Source: UNIVERSITY OF FLORIDA submitted to
SWEET CAP: INTEGRATED TECHNOLOGIES TO IMPROVE SWEET CORN PRODUCTION AND MARKETABILITY
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
EXTENDED
Funding Source
Reporting Frequency
Annual
Accession No.
1016512
Grant No.
2018-51181-28419
Project No.
FLA-HOS-005730
Proposal No.
2018-03344
Multistate No.
(N/A)
Program Code
SCRI
Project Start Date
Sep 1, 2018
Project End Date
Aug 31, 2022
Grant Year
2019
Project Director
Resende, M.
Recipient Organization
UNIVERSITY OF FLORIDA
G022 MCCARTY HALL
GAINESVILLE,FL 32611
Performing Department
Horticultural Sciences
Non Technical Summary
Sweet CAP is a coordinated agricultural project that will develop breeding tools and resources to improve the genetic foundation of sweet corn. Annual sweet corn production value, approximately $1 billion, is only 2% of field corn, which limits private investment in new technologies. However, sweet corn is the fifth most popular vegetable in the United States and breeders need to be able to address emerging challenges for the crop. For example, the percentage of fresh market corn that is shipped across the country is increasing and sweet corn needs to have a longer shelf-life. Similarly, emerging insect and microbial pests could be addressed with genetic resistance.The project brings together a multidisciplinary team with expertise in sweet corn breeding, plant genomics, plant pathology, plant-insect interactions, high throughput phenotyping, plant biochemistry, food science, and agricultural economics. Goals include:Sequencing the sweet corn genomeCoordinating public breeding resourcesDevelopment of new breeding technologiesImproving insect and pest resistance in sweet cornImproving tolerance to early season plantingDetermining the factors that drive consumer preferences for different types of sweet cornEconomic analysis will identify the breeding technologies and traits that have the highest potential return and educate breeders, growers, and processors on the most promising innovations. The CAP team will work with breeders, processors, and growers to ensure that the project addresses needs through the chain of production.
Animal Health Component
0%
Research Effort Categories
Basic
10%
Applied
80%
Developmental
10%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011480108010%
2021480108150%
2041480301010%
2041480309010%
2021480100010%
2011480105010%
Goals / Objectives
This Coordinated Agricultural Project (CAP) addresses needs expressed by sweet corn breeders, processors, and growers. Annual sweet corn production value, approximately $1 billion, is only 2% of field corn, which limits private investment in new technologies. The CAP will develop breeding tools and resources to address the stakeholder consensus that the genetic foundation of sweet corn needs improvement. The project goals are to addresses four SCRI focus areas: 1) breeding, genetics, and genomics; 2) address threats from pests and diseases; 3) improve production efficiency, productivity, and development; 4) innovations and technology development.Sweet CAP has five inter-related objectives. Objective 1 will develop genomics, germplasm diversity resources, and doubled haploid breeding. These resources will be used to study traits identified by stakeholders as having high value. Objective 2 focuses on insect and disease resistance to reduce inputs and improve marketability. Objective 3 focuses on early season cold tolerance to aid growers and processors. Objective 4 seeks to improve sweet corn eating quality based on consumer preferences. Objective 5 will integrate and extend the knowledge developed. Economic analysis will identify the technologies and traits that have the highest potential return and educate stakeholders on the most promising innovations.
Project Methods
The reference Sweet Corn genome sequence will be generated with a combination of next generation sequencing methods including Illumina short reads, PacBio long reads, and Hi-C sequencing for assembly. The diversity panel will be selected from sweet corn germplasm that is able to grow in both Florida and Wisconsin. Genotyping will be completed by short read, whole genome sequencing. Plant phenotypes will be assessed in the field. Cold tolerant emergence will be assessed using a machine vision growth chamber assay. Eating quality traits will be assessed with analytical chemistry and physical measurements. Mature kernel phenotypes will be predicted from near infrared spectroscopy based on calibrations developed during the project. GWAS will use statistical methods developed for field corn. Associations for specific traits will be validated for a few test cases when maize genomic resources have appropriate genetic stocks available.Doubled-haploid breeding will be improved by identifying superior haploid inducers for sweet corn germplasm and developing high-oil inducer lines. Haploid selection will be improved by developing near infrared spectroscopy sorting capabilities for high-oil inducer lines. Haploid doubling frequency will be improved by screening for spontaneous haploid genome doubling traits within the diversity panel.A subset of the diversity panel will be screened for resistance to seedling blights caused by Pythium ultimum. Genetic inheritance patterns will be tested for any resistance sources found. Silkfly resistance will be further introgressed into elite sweet corn germplasm to produce commercial quality lines for licensing. Eating stage ear volatile emissions from resistant and sensitive lines will be compared.Transgenes expressing starch synthesis genes late in kernel development will be constructed and tested for improved cold tolerance at germination and emergence.To improve eating quality, novel genetic combinations of starch synthesis mutants will be generated and evaluated for production of sugars and phytoglycogen. Phytoglycogen synthesis will be studied in bacteria using a synthetic biology approach. Mature kernel sugar and starch levels along with pericarp thickness will be correlated with eating stage values to determine if eating quality can be predicted prior to planting. Near infrared spectroscopy will be used to predict these mature kernel traits.Eating quality will be assessed in consumer panels using flash frozen corn from the diversity panel. Consumers will rate overall liking and participate in auctions of the varieties tasted. Parallel analytical chemistry will correlate sugars, volatiles, pericarp thickness, and color traits to consumer preferences. Economic models will be developed to determine the willingness to pay for specific quality traits. Partial budget analysis will determine the relative value of traits for improvements in breeding, production, and shelf-life.The CAP will be evaluated by a stakeholder advisory panel representing scientists, breeders, processors, and growers. Knowledge developed will be extended to the target audiences mentioned in previous sections.

