoV resistance loci in maize and evaluate the effects of disease resistance on seed contamination and transmission.
Sub-objective 2.B: Identify and characterize loci conferring tolerance/resistance to maize yellow mosaic virus.
Sub-objective 2.C: Identify bean pod mottle virus resistant Glycine accessions and incorporate resistance into a cultivated soybean background.
Objective 3: Fine map, clone, and characterize virus resistance genes, facilitating the investigation of host-pathogen interactions.
Sub-objective 3.A: Fine map the WSMV resistance gene, wsm3, and examine pathogenesis of WSMV in resistant and susceptible maize.
Sub-objective 3.B: Fine map MCMV resistance loci in maize inbred lines and develop near isogenic lines to study host-pathogen interactions.
Approach
Corn and soybean production in the United States is valued at more than $80 billion annually. Pathogens, including plant viruses, constitute a major component of crop loss, reducing U.S. corn and soybean yields by approximately 15%. Furthermore, pathogen contamination of grain poses major phytosanitary concerns for international trade. The spread of invasive pests and pathogens due to increased global trade and changing habitats, necessitates continued monitoring and identification of emerging viruses and their vectors to inform appropriate disease management strategies. The overarching goals of our research are to detect and characterize important viruses of corn and soybean, identify and develop virus resistant germplasm, map resistance loci, and elucidate mechanisms of host-vector-virus interactions. Using serological, molecular, and next generation sequencing techniques, we will identify key endemic and emerging maize and soybean viruses, evaluate virus population structures, and develop diagnostic assays. Host range and insect-vectors will be determined to reveal factors important for pathogenesis and transmission. We will identify resistant germplasm and develop molecular breeding tools to combat emerging maize viruses, such as high plains wheat mosaic virus (HPWMoV) and maize yellow mosaic virus (MaYMV). Secondary and tertiary soybean gene-pools will be evaluated to identify bean pod mottle virus (BPMV) resistant germplasm and resistance will be incorporated into cultivated soybean lines. Fine mapping and map-based cloning approaches will used to delineate the genomic loci associated with maize chlorotic mottle virus (MCMV) and potyvirus resistance genes, helping to determine mechanisms of host-resistance and to broaden our overall understanding of virus resistance in plants. Seed producers, breeders, researchers, and farmers will benefit from new disease diagnostic and molecular breeding tools, leading to improved corn and soybean yields.
Progress Report
Significant progress was made on all three project plan objectives in the third year of the project.
Objective 1: Identify, diagnose and characterize insect-transmitted pathogens of maize and soybean.
Twenty-one High Plains wheat mosaic virus (HPWMoV) isolates were collected from the Pacific Northwest and their genomes were sequenced and assembled. A remarkable level of genomic diversity was discovered with as little as 80% nucleotide identity found in some pairwise comparisons between isolates. Some regions showed as little as 70% nucleotide identity, bordering on designation as different viral species. Multiple distinct variants for all eight RNA segments were identified, sometimes within a single isolate. This vast isolate collection was used to test the ability of current diagnostic methods to detect diverse variants of the virus. It was found that while a new diagnostic primer set we developed detected all isolates, the most widely used existing diagnostic primer set was unable to detect 20% of isolates. Leveraging the virus genome sequences, new primers that detect all isolates were developed to replace the less effective primer set that will be shared with collaborators at diagnostic clinics. Work continued to assess the effects of maize yellow mosaic virus (MaYMV) and maize dwarf mosaic virus on aphid vector behavior. Host preference experiments were conducted to determine whether the vector of both viruses, Rhopalosiphum maidis, the corn leaf aphid, prefers uninfected, MaYMV-infected, or MDMV-infected plants and if this preference changes after the insects acquire one or both viruses. Understanding how viruses can alter vector behavior and preference can help to elucidate the dynamics of vector and virus movement in the field, especially in complex co-infection contexts, leading to improved strategies to disrupt and limit the spread of both the vector and viruses.
Objective 2: Develop genetic markers and germplasm associated with corn virus resistance genes, and transfer information for practical management solutions.
Four field corn lines and approximately 80 sweet corn lines were screened for their response to infection by HPWMoV. Most lines were discovered to become infected with the virus when tested by sensitive diagnostic tests, however the majority outgrew symptoms during early vegetative maturity stages. Field corn recombinant inbred line populations derived from HPWMoV susceptible (Oh28) and resistant (Pa405, Oh1VI) parents have been increased for mapping HPWMoV resistance loci. Mapping populations are also being derived from crosses between the most resistant and most susceptible sweet corn lines that were identified from this screening process to map genomic loci associated with resistance. Asymptomatic and HPWMoV susceptible field and sweet corn lines were inoculated with the virus and grown to seed. Several HPWMoV infested seed lots were obtained from susceptible corn lines. However, none of the seed lots from asymptomatic lines tested positive for the virus, indicating that genetic resistance could be a viable management strategy to reduce seed infestation rates, thus facilitating seed export from the United States. Preliminary grow-out tests were conducted to determine the transmission rate of the virus from seed to seedling using 1,152 seed from HPWMoV susceptible infested seed lots, and the transmission frequency of the virus through seed was found to be 0.12%.
A genome wide association study was conducted for MaYMV resistance in the Flint-Goodman diversity panel. Preliminary analysis detected the presence of genomic loci on chromosomes 2, 3, 4, 5, and 6 associated with the severe reddening response induced by MaYMV infection. A semi-quantitative serological assay for virus detection developed by our research group will facilitate further mapping of resistance for this emerging virus. A recombinant inbred line population derived from B73 (MaYMV susceptible) and Ki3 (MaYMV resistant) was increased and will be used to map MaYMV resistance quantitative trait loci. Five soybean accessions with strong resistance to bean pod mottle virus were identified and crosses were made between the most resistant and susceptible lines Williams 82 and Dwight for F2 mapping population development.
