Source: MICHIGAN STATE UNIV submitted to
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
Funding Source
Reporting Frequency
Accession No.
Grant No.
Project No.
Proposal No.
Multistate No.
Program Code
Project Start Date
Jun 1, 2020
Project End Date
May 31, 2023
Grant Year
Project Director
Thompson, A.
Recipient Organization
Performing Department
Non Technical Summary
Tar spot is a fungal disease that causes black lesions on maize leaves. Though it was first described in Mexico in the early 1900s, it wasn't reported in the United States until 2015, in the Great Lakes region. The disease subsequently spread to 7 states, with multiple reports of yield losses up to 50 bu/A. Our goals in this study are to i) identify and verify genomic regions contributing to tar spot resistance in maize, ii) model levels of disease with aerial spectral data, and iii) produce, sequence, and evaluate doubled haploids from resistant varieties crossed to elite temperate germplasm. We will screen a population of 300 diverse temperate inbreds and 200 tropical introgression lines in three Great Lakes states, with spectral imaging in one location in order to establish a faster and more efficient approach for future scouting and screening. Using preliminary data and resistance screening results, doubled haploids will be created from backcrosses of resistant to elite germplasm. Doubled haploids will be sequenced for marker discovery and screened in the three Great Lakes states to validate the effect of the introgressed genetic regions by re-estimating the effects of the haplotype blocks. This project will create a valuable resource for future research and breeding that will be utilized by both the public and private sectors to reduce the impact of tar spot on farmers' productivity. It is directly relevant to the program goals of resistance to pests and diseases, pre-breeding and germplasm enhancement, applied quantitative genetics, and phenomics.
Animal Health Component
Research Effort Categories

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1510 - Corn;

Field Of Science
1081 - Breeding; 1080 - Genetics;
Goals / Objectives
Our proposed work has three main goals:1) Map and validate resistance to tar spot by screening diverse temperate maize germplasm across affected locations in multiple years2) Generate new resistant material for breeders by backcrossing resistant varieties into elite germplasm and testing subsequent doubled haploid lines3) Establish resources (doubled haploid germplasm, marker data, and new quantitative genetics and remote sensing approaches) for future research
Project Methods
Objective 1. Map and validate resistance to tar spot by screening diverse temperate maize germplasm across affected locations in multiple years.A subset of 400 lines of field corn from the Wisconsin Diversity Panel will be screened for tar spot resistance in Michigan, Wisconsin, and Indiana. The 942 lines of the full Panel were initially selected to represent as much of the diversity of maize as possible while restricting phenology to material that is able to flower in Great Lakes climates. The subset of 400 were chosen as a subset that focused on field corn (rather than popcorn, sweet corn, or ornamental varieties) in order to be more uniform for management in on-farm trials. These varieties represent diverse public and private temperate germplasm. As the US did not have tar spot disease until 2015, there is no expectation of strong levels of resistance (unless by random chance) in this material since it would not have been under selection. However, the genetic resources in the population enable rapid progress in genetic mapping and downstream gene discovery should any level or type of resistance be present.In addition, 100 Germplasm Enhancement of Maize (GEM) lines and 100 BGEM doubled haploid lines that flower in the region will be screened, as they contain 25% tropical introgressions and may harbor unique resistance to tar spot. The GEM and BGEM lines were developed by backcrossing tropical maize germplasm to PHB47 or PHZ51, two temperate lines. The tropical donor parents are more likely to harbor some resistance to tar spot, as they come out of regions in Central and South America where the disease has been present for over a century. The 100 lines of each (GEM and BGEM) were chosen based on a) diverse representation of donor countries of origin, and b) ability to flower in the upper Midwest based on previous observations. The BGEM population, as doubled haploids, is entirely inbred and has marker data available. The GEM lines, on the other hand, are still segregating, meaning that each plant within a plot would have a unique (but related) combination of alleles present. Ideally, we can find resistance within the Wisconsin Diversity Panel, but if not, the BGEM lines would be the next logical choice. The segregating GEM lines are included as a backup; if we were to use them as our resistant donor sources we would be identifying a specific highly resistant plant within a segregating plot.We plan to collect agronomic and yield data on these lines in addition to taking severity ratings at all locations on at least three dates. Association mapping will be conducted on tar spot and eye plot severity and their combined tar spot index at each of three timepoints, as well as area under the disease progress curve (AUDPC).Objective 2. Generate new resistant material for breeders by backcrossing resistant varieties into elite germplasm and testing subsequent doubled haploid linesUsing preliminary data from Summer 2019 trials, approximately 20 potentially-resistant lines will be crossed to LH244 or another modern elite Ex-PVP line to start generating backcross material, and advanced until 75% elite. LH244 is a stiff-stalk line that grows well in the region of interest, is a very recent and highly used industry breeding line, and has modern genomic resources available. It is not expected to have resistance to tar spot, though this will be confirmed in summer 2019 before proceeding. In the event that LH244 is resistant or the donor resistant lines are non-stiff-stalk, a different recurrent parent will be chosen from recent Ex-PVP material.In subsequent inbred trials, identification and validation of resistance will refine the targeted resistant donor inbreds to 2-3. From each of these select populations, 100 to 150 doubled haploids will be induced, for a total of 300 lines, which will then be sequenced and tested in three locations. Doubled haploid production will occur as a fee-for-service at the Iowa State University facility (see quote in supporting documents). Sequencing for SNP calling will be completed using tGBS by Freedom Markers in order to ensure high-quality calls and reduce the quantity of missing data (see quote in supporting documents).Objective 3. Establish resources (doubled haploid germplasm, marker data, and new quantitative genetics and remote sensing approaches) for future researchSo far, observed levels of partial resistance in maize hybrid yield trials may only be due to hybrids escaping the moderate levels of disease pressure present thus far (Chilvers et al. 2018b). Therefore, these resources are crucial, and will be released immediately upon publication, if not before. Generation of germplasm and marker data will occur as described in Objective 2, and all resources generated will be made publicly available. PD Thompson has been in conversation with the maize curator at GRIN, the germplasm repository, and it is anticipated that these new lines (and accompanying marker data) may be a highly sought-after resource. The extreme ends of phenotypic distribution are likely to be popular, as well as potentially the whole population for linkage studies. Seed increases performed as part of the project will take this demand into account.Drone-based multispectral data will be acquired at the Michigan location and compared to ground-based data collection in order to model relationships between yield, disease severity, AUDPC, and spectral indices. Using phenotypic observations and generated SNP marker data, genetic effects will be re-estimated in the doubled haploids. This provides validation of the mapping results as well as helping to determine whether to approach further selection and introgression via tracking of large chromosomal segments (in the case of beneficial chunks in consolidated regions) vs genomic prediction (in the case of many small-effect regions spread throughout the genome).