Progress 09/01/20 to 08/31/21

Outputs
Target Audience:Our primary target audience are stakeholders in the production and distribution of sweet corn. Our stakeholders include members of sweet corn breeding programs in seed companies, processors who decide on hybrids for contracts with growers, and sweet corn growers. Changes/Problems:A derecho in August of 2020 did have substantial impact on how much seed we were able to harvest from our 2020 nursery at ISU. Unfortunately, most of the induction crosses completed during July of 2020 were destroyed and will thus be repeated during summer of 2021. The COVID19 pandemic caused the USDA location in Gainesville, Florida to switch to maximum telework. Dr. Anna Block's group obtained permission to perform only a limited amount of lab and field work. This has significantly slowed progress planned for Dr. Block's group during this reporting period. At UF, COVID19 caused all sensory testing to be suspended from March - September 2020. Two sensory panels were cancelled during the suspension. COVID19 restrictions also made hiring undergraduate help at UF difficult for the Fall of2020. Furthermore, our fall nursery in 2020 was impacted by unusual amounts of rain in September 2020, which limited our ability to phenotype the sweetCAP diversity population and caused several inducer crosses to fail. We had to stop taste panels at UW. Therefore, we switched to using annual USDA consumption and price data to estimate own price, cross price, and income elasticities for both fresh and processed sweet corn over time. This work will not directly address the specific goals of the project but does document the broader context of consumer trends in sweet corn consumption that set the stage for the project's more detailed analysis based on the consumer panels. Equipment failure at WSU resulted in a >4 month delay in screening the SweetCAP panel for resistance to F. verticilloides. Temperature control of the Percival Scientific growth chamber used to initiate the screen failed. By the time the growth chamber was repaired effectively, we had found out about an opportunity to do the resistance screening in a large, underground room with excellent temperature control located at the WSU Puyallup REC. The silver lining in the delay caused by the growth chamber failure is that we anticipate being able to screen the entire association panel over ~6 weeks (August-September 2021) in this facility instead of over ~15 months with the original growth chamber that can only accommodate screening 42 lines at a time. At UW-Madison our efforts in the 2020 growing season were reduced by more than 50% due to COVID19 restrictions. What opportunities for training and professional development has the project provided?Graduatestudents and post doc trainees present their data at monthly Sweet CAP project meetings. These trainees are also participating in professional development at their respective instuitional programs, which includes developing research proposals, presenting research at local meetings, and writing manuscripts. Additionally, a total of 20 presentations were given by members of the team at various conferences across the country. These presentations have all been reported under "Products". How have the results been disseminated to communities of interest?We published a total of 15 peer reviewed articles, and have submitted an additional 8 manuscripts. A total of 20 presentations were given at various conferences throughout the year by Sweet CAP personnel (reported under "Products" in greater detail). Additionally, 6 seminars were given by Sweet CAP personnel. Details of these seminars are listed below. Past, Present, and Future of Maize Doubled Haploid Technology. T. Lubberstedt. Invited Seminar. The Frontiers of Science and Technology in Crop Breeding and Production (Virtual). June 2021. Maize Volatiles in plant-pest interactions. A. Block. Invited Seminar. UF Department of Entomology and Nematology Seminar Series. December 2020. The Impact of Cooking on Sweet Corn Aroma. J. Yactayo-Chang. Postdoc Seminar. ARS Postdoc Network Seminar Series. October 2020. Cold Season Tolerance and Prevalence of Seedling Blights in Sweet Corn in the Columbia Basin of Washington. R. Solemslie. Masters thesis defense seminar (Virtual). Washington State University. November 2020. The Third Eye: Computer Vision for Sweet Corn Breeding. J. Gonzalez. Guest Lecture. University of North Florida Biology Lecture Series (Virtual). Genomics and Phenomics Applied to Sweet Corn Breeding. M. Resende. Invited Seminar. University of Illinois Urbana-Champaign Seminar Series (Virtual). What do you plan to do during the next reporting period to accomplish the goals?Objective 1: -Finalize all the GWAS for the multiple traits collected in the project so far. -The 4 haploid inducers selected at ISU will be evaluated at UF to determine induction rates in Florida and potential inducer by environment interactions. -Haploid seed will be produced from the 9 lines identified at ISU with elevated haploid male fertility. These lines will be re-evaluated in the Summer of 2022. Additionally, we will re-evaluate lines for HMF that we were unable to evaluate due to damage from the 2021 derecho. - A 2nd GWAS will be completed at ISU with 384 lines as data becomes available from UF during 2022. -We are considering incorporating a major HMF/SHGD QTL into sweet corn, which was identified in field corn by the Lubberstedt group at ISU. This idea will be discussed further in an upcoming meeting. -We will continue to test our high-pressure chamber at UF for use in haploid doubling. Objective 2: -We will identify/create UniformMu or CRSPR/Cas9 loss-of-function mutants in genes identified in our fall armyworm induced volatile GWAS study. -We will screen the entire SweetCAP panel for resistance to the seedling blight pathogen F. verticillioides. Objective 3: -The last replicate of the of the seedling emergence assay using the machine vision program VIGOR will be completed at UF. Results will be analyzed and used for GWAS. -Hybrid seed from the introgression of a heat stable 6-phosphogluconate dehydrogenase into Florida Stay Sweet parental inbred lines will be evaluated in the spring of 2022 to see if there was improved kernel set under heat stress. Objective 4: -We plan on conducting 3 more sensory tests at UF, where sensory testing has already resumed. In person testing is scheduled to resume at UW in Fall of 2021. -Volatile analysis will be completed alongside the sensory panels. Objective 5: -We will write up the analysis results of consumer trends in sweet corn consumption based on USDA data for submission to peer-reviewed journal. -We will write and pursue publication of 1-2 additional UF EDIS extension publications focused on sweet corn over the next reporting period.

Impacts
What was accomplished under these goals? 1.1. We completed the sequencing and assembly of Ia453-sh2, and an accompanying analysis that estimated regions of the maize genome uniquely under selection in sweet corn. Results also suggest a single haplotype of origin for the different sugary1 alleles found in North America. The Ia453-sh2 genome was also used as reference for the alignment of the whole genome sequenced samples. We have sequenced and analyzed the ~700 samples that compose the Sweet CAP Diversity Panel. SNPs were called using two different callers. Approximately 28 million SNPs were detected, annotated, and made available toco-PIs for downstream analysis. 1.2. AT UF, best linear unbiased estimates (BLUEs) were generated for all phenotypes collected so far. Preliminary GWAS was performed using different models and SNP sets. Results are promising and the analysis is currently being refined. Linkage disequilibrium and population genetic parameters were also estimated. 1.3. 20 experimental haploid inducers sent from ISU to UF in 2019 were used for a first round of inductions in 2020. Resulting seed was sent to ISU for evaluation; colchicine-treated haploids were returned to UF. From the list of 20 haploid inducers, 4 were selected which best met criteria for use at UF. A second set of test inductions was done at UF with these 4; resulting seed was sent to ISU and colchicine-treated haploids were transplanted to the ISU nursery in 2021. Additionally, Dr. Gustin designed a high-pressure chamber that is being tested at UF for the ability to induce chromosome doubling without colchicine. MTC inducers were crossed with various hybrid lines. Haploid kernels were selected and treated with N2O at high pressure. Resulting plants were transplanted to the greenhouse, where fertile sectors of haploid anthers were observed. We are collaborating with USDA-ARS Research Agricultural Engineer Dr. Paul Armstrong to develop a high-speed single kernel sorting device to separate haploid and diploid kernels from bulk haploid induction populations. Dr. Armstrong has constructed a high-throughput skNIRS sorter based on the original design but augmented with an automated kernel feeder and a high-speed sorting gate. Dr. Armstrong expects to deliver high-speed sorters to UF and ISU before the end of 2021. We expect to begin developing haploid discrimination models for each device in 2022 using induction populations produce from the ISU high oil haploid inducer. 4 promising high oil haploid inducer liners (HOHI) were isolated, showing induction rates of over 10%. Self-pollinated progeny of these lines has average oil contents around 10%. Haploid and hybrid kernels were analyzed by skNIR, with on average a 1% oil content difference. In the summer 2021 season test inductions with all 4 lines in 6 different genetic backgrounds is underway. To increase the oil content of inducer lines further, the development of BC2 derived materials was continued. Results suggest that high oil and induction ability are negatively correlated. 