Objective 3: Fine map, clone, and characterize virus resistance genes, facilitating the investigation of host- pathogen interactions.
An RNA-seq experiment was conducted to investigate gene expression in wheat streak mosaic virus resistant and susceptible near isogenic corn lines. Corn plants were inoculated or mock-inoculated with wheat streak mosaic virus and tissue was collected at 0, 6, 9, and 18 days post inoculation. RNA was isolated from tissue samples and subsequently sent for transcriptome sequencing. The RNA-seq data is currently being analyzed to identify differentially expressed genes between different genotypes and treatments. Fine mapping of maize chlorotic mottle virus resistance genes is ongoing in both N211 x Oh28 and CML333 x B73 fine mapping populations. Recombinant N211 x Oh28 backcross families were propagated in the field and are awaiting genotyping by an external collaborator prior to making informed selections to facilitate efficient phenotyping.
Additional rounds of backcrossing were performed for the CML333 x B73 backcross populations and the BC3S1 segregating families were planted in 2024 for genotyping and selection to perform the fine mapping experiments.
Accomplishments
1. Widespread susceptibility of commercial corn varieties to sugarcane mosaic virus and yield penalties up to 30% are prevented by improved potyvirus resistance. Maize dwarf mosaic (MDM) disease is one of the most important virus diseases of maize worldwide. MDM is caused by one of several potyviruses, most commonly maize dwarf mosaic virus (MDMV) or sugarcane mosaic virus (SCMV). Despite being widespread, little is known about the susceptibility of commercial field corn varieties or the associated yield impact of MDM disease in the United States. ARS scientists in Wooster, Ohio determined that 100% of the 78 high yielding commercial field corn varieties that were tested are susceptible to SCMV, and just one was susceptible to MDMV. Furthermore, among the susceptible varieties, yields were reduced on average by 10% and by nearly 30% in some varieties when inoculated with SCMV. Growing corn with all three major potyvirus resistance genes was found to eliminate disease symptoms, suggesting that incorporating potyvirus resistance genes into commercial varieties would be a viable management strategy for reducing the yield impact of MDM in the United States. This information can be used by commercial seed companies and corn breeders to develop varieties with improved potyvirus resistance, leading to better yields for growers.
2. 02 Potyvirus resistance is an effective control strategy for managing maize lethal necrosis disease. Maize lethal necrosis (MLN) disease is a devastating virus disease of corn caused by simultaneous infection of corn by maize chlorotic mottle virus (MCMV) and a potyvirus such as sugarcane mosaic virus (SCMV). Co- infection with these two viruses produces more severe disease symptoms than the combined effects of each virus individually, a phenomenon termed synergy. ARS researchers in Wooster, Ohio discovered that MLN disease synergy is more effectively managed by growing lines with elite potyvirus resistance rather than lines with MCMV resistance. Levels of SCMV were as much as 2-million fold lower in SCMV resistant corn compared to the most susceptible. In contrast, MCMV levels were initially lower in MCMV resistant lines, but by 14 days after virus inoculation, virus levels were no different from the susceptible control. Furthermore, while SCMV and MCMV synergy occurred in MCMV resistant lines co-infected with both viruses, no virus synergy was detected in the most potyvirus resistant lines. Thus, potyvirus resistance in corn should be a priority for effective MLN management. This information can be used by seed breeding companies to prioritize the development of corn varieties with better potyvirus resistance to effectively manage MLN, which will greatly benefit growers suffering from the devastating effects of this disease.
3. 03 Drone imaging data, combined with machine learning, predicts maize dwarf mosaic disease with greater than 70% accuracy. Maize dwarf mosaic (MDM) disease is one of the most widespread and important virus diseases of maize globally. Efficient and effective detection and monitoring of disease presence is critical for monitoring virus spread and disease management strategies. However, manual scouting and testing for MDM is laborious and expensive. ARS scientists in Wooster, Ohio discovered that multispectral imaging collected using drones equipped with a cost-effective multispectral camera could be used to predict the presence of MDM. A model was developed using machine learning and multispectral imaging that could effectively predict the presence or absence of virus infection with greater than 70% accuracy: a similar or better accuracy to that of traditional human based scouting for MDM based on comparisons of human scouting with subsequent validation by diagnostic testing. This discovery can be used to facilitate rapid and cost-effective detection of MDM disease by growers to inform crop rotations, weed management, and rogueing of infected plants, leading to improved yields.
Review Publications
Gentzel, I.N., Paul, P.A., Wang, G., Ohlson, E.W. 2024. Effects of maize chlorotic mottle virus and potyvirus resistance on maize lethal necrosis disease. Phytopathology. 114(2): 484-495. https://doi.org/10.1094/phyto-05-23-0171-r .
Jones, M.W., Ohlson, E.W. 2024. Susceptibility and yield response of commercial corn hybrids to maize dwarf mosaic disease. Plant Disease. https://doi.org/10.1094/pdis-01-24-0155-re.
Ohlson, E.W., Khatri, N., Wilson, J.R. 2024. Experimental host and vector ranges of the emerging maize yellow mosaic polerovirus. Plant Disease. 108(5):1246-1251. https://doi.org/10.1094/PDIS-06-23-1124-RE.