Progress 06/01/21 to 05/31/22

Target Audience:Scientists, breeders (public and private), and farmers Changes/Problems:We were funded to produce and assess one set of doubled haploids. Through public-private partnership, we have negotiated to produce TWO sets -- we will have several hundred lines using B73 (public) and another several hundred using LH244 (private) -- both will be made fully public and available, and will include marker data. We are happy that these collaborations allowed us to double our outputs. What opportunities for training and professional development has the project provided?After the previous graduate student on this project successfully graduated, one of the undergrads involved on the project decided to stay on for a MS starting in Fall 2021. She has been the lead on the project, and has started training multiple undergraduates on the project as well. Another graduate student has been utilizing the field site and ratings to start a computer vision project on estimating tar spot disease severity from cell phone imagery. In addition, the lab group held an internal training session to process and analyze drone imagery for this project. How have the results been disseminated to communities of interest?Breaking barriers and building bridges: Identifying and addressing bottlenecks in interdisciplinary and translational plant science; invited talk at MSU Genomics Symposium, May 2022 Tar spot and other stories about maize breeding, genetics, and phenomics; Brewbaker Lecture at University of Hawaii, November 2021 Tar spot presentation and discussion with National Corn Growers SARAT committee, 1/11/2022 Field and lab research demonstration site for visiting VIPs: MSU Trustees Renee Knake Jefferson, Rema Vassar, and Dianne Byrum; and Interim Dean Kelly Millenbah, 9/13/2021 Senator Curtis Hertel, 7/29/2021 Representative Julie Brixie, 7/22/2021 Corn Marketing Program of Michigan, 7/20/2021 and 3/2/2022 What do you plan to do during the next reporting period to accomplish the goals?Test new germplasm (doubled haploids) in the field; perform further increases; obtain marker data for LH244 populations Establish collaborations to test cross doubled haploid lines for future work Finish analyzing, writing, and publishing datasets Deposit germplasm of interest into the repository in Ames so that it is available concurrently with publication

What was accomplished under these goals? 1. Validated resistance by screening stiff-stalk MAGIC population in 3 states 2. Continued backcrossing efforts in both field corn and sweet corn, and continued to produce/increase doubled haploid lines 3. Continued collaborations with public/private breeders to generate germplasm and marker data


    Progress 06/01/20 to 05/31/21

    Target Audience:Breeders, plant scientists, and farmers Changes/Problems:The pandemic shut down activity for some time in 2020, but we were able to proceed more or less as planned, especially since we had packaged and shipped our seed to off-site locations prior to the shutdown. Our trips to our off-site location throughout the summer were less well-staffed than normal because we were limited to 1 person per vehicle, but we collected the necessary data. What opportunities for training and professional development has the project provided?This was the primary thesis project for lead grad student, Blake Trygestad, who has now graduated with his MS. This was also the primary project for two undergraduate students, one of whom will start as a MS student in fall 2021 on this project. How have the results been disseminated to communities of interest?Corn field day presentation to farmers on tar spot work - 9-9-2020 MI Ag Ideas to Grow With Conference: Field Crops and Forage Session - 2-16-2021 MICENT Young Farmer's Workshop with Michigan Corn - 3-10-2021 Multi-scale image-based innovations for plant breeding research, invited talk at student-run 1st Annual Cell and Molecular Biology Research Symposium on "Discovery through imaging", MSU, May 2021 (virtual) Improving Methods for Maize Breeding and Genetics, invited talk at Plant Breeding Circle, TAMU, Sept 2020 (virtual) Improving Methods for Maize Breeding and Genetics, invited talk for NC State seminar series, Oct 2020 (virtual) Futures Magazine article on Addie Thompson in MSU's publication on plant health - July 2020 What do you plan to do during the next reporting period to accomplish the goals?Validate resistance in a different population Test doubled haploid lines for tar spot resistance Continue breeding goals

    What was accomplished under these goals? 1. Mapping resistance and screening diverse temperate germplasm was completed. 2. Crosses were completed, doubled haploids were induced, and agreements were started with companies to cross into their germplasm as well. 3. Doubled haploids were induced and recovered, and data was generated for future use.