313 lines were evaluated for haploid male fertility (HMF) at two locations in Iowa. 9 lines were selected for elevated levels of HMF. Evaluation is ongoing. 2.1. Dr. Block's group identified a receptor like kinase in corn that impacts resistance to the fungal diseases southern leaf bight and Fusarium graminerum. In summer of 2020, 86 SweetCAP lines were screened at WSU for resistance to Fusarium verticilloides. Results suggested that a higher inoculation rate was needed. In Spring of 2021 a screen of 42 SweetCAP lines was begun for resistance to a highly virulent strain of F. verticilloides. However, by 14 days, equipment failure caused majors delays. Read more details in the "Changes/Problems" section. 2.2.We have tested all of University of Florida's insect resistant, sweet corn germplasm but have not yet found a resistant line to the silk fly complex in South Florida. We have moved our search into field corn in hopes of finding an acceptably resistant/tolerant line that we can convert to sweetcorn.So far, no resistant field corn line has shown consistent resistance in multiple seasons. We will continue to evaluate these resistant lines and new populations and hybrids made from these lines for silk fly resistance. 2.3. We completed GWAS for fall armyworm induced volatiles and identified promising candidate genes for the production of several volatiles. We performed fall armyworm oviposition choice assays on corn plants supplemented with different volatiles and identified 4 volatiles that impact fall armyworm behavior. 2.4. One nursery at UW-Madison is being utilized for screening SweetCAP materials for resistance to the sugarcane mosaic virus. Evaluation is ongoing and genetic variability is present. 3.1. Data from our 2nd cold field trial at WSU has been analyzed for stand count, emergence, vigor, and seedling abnormalities. Results identified several lines from the SweetCAP panel with greater tolerance to cold stress than some commercial hybrids. 583 lines from the panel have been scored for seedling emergence in controlled temperature conditions via our machine vision assay (VIGOR) at UF. Results from cold and warm plantings were used to identify top lines for emergence frequency and variability. 3.2 We transformed a dCas9-Adenine deaminase-based editor to engineer new weak sh2 alleles. The transformants did not contain the base editor. We are redesigning the construct. 3.3. We introgressed a heat-stable 6-phosphogluconate dehydrogenase trait (Ribeiro et al. 2020 - https://doi.org/10.1073/pnas.2010179117) into Florida Stay Sweet parental inbred lines. Hybrid seed was produced and will be evaluated for heat tolerance. We have also characterized a subset of the sweetCAP population for the limited-transpiration trait in response to high temperatures. 4.1. We completed a sensory test in 5/21 at UF using 5 varieties and including volatile analysis. We have now assembled a master data sheet containing results from all 4 panels from this project so far. We also characterized sweet corn cob volatiles from a commercial hybrid for the impact of both cooking and post-harvest storage on aroma volatile production. 4.2. We made progress in setting up the starch biosynthetic system in Saccharomyces cerevisiae. The strain was transformed with 12 maize genes the resulting carbohydrate was physically characterized. We've made novel observations on the function of Starch phosphorylase 1 and its interactions with Starch synthase 4 and 5. 4.3. NIR prediction of mature sweet corn pericarp thickness was improved by collecting alternative thickness data for thick pericarp samples. We observed that the pressure micrometer inflated pericarp thickness in kernels with pericarps over 100µM thick. This bias in the reference data increased the error in the NIR prediction model. Accuracy was improved by replacing pressure micrometer data for 16 thick pericarp kernels with data collected using high resolution non-computed tomography. 5.1. We completed economic analysis of consumers' willingness to pay using consumer panel data from our May 2021 trial. Due to COVID limitations on consumer experiments, switched to examining consumer trends in sweet corn consumption based on USDA data. Developed own price, cross price, and income elasticity estimates over time for both fresh and processed sweet corn. 5.2. In 2020/21, we presented updates of our SweetCAP project to the Sunshine Growers Association of Florida. The meeting included 36 growers which provided suggestions and input on steps moving forward. We have also chaired and organized the International Sweet Corn Developers Association (ISCDA). Several SweetCAP scientists and students presented results and a stakeholder panel was organized to discuss future steps. We have also prepared one outreach article focused on sweet corn origins and current industry status. We are in the process of submitting this article to the UF EDIS publication system.

Publications

  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Baseggio, M., Murray, M., Wu, D., Ziegler, Kaczmar, N., Chamness, J., Buckler, E.S., Hamilton. J.P., Buell, C.R., Vatamaniuk, O.K., Buckler, E.S., Smith, M.E., Baxter, I., Tracy, W.F., and Gore, M.A. 2021. A genome-wide association study reveals an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels . G3-2021-402240
  • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Zystro, Jared, Tessa Peters, Kathleen Miller, and William F. Tracy 2021. Classical and genomic prediction of synthetic open pollinated sweet corn performance in organic environments. Crop Science (accepted)
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Revilla, P., Anibas, C.M. and Tracy, W.F. 2021. Sweet Corn research around the world 2015 2020. Agronomy 2021, 11, 534. https://doi.org/10.3390/agronomy11030534
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Ivancic, K., A. Locatelli, W.F. Tracy, and V. Picasso. 2021 Kernza intermediate wheatgrass (Thinopyrum intermedium) response to a range of vernalization conditions. Canadian Journal of Plant Science 10.1139/CJPS-2020-0251
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Zystro, Jared, Tessa Peters, Kathleen Miller, and William F. Tracy 2021. Inbred and hybrid sweetcorn genotype performance in diverse organic environments. Crop Science 10.1002/csc2.20457
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Rapid Phenotyping of Sweet Corn with Computer Vision. J. Gonzalez, K. Leach, M. Resende. Oral presentation. International Sweet Corn Development Association  Virtual Meeting. Dec 2020.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2021 Citation: Deploying Genomic Selection in the University of Florida Sweet Corn breeding program. M. Resende. Oral presentation. International Sweet Corn Development Association  Virtual Meeting. Dec 2020.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Utilizing Spontaneous Haploid Genome Doubling in Sweet Corn Breeding. T. Foster. Oral presentation. International Sweet Corn Development Association  Virtual Meeting. Dec 2020.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Recent Advances in Maize Haploid Inducer Development. U. Frei. Oral presentation. International Sweet Corn Development Association  Virtual Meeting. Dec 2020.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: The Impact of Storage and Cooking on Sweet Corn Aroma. J. Yactayo-Chang. Oral presentation. International Sweet Corn Development Association  Virtual Meeting. Dec 2020.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Screening the USDA SCRI Sweet CAPs Sweet Corn Germplasm for Cold Tolerance in the Columbia Basin of Washington R. Solemslie. Oral presentation. International Sweet Corn Development Association  Virtual Meeting. Dec 2020.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Insights in the Regulation of Starch Biosynthesis in Different Sweet Corn Genetic Backgrounds. C. Finegan. Oral presentation. International Sweet Corn Development Association  Virtual Meeting. Dec 2020.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Breeding Vegetable Corn: Selection Strategies for Quality Traits. L. Baker. Oral presentation. International Sweet Corn Development Association  Virtual Meeting. Dec 2020.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2021 Citation: Exploring the Genetic Variation of Haploid Induction Rate for High Level Maternal Haploid Inducer Breeding. YR. Chen. Poster presentation. Baker Symposium at ISU. April 2021.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2021 Citation: Prospect of Utilizing Haploid Male Fertility for Doubled Haploid Production in a Maize Breeding Program. T. Foster. Poster Presentation. Baker Symposium at ISU. April 2021.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2021 Citation: The Production and Function of Maize Chemical Defenses in Plant-Pest Interactions. A. Block. Keynote Speaker Presentation. Plant Molecular and Cellular Biology Workshop by UF. May 2021.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2021 Citation: Engineered 6-Phosphogluconate Dehydrogenase in Amyloplasts Assessed in Field Corn Hybrids for Mitigation of Grain Yield Loss Under Heat Stress. H. Hersh. Oral presentation. Plant Molecular and Cellular Biology Workshop by UF. May 2021.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2021 Citation: Computer Vision for High-Throughput Quantitative Genetics in Sweet Corn. J. Gonzalez. Oral presentation. Plant Molecular and Cellular Biology Workshop by UF. May 2021.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2021 Citation: Implications of Consumer Sweet Corn Trends for Wisconsin. P. Mitchell, F. Dong. Oral presentation. Central Wisconsin Processing Crops Meeting (virtual). March 2021.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Optimizing and accelerating sweet corn breeding through genomics and phenomics. M. Resende. Oral presentation. Florida AgExpo 2020 (virtual).
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: The Third Eye: Computer Vision for Sweet Corn Breeding. J. Gonzalez. Graduate Student Oral Presentation. SACNAS Annual Conference (Virtual). October 2020.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Use of Computer Vision to Quantitatively Screen Leaf Blight Resistance in Sweet Corn. . J. Gonzalez. Graduate Student Oral Presentation. SACNASs South Eastern Regional Symposium. February 2020.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Genomic Dissection and Molecular Breeding of Nitrogen Use Efficiency in Sweet Corn. C. Finegan. Poster presentation. 4th Annual UF Plant Science Symposium: Big Data in Plant Science. January 2020.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Gustin, JL, Frei, UK, Baier, J, Armstrong, P, L�bberstedt, T, Settles, AM. Classification approaches for sorting maize (Zea mays subsp. mays) haploids using single-kernel near-infrared spectroscopy. Plant Breed. 2020; 139: 1103 1112. https://doi.org/10.1111/pbr.12857
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Vanous, K., L�bberstedt, T., Ibrahim, R., Frei, U.K. (2020) MYO, a candidate gene for haploid induction in maize causes male sterility. Plants 9:773; doi:10.3390/plants9060773
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Verzegnazzi, A., Goncalves, I., Frei, U.K., Krause, M., Hufford, M., Frei, U., Campbell, J., Almeida, V., Tonello Zuffo, L., Boerman, N., L�bberstedt, T. (2021) Major locus for spontaneous haploid genome doubling detected by a case-control GWAS in exotic maize germplasm. Theor. Appl. Genet. DOI: 10.1007/s00122-021-03780-8
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2021 Citation: Muhammad-Aboobucker, S., Jubery, Z., Frei, U.K., Foster, T., Chen, Y.-R., Ganapathysubramanian, B., L�bberstedt, T. (2021) Protocols for in vivo doubled haploid (DH) technology in maize breeding: From haploid inducer to haploid genome doubling. Methods Molecular Biology (in press)
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Yactayo-Chang, J.P, Tang, H.V., Mendoza, J., Christensen, S.A., and Block, A.K. (2020) Plant defense chemicals against insect pests. Agronomy 10:1156 doi:10.3390/agronomy10081156.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Block, A.K., Mendoza, J., Rowley, A., Stuhl, C., Meagher, R.L. (2020) Approaches for assessing the impact of Zea mays (Poaceae) on the behavior of Spodoptera frugiperda (Lepidoptera: Noctuidae) and its parasitoid Cotesia marginiventris (Hymenoptera: Braconidae). Florida Entomologist 103(4):505-513.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Block, A.K., Xin, Z., Christensen, S.A. (2020) The 13?lipoxygenase MSD2 and the ??3 fatty acid desaturase MSD3 impact Spodoptera frugiperda resistance in Sorghum. Planta 252:62 doi.org/10.1007/s00425-020-03475-2.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Perez VE, Dai R, Bing Bai B, Tomiczek B, Askey B, Zhang Y, Ding Y, Grenning A, Block AK, Kim J. (2021) Aldoximes are precursors of auxins in Arabidopsis and maize . New Phytologist doi:10.1111/nph.17447
  • Type: Journal Articles Status: Submitted Year Published: 2021 Citation: Yactayo-Chang JP, Mendoza J, Willms SD, Rering CC, Beck JJ and Block AK Zea mays Volatiles that Influence Oviposition and Feeding Behaviors of Spodoptera frugiperda. Journal of Chemical Ecology (submitted)
  • Type: Journal Articles Status: Submitted Year Published: 2021 Citation: Block AK, Tang HV, Hopkins D, Mendoza J, Solemslie RK, du Toit LJ, and Christensen SA A Maize Leucine-Rich Repeat Receptor-Like Protein Kinase Mediates Responses to Fungal Attack. Planta (submitted)
  • Type: Theses/Dissertations Status: Other Year Published: 2020 Citation: Cold season tolerance and prevalence of seedling blights in sweet corn in the Columbia Basin of Washington (PDF). MS thesis, Washington State University, Pullman, WA. 186 pp.
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Solemslie, R., du Toit, L.J., Tracy, W.F., and Stearns, T. 2021. Evaluation of steam treatments for Fusarium spp. and other fungi on sweet corn seed, 2020. Plant Disease Management Reports 15:CF017
  • Type: Journal Articles Status: Submitted Year Published: 2021 Citation: Gonzalez J., Ghosh N., Colantonio V., Pereira F.C., Pinto Jr R, Leach K., Resende. MFR - EARCV: An Open-Source Package For Sweet Corn Ear Phenotyping. Submitted
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Ying Hu, Vincent Colantonio, B�rbara SF M�ller, Kristen A Leach, Adalena Nanni, Christina Finegan, Bo Wang, Matheus Baseggio, Carter J Newton, Emily M Juhl, Lillian Hislop, Juan M Gonzalez, Esteban F Rios, L Curtis Hannah, Kelly Swarts, Michael A Gore, Tracie A Hennen-Bierwagen, Alan M Myers, A Mark Settles, William F Tracy, Marcio FR Resende. Chromosome-scale genome assembly and population genomic analysis provides insights into origin and evolution of modern sweet corn. Nature Communications. 12, 1227. 2021
  • Type: Journal Articles Status: Submitted Year Published: 2021 Citation: Colantonio V., et al. RESENDE M.F.R.. Metabolomic Selection for Enhanced Fruit Flavor. Submitted, PNAS
  • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Colley, M.C., J. C. Dawson, C. McCluskey, J. R. Myers, W. F. Tracy, E. T. Lammerts van Bueren. 2021. Exploring the emergence of participatory plant breeding in countries of the global North  a review The Journal of Agricultural Science (accepted with revisions)
  • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Hislop, L., E. Stephanie, P.J. Flannery, M. Baseggio, M.A. Gore, and W.F. Tracy. Sugarcane Mosaic Virus Resistance in the Wisconsin Sweet Corn Diversity Panel Journal of American Society of Horticultural Science (accepted with revisions)
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: McCluskey, C. and W.F. Tracy. 2021. Engaging Farmer Stakeholders: Maize Producers Perceptions and Strategies for Managing On-Farm Genetic Diversity in the Upper Midwest. Sustainability https://www.mdpi.com/2071-1050/13/16/8843/htm


Progress 09/01/19 to 08/31/20

Outputs
Target Audience:The major goal of Sweet CAP is to identify genetic resources, high-value traits, and breeding tools needed for long term sustainability of the sweet corn agricultural system. Our primary target audience are stakeholders in the production and distribution of sweet corn. Our stakeholders include members of sweet corn breeding programs in seed companies, processors who decide on hybrids for contracts with growers, and sweet corn growers. Changes/Problems: Last year we reported difficulties hiring a project manager. We hired a full time Research Coordinator in spring 2020, who completes project management tasks for the Sweet CAP team. Therefore, we now expect to develop the scientific content for the project website and publish extension publications at UF over the next reporting period. Hurricane Dorian caused a taste panel originally planned for UF to be re-located to UW in the fall of 2019. In Dr. Mark Settles' lab at UF, a large growth room was irreparably damaged during infrastructure renovations by the college. This delayed the start of cold emergence assays, but we have been assigned a cold room replacement to complete the emergence assays. The COVID19 pandemic has caused setbacks for many Sweet CAP objectives, though research was able to continue in most cases with alterations. Laboratory access was heavily restricted at all campuses involved through spring 2020, causing experiments to be postponed and field plantings were more limited. COVID19 travel restrictions prevented data from being collected for field trials. In order to repeat trials in year 3, a subset of Sweet CAP diversity panel accessions will require a new round of seed increases. We were also unable to hire undergraduate researchers for the 2020 summer season. This limited field activities and student training/outreach. All sensory panels were cancelled since March 2020. Human subject research is currently allowed, but our next opportunity for consumer panels will be spring 2021. The in-person Annual Maize Genetics Conference was cancelled as a result of COVID19. A majority of Sweet CAP scientists and students had planned to attend and/or present at this conference. Several students presented posters at the virtual meeting in June, 2020. What opportunities for training and professional development has the project provided?Graduate student and post-doc trainees present their data at biweekly project meetings. These trainees are also participating in professional development in their respective institutional programs, which includes developing research proposals, presenting research at local meetings, and writing manuscripts. Additionally, talks and posters were presented by students and faculty of the Sweet CAP team at scientific conferences throughout the year, which are listed below: Solemslie, R., Derie, M., Morgan, P., Gyawali, S., and du Toit, L. 2019. Sweet corn production in the Columbia Basin of Washington: Causal agents of seedling blights and prevalence of mefenoxam resistance. Phytopathology 109:S2.168. Poster presented at the 2019 Annual Meeting of the American Phytopathological Society, 3-7 Aug. 2019, Cleveland OH. (Abstr.) Solemslie, R. and du Toit, L.J. 2019. Sweet corn production in the Columbia Basin of Washington: Screening for cold tolerance and resistance to seedling blights. Page 8, Abstracts of the 2019 Annual Meeting of the International Sweet Corn Development Association, 9-10 Dec. 2019, Chicago, IL. (Abstr.) Lillian Hislop, Elizabeth Stephanie, Pat Flannery, Michael A. Gore, William F. Tracy (2020) Sugarcane Mosaic Virus Resistance in the Wisconsin Sweet Maize Diversity Panel. Poster. Plant and Animal Genome Conference 2020, San Diego, California. Lillian Hislop, Elizabeth Stephanie, Pat Flannery, Michael A. Gore, William F. Tracy (2020) Sugarcane Mosaic Virus Resistance in the Wisconsin Sweet Maize Diversity Panel. Poster. Corn Breeding Research Meeting and the International Sweet Corn Development Association meeting, Chicago, IL Gonzalez J.M., Leach K., Dufault N., Beckham K., RESENDE M. F. R. Genome Wide Association Study of Leaf Blight Resistance in Sweet Corn. Oral presentation, 2020 -SACNAS - Advancing Chicanos/Hispanics and Native Americans in Science, Gainesville. Y Hu, Colantonio V., K Leach, M Baseggio, K Swarts, M Gore, WF. Tracy, RESENDE M. F. R.. The Sweet Corn Genome Assemblyand Comparative Analysis with Other Field Corn Genomes. Oral presentation, 2020,Plant and Animal Genome XXVIII Conference,San Diego, California, USA Colantonio V., Hu Y., Swarts K., Hislop L., Gore M., Settles M., Tracy W., RESENDE M. F. R.. (2019). Population Genomic Analyses of Sweet Corn. Joint meeting - Corn Breeding Research Meeting and the International Sweet Corn Development Association meeting, Chicago, IL Gonzalez J.M., Leach K., Dufault N., Beckham K., RESENDE M. F. R. Use of Oxford Nanopore Genome Sequencing Technology towards Diagnostic Marker Development and Dissection of Disease Resistance in Sweet Corn - Florida Phytopathological Society, 2019 Finegan C., Leach K., RESENDE M. F. R. Molecular Breeding of Nitrogen Use Efficiency in Sweet Corn. National Association of Plant Breeding 2019 Annual Meeting, Mountain Pine, Georgia, 2019. Gonzalez J.M., Leach K., Dufault N., Beckham K., RESENDE M. F. R. Genome Wide Association Study of Leaf Blight Resistance in Sweet Corn. Sweet Corn. National Association of Plant Breeding 2019 Annual Meeting, Mountain Pine, Georgia, 2019. Mitchell, P., and F. Dong. Influence of Sweet Corn Quality Traits on Willingness to Pay for Fresh Sweet Corn. Oral presentation. International Sweet Corn Development Association Annual Meeting. Chicago, IL Dec 9-10, 2019. Mitchell, P. Agricultural Economy Outlook: Implications for Processing Vegetables. Oral presentation. MidWest Food Products Association, Processing Crops Conference, Wisconsin Dells, WI, Dec 3, 2019. Dao, L., Gustin, J., Ryan, S., Spalding, E., Miller, N., du Toit, L., Resende, M., and Settles, A.M. (2019) Comparing Controlled Environmental Conditions to Simulate Field Trial Emergence in Sweet Corn. Oral presentation. Corn Breeding Research Meeting and the International Sweet Corn Development Association meeting, Chicago, IL. Hersh, H., Boehlein, S., Gustin, J., Resende, M., and Settles, A.M. (2019) Predicting Sugar and Starch in Mature Sweet Corn Kernels. Oral presentation. Corn Breeding Research Meeting and the International Sweet Corn Development Association Meeting, Chicago, IL. Boerman, N.A., Frei, U.K., Lubberstedt, T. (2019) Utilizing Doubled Haploids in Sweet Corn Breeding: Haploid Induction and Selection. Oral presentation. Corn Breeding Research Meeting and the International Sweet Corn Development Association Meeting, Chicago, IL. Tracy, W.F. (2019). Recent developments tweaking starch biosynthesis and creating new products in fresh corn. Oral presentation. Corn Breeding Research Meeting and the International Sweet Corn Development Association Meeting, Chicago, IL. Gustin, J., Williams, J., Baier, J., Armstrong, P., Resende, M., Tracy, W., and Settles, M. (2019) Expanding the Vision of Near-Infrared Spectroscopy to Create Novel Breeding Tools for Sweet Corn. Oral presentation. Corn Breeding Research Meeting and the International Sweet Corn Development Association Meeting, Chicago, IL. Block, A. (2019) Maize Volatiles That Guide the Behavior of the Insect Pest Fall Armyworm. Oral Presentation. Corn Breeding Research Meeting and the International Sweet Corn Development Association Meeting, Chicago, IL. How have the results been disseminated to communities of interest?We published 15 peer reviewed scientific papers, and submitted 4 additional papers. A total of 18 presentations were given at professional scientific conferences by Sweet CAP personnel. Finally, Dr. Mark Settles and Dr. Charles Sims were interviewed for an article in Food Technology magazine titled "The Sweet State of Corn" regarding the Sweet CAP project. What do you plan to do during the next reporting period to accomplish the goals?Objective 1 Bioinformatics on 697 whole genome sequences will be completed to score SNPs and other polymorphisms in all Sweet CAP diversity panel accessions. Sweet CAP diversity panel seed will be further increased to plant and collect agronomic phenotypic data. GWAS will be initiated for traits with sufficient data. Doubled haploid breeding programs will be initiated at both UF and UW in collaboration with ISU. High oil haploid inducer lines identified in 2020 will be inbred and evaluated on diverse donor lines. High oil haploid inducer families will be intercrossed to generate a synthetic population for further oil content selection. Haploid/hybrid kernel sorting using skNIR will be further developed. Objective 2 The Sweet CAP diversity panel will be screened for blight resistance to F. verticillioides, isolate Fus627. Evaluate steam treatments on Sweet CAP diversity panel seeds. Screen diverse corn lines for silk fly resistance in Belle Glade, FL. Complete GWAS on fall armyworm-induced volatiles. Objective 3 Complete a third cold emergence field trial at WSU. Complete growth chamber emergence phenotyping of the Sweet CAP Diversity Panel at UF. Develop transgene constructs for a late endosperm expressed Sh2 gene. Isolate weak alleles of sh2 using the adenine deaminase base editor transgenics. Complete field trials to test heat stable 6-phosphogluconate dehydrogenase for mitigation of heat stress yield losses in Florida Stay Sweet hybrid corn. Repeat heat stress field trial in Mendoza, Argentina to obtain phenotype data for tassel blasting. Objective 4 Sensory panels will hopefully resume in spring 2021 at UF and summer 2021 at UW. Our next window for planting trials is winter 2020/2021. Characterize physical properties of carbohydrates produced by yeast carrying maize starch synthesis enzymes. Complete field trials to test for phenotype relationships between mature kernel phenotypes and eating stage phenotypes. Analyze impact of post-harvest storage and cooking on flavor-associated volatiles. Objective 5 Publish extension documents on sweet corn history, nutrition, economics, and breeding technologies in the UF/IFAS electronic data information source (EDIS). Develop a Sweet CAP website. Continue to analyze the Nielsen retail data we recently obtained to answer the research topic "what caused the decline in consumption of sweet corn in recent years?" This project was initiated during the time of COVID restrictions while we wait to resume consumer experiments at UW-Madison. Present year 2 results to stakeholders at the ISCDA annual conference. Hold a virtual advisory group and stakeholder meeting in December 2020.

Impacts
What was accomplished under these goals? Objective 1 1.1Genomics. We sequenced and assembled a reference sweet corn inbred line, Ia453, with a mutated shrunken2 reference allele (Ia453-sh2). This genome revealed the complete structure of the sh2 allele. Comparisons to other maize genome data identified sequences under selection and candidate genes associated with sweet corn traits, such as early flowering, high sugar content and tassel size. Whole genome sequences for 697 sweet corn accessions in the Sweet CAP Diversity Panel were completed. Bioinformatic analysis is on-going with a preliminary evaluation identifying ~30 million SNPs. 1.2GWAS. This sub-objective is scheduled for years 3-4. We planted the diversity panel in two Florida environments and collected agronomic phenotypes as well as tissue samples in Citra, FL. Covid-19 impacted phenotype scoring in our Belle Glade, FL planting. 1.3Doubled Haploid Breeding. More than 180 experimental haploid inducers were evaluated at ISU. Inducer line BHI306 was sent to UW for initiation of a doubled haploid breeding program there. Twenty experimental haploid inducers were bulked at ISU, sent to UF, and evaluated for agronomic performance. Two promising high oil haploid inducer (HOHI) lines were isolated. Single-kernel NIR (skNIR) found that both lines contain over 10% kernel oil content and testcrosses to a Viking hybrid donor showed that both lines induced over 10% haploids. Haploid and hybrid kernels from test crosses from the HOHI lines were analyzed by skNIR, with a 2% relative oil content difference between hybrid and haploid kernels. Partial least squares linear discriminant analysis of the skNIR spectra can sort haploid kernels from hybrid with accuracy similar to human sorting. Haploid induction crosses were completed with a subset of the Sweet CAP diversity panel. Haploid kernels were selected and planted at ISU to score spontaneous haploid genome doubling frequencies in summer 2020. Objective 2 2.1 Seedling blights. Forty-seven sweet corn fields were surveyed in 2018 in the Columbia Basin of Washington. Pathogens from stunted plants were isolated with 23 species of Fusarium, Pythium, and Rhizoctonia identified. A subset of 50 isolates were screened for pathogenicity on sweet corn in growth chambers. The most pathogenic isolate of F. verticillioides, Fus627, was selected to screen a subset of the Sweet CAP diversity panel. We are comparing the growth chamber seedling assay to seedling leaf volatiles with three corn lines characterized by Anna Block at the USDA-ARS in Gainesville. We also initiated trials to examine the effects of steam treatments on sweet corn seed quality with Tom Stearns from High Mowing Seeds. We are evaluating for potential phytotoxicity of the treatments on seed quality using warm and cold germination assays completed every three months, and for efficacy of the treatments at eradicating seedborne fungal inoculum by completing seed health assays. 2.2 Silk fly resistance. We continue to test inbreds and populations of sweet corns for resistance/tolerance to silk fly in South Florida. We have tested most of UF's insect resistant germplasm but have not yet found a resistant line that also has consumer accepted silk and cob color. We have moved our search into field corn in hopes of finding an acceptably resistant line. 2.3 Plant Volatiles Influencing Insects. We collected and analyzed fall armyworm-induced volatiles from 347 diverse sweetcorn lines. We tested flooding impacts on insect resistance, herbivore induced volatiles, and other compounds in corn. 2.4. SCMV resistance. Eight replicates of 563 sweet corn accessions, a subset of which were sweet CAP panel inbreds, were tested for sugar cane mosaic virus (SCMV) resistance. We genotyped 92971 marker sites using Genotyping By Sequencing for 417 of the tested accessions. Population structure was observed and GWAS was conducted to identify loci related to resistance. The Scm1 loci was confirmed with GWAS through the presence of significant loci flanking the Scm1 gene. Objective 3 3.1 Early season cold tolerance. A second cold emergence field trial was completed by WSU to screen 580 Sweet CAP Diversity Panel lines in Spring of 2020. The trial was enabled with assistance from Doug Plaisted and Kevin Moe from Syngenta. We continued development of a machine vision assay (VIGOR) to score sweet corn seedling emergence in controlled conditions. The assay was evaluated by comparing results to hand scoring methods using a subset of the Sweet CAP diversity panel. Emergence assays are in progress to screen 583 lines from the diversity panel in an augmented incomplete random block design. 3.2 Engineer altered starch synthesis in sweet corn. We completed transcript profiling of late developmental stages of sweet corn endosperm to identify late expressed genes. Promoters from these genes will be used to develop late Sh2 expression transgenics. We transformed a dCas9-Adenine deaminase based editor to engineer new weak sh2 alleles. Eighty primary transformants are being evaluated for presence of the transgene and gene editing efficiency. 3.3 Heat tolerance. We introgressed a heat-stable 6-phosphogluconate dehydrogenase trait into Florida Stay Sweet parental inbred lines. Hybrid seed will be produced and evaluated for improved kernel set under heat stress in 2021. We screened 300 Sweet CAP diversity panel lines for tassel heat sensitivity in Mendoza, Argentina as part of a supplemental bulk up of the panel. Objective 4 4.1 Consumer panels. We completed a consumer panel taste test and economics experiment (objective 5), at the UW-Madison Sensory Analysis Laboratory in Sept. 2019. Sweet corn was planted for UF consumer panels at Stewart Stein Farms in Belle Glade, FL, but Covid-19 restrictions stopped further human subject research for 2020. 4.2 Synthetic biology starch model system. We obtained a yeast strain that synthesizes starch using Arabidopsis enzymes. Maize branching and debranching enzymes, starch synthases, and isoamylases were used to replace the Arabidopsis enzymes. The maize synthetic pathway produces carbohydrate polymers, which are now being characterized for physical properties relative to maize starch. 4.3 Mature kernel phenotypes. We developed Partial Least Squares (PLS) regression models to predict pericarp thickness, total sugars, and starch in mature sweet corn kernels. Analytical data was from a panel of 100 Sweet CAP diversity panel accessions consisting of equal parts su1 and sh2 genotypes. Pericarp thickness was measured with a pressure micrometer and carbohydrates were quantified with enzymatic assays. We collected skNIR data for 585 Sweet CAP diversity panel lines and predicted these traits using the models. Objective 5 5.1 Experimental Auctions. We completed economic analysis of consumers' willingness to pay using consumer panel data from year 1 experiments at UF and the year 2 panel at UW. 5.2 Stakeholder outreach. In 2019, Co-PI Dr. Marcio Resende chaired and organized the International Sweet Corn Developers Association (ISCDA) meeting which was held joint with the Corn Breeding Research group. Five Sweet CAP graduate students and four investigators gave talks on Sweet CAP objectives. One Sweet CAP graduate student won the best student presentation award. We held a stakeholder and advisory group meeting at the end of the conference with five companies and one outside sweet corn academic program represented.

Publications

  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Andorf, C., Beavis, W.D., Hufford, M., Smith, S., Suza, W., Wang, K., Woodhouse, M., Yu, J., L�bberstedt, T. (2019) Technological advances in maize breeding: Past, present and future. Theoretical and Applied Genetics. 132: 817-849.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Yang, J., Qu, Y., Chen, Q., Tang, J., Lubberstedt, T., Li, H., and Liu, Z. (2019) Genetic dissection of haploid male fertility in maize (Zea mays L.). Plant Breeding. 138: 259-265 https://doi.org/10.1111/pbr.12688
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Vanous, K., Jubery, T.Z., Frei, U.K., Ganapathysubramanian, B., and Lubberstedt, T. (2019). Utilization of reduced haploid vigor for phenomic discrimination of haploid and diploid maize seedlings. The Plant Phenotype Journal. 2:1. doi: 10.2135/tppj2018.10.0008
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Ren, J., Boerman, N.A., Liu, R., Wu, P., Trampe, B., Vanous, K., Frei, U.K., Chen, S., and Lubberstedt, T. (2020). Mapping of QTL and identification of candidate genes conferring spontaneous haploid genome doubling in maize (Zea mays L.). Plant Science. 293:110337 https://doi.org/10.1016/j.plantsci.2019.110337
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Boerman, N.A., Frei, U.K., L�bberstedt, T. (2020) Impact of Spontaneous Haploid Genome Doubling in Maize Breeding. Plants. 9:369. doi: 10.3390/plants9030369
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Trentin, H.U., Frei, U.K., L�bberstedt, T. (2020) Breeding Maize Maternal Haploid Inducers. Plants. 9: 614. doi:10.3390/plants9050614
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: De la Fuente, G., Frei, U.K., Trampe, B., Ren, J., Bohn, M.O., Yana, N., Verzegnazzi, A., Murray, S.C., L�bberstedt, T. (2019) A diallel analysis of a maize donor population response to in vivo maternal haploid induction. II: Haploid Male Fertility. Crop Science. doi: 10.1002/csc2.20021
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Qu, Y., Wu, P., Ren, J., Liu, Z., Tang, J., L�bberstedt, T., Chen, S., Li, H. (2020) Mapping of QTL for kernel abortion caused by in vivo haploid induction in maize (Zea mays L.). PloS One. 15: e0228411
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Costa Almeida, V., Trentin, H.U., Frei, U.K., L�bberstedt, T. (2020) Genomic prediction of maternal haploid induction rate in maize. The Plant Genome. doi: 10.1002/tpg2.20014
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Trampe, B., Goncalves, I., Frei, U.K., Ren, J., Chen, S., L�bberstedt, T. (2020) QTL mapping of Spontaneous Haploid Genome Doubling using genotyping-by-sequencing in maize (Zea mays L.). Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-020-03585-1
  • Type: Journal Articles Status: Submitted Year Published: 2020 Citation: Trentin, H.U., Costa Almeida, V., Rotarenco, V., Frei, U.K., L�bberstedt, T. (2020) A genome-wide association study to identify genes affecting the haploid induction rate of maize maternal haploid inducers adapted to Midwest U.S. (Submitted)
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Block, A K., Hunter, CT., Sattler, SE., Rering, C., McDonald, S., Basset, GJ. and Christensen, SA. (2019) Fighting on Two Fronts: Elevated Insect Resistance in Flooded Maize. Plant Cell and Environment doi: 10.1111/pce.13642.
  • Type: Journal Articles Status: Submitted Year Published: 2020 Citation: Ribeiro, C., Hennen-Bierwagen, T.A., Myers, A.M., Cline, K., Settles, A. M. (2020) Engineering 6-phosphogluconate dehydrogenase to improve heat tolerance in maize seed development. BioRxiv, pre-print. (https://doi.org/10.1101/2020.05.21.108985)
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Hacisalihoglu G., Freeman J., Armstrong P.R., Seabourn B.W., Porter L.D., Settles A.M., Gustin J.L. (2020) Protein, weight, and oil determination by single-seed near-infrared spectroscopy for selection of seed quality and yield traits in pea (Pisum sativum). J. Science Food Agriculture. (https://doi.org/10.1002/jsfa.10389)
  • Type: Journal Articles Status: Submitted Year Published: 2020 Citation: Hacisalihoglu, G., Beisel, N.S., and Settles, A.M. 2020. (2020) Characterization of pea seed mineral nutritional value within a diverse collection of pea (Pisum sativum) genotypes. Scientific Reports. (Submitted).
  • Type: Book Chapters Status: Published Year Published: 2020 Citation: Settles A.M. (2020) EMS mutagenesis of maize pollen. Methods in Molecular Biology. 2122:25-33. (https://doi/10.1007/978-1-0716-0342-0_3).
  • Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Gustin J, Frei UK, Baier J, Armstrong P, L�bberstedt T, Settles AM. (2020) Maize (Zea mays subsp. mays) Haploid Classification using Single Kernel Near-Infrared Spectroscopy. Plant Breeding. (Accepted).
  • Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Gillmor C.S., Settles A.M., Lukowitz W. (2020) Genetic screens to target embryo and endosperm pathways in Arabidopsis and maize. Methods in Molecular Biology. 2122:3-14. (https://doi/10.1007/978-1-0716-0342-0_1).
  • Type: Journal Articles Status: Other Year Published: 2020 Citation: Hislop, L., Stephanie, E., Flannery, P., Gore, M.A., and Tracy, W.F. (2020) Sugarcane Mosaic Virus Resistance in the Wisconsin Sweet Maize Diversity Panel. The Plant Genome. (In prep).
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Liu, R., Boehlein S.K., Tracy W.F., RESENDE M.F.R., Hudalla G.A. (2020) Characterizing the Physical Properties and Cell Compatibility of Phytoglycogen Extracted from Different Sweet Corn Varieties. Molecules. 25(3): 637
  • Type: Journal Articles Status: Under Review Year Published: 2020 Citation: Y Hu, Colantonio V., K Leach, M Baseggio, Muller B., Finegan C., K Swarts, M Gore, Settles, M., WF. Tracy, RESENDE M. F. R.. (2020) Chromosome-scale genome assembly and population genomic analysis provides insights into origin and evolution of modern sweet corn. Nature Communications. (Under review).


Progress 09/01/18 to 08/31/19

Outputs
Target Audience:Target audiences: The major goal of the Sweet Corn CAP is to identify genetic resources, high-value traits, and breeding tools needed for long-term sustainability of the sweet corn agricultural system. Our primary target audience are stakeholders in the production and distribution of sweet corn. Our stakeholders include members of sweet corn breeding programs in seed companies, processors who decide on hybrids for contracts with growers, and sweet corn growers. We engaged with these groups in the first year of the project. Sweet CAP organized a special session at the International Sweet Corn Developers Association (ISCDA) conference on November 26-27, 2018. We invited our stakeholder advisory board with representatives from Bayer, Syngenta, Crookham, National Frozen Foods, and Sunshine Sweet Corn Farmers of Florida. The ISCDA was held in conjunction with the Midwest Food Processors Association (MWFPA) Annual Convention and we interacted with sweet corn growers, processors, and breeders at this conference. Efforts: At the end of the ISCDA conference, we held an open forum with approximately 20 seed company representatives. The primary focus of discussion was on our proposed consumer taste panels. Industry representatives made a very convincing argument that their primary goals for long-term improvement of sweet corn is focus on the fresh market. This is the only sector of sweet corn that has shown any improvement in consumption and our stakeholders are most interested in the high-value traits for consumers in this market. At the MWFPA Convention, we presented an overview talk to the Processing Crops Conference with an audience of 100-150 attendees. Drs. Tracy and Mitchell conducted one-on-one interactions with stakeholders throughout this conference. U. of Florida, Washington State U., and U. of Wisconsin had direct interactions with seed company breeders during the project. At Florida and Wisconsin, these interactions are primarily to test University X Company hybrids. At Washington, we completed a cold stress field emergence trial with a commercial grower and seed industry field representative. Changes/Problems:We had a significant delay in identifying and appointing a Project Manager. University of Florida policies regarding hiring relatives on the same grant were reinterpreted by the Provost's office in 2018. This required two searches to identify a qualified candidate for the position. The extended search delayed efforts in project website development and drafting extension publications at the University of Florida. We now have a qualified candidate and are negotiating an offer of employment. What opportunities for training and professional development has the project provided?Six graduate students and three post-docs were recruited for training on Sweet CAP. Each of the participating institutions have at least one trainee. The students who were appointed in fall 2018 attended the ISCDA conference and participated in the stakeholder forum. One postdoc presented a 30 minute talk on the sweet corn genome at the ISCDA conference. A subset of the trainees attended the 61st Annual Maize Genetics Conference. One post-doc and one graduate student presented posters on their sweet corn research at this conference. The trainees are also attending our monthly project meetings and presenting their data at these meetings. We devoted part of one meeting to discussing annual reporting to provide insight for the trainees about project management. The graduate students are participating in professional development in their respective programs, which includes developing dissertation and thesis proposals as well as presenting research at graduate student seminars and local meetings. How have the results been disseminated to communities of interest?We organized a special session at the ISCDA conference and presented seven talks to sweet corn stakeholders. We also presented research results on our Columbia Basin seedling pathogen survey at the Pacific Northwest Vegetable Association Annual Convention & Trade Show. What do you plan to do during the next reporting period to accomplish the goals?Objective 1 Finish assembly and annotation of the Ia453-sh2 genome Whole genome sequencing of the Sweet CAP Diversity Panel accessions First round of in-field phenotyping of the Diversity Panel Evaluate ISU inducers in south Florida growing conditions Continue breeding high-oil inducers lines Collect single-kernel NIR data from haploid and hybrid kernels using sweet corn donor lines Evaluate induction frequencies of sweet corn inducer lines. Objective 2 Begin evaluating sweet corn diversity panel for resistance to Pythium, Rhizoctonia, and Fusarium in growth chamber assays. Develop mapping populations for silk fly resistance Begin profiling diversity panel for insect-induced volatiles. Objective 3 Begin growth chamber assays for cold emergence of the diversity panel Complete a second field emergence trial in the Columbia Basin Complete sweet corn endosperm RNA-seq to identify late-expressed promoters Objective 4 Continue consumer panels for hybrid fresh market corn. Introgress wx1, du1, sh1 into su1 sweet corn inbreds. Begin replacing Arabidopsis starch synthesis genes with maize genes in the yeast synthetic starch strain. Develop single-kernel NIR models for mature sweet corn kernel traits. Collect NIR data from diversity panel kernels. Objective 5 Refine economic assessment questions and auction set-up for consumer panels Collect data for partial budget analysis of sweet corn agricultural system. Organize Sweet CAP session and Stakeholder forum at the 2019 ISCDA conference Develop a Sweet CAP website Publish extension documents on sweet corn nutrition, economics, and breeding technologies in the UF/IFAS electronic data information source (EDIS). Present sweet corn talks at the MWFPA, PNVA, and other regional stakeholder meetings.

Impacts
What was accomplished under these goals? Objective 1: genomics, germplasm diversity resources, and doubled haploid breeding. 1.1: Genomics. We made significant progress on the Ia453-sh2 reference genome sequence. Long read sequencing combined with a Dovetail HiRise assembly resulted in 56x coverage of and genome length of 2,234.9 Mb. Annotation used the Maker-P pipeline using Pacbio Iso-seq transcriptomes from leaf, stem, silk, husk, ear, and pollen tissues as well as short read endosperm mRNA-seq. The current annotation has a working gene set of 47,698 genes. BUSCO analysis of single-copy orthologs suggests the Ia453-sh2 assembly has a similar quality to the B73_v4 genome assembly, which is higher quality than recently published W22 and Mo17 genomes. To further improve assembly, we contracted with Corteva to complete Bionano optical mapping of the genome. Physical maps that are readily assigned to B73_v4 chromosomes cover 92.2% of the assembled sequence. Corteva is currently integrating the physical map with the DoveTail assembly. We made progress in developing the Sweet CAP Diversity Panel. Collaborations between the Florida and Wisconsin breeding programs identified a panel of 693 inbred lines and landraces that are selected to be genetically diverse. For example, 55 inbred lines from the current Florida breeding program and 17 lines are included from the historic Hawaiian breeding program. We also included a significant number of tropical and South American temperate lines. The diversity panel was planted this spring in south and central Florida and is being planted in Wisconsin for a first evaluation of the lines. We will narrow the panel based on lines that have such poor adaptation that they cannot be phenotyped in multiple locations. 1.2 GWAS. This sub-objective is scheduled for years 3-4. 1.3 Doubled haploid breeding technology. Material Transfer Agreements are in place for Iowa State University (ISU) inducers to tested southern Florida field trials for fall season of 2019. For high-oil inducers, Iowa State University crossed their BHI inducer to Illinois High Oil (IHO) inbred lines. BC1 and F2 kernels were selected for the kernel color marker and high oil content. BC1S1 and F2xIHO crosses were made in the 2019 winter nursery and new selections for high oil were completed at Florida. These selected kernels were planted in the Iowa summer nursery. ISU has also planted a screen for spontaneous haploid genome doubling (SHGD). A panel of ~300 sweet corn lines are being crossed by haploid inducers to generate haploid kernels. These will be selected and screened for spontaneous fertility in 2020. Objective 2: insect and disease resistance. 2.1 Seedling blights. In 2018, Washington State University (WSU) surveyed 47 commercial sweet corn fields in the Columbia Basin and isolated over 20 species of Pythium, Rhizoctonia, and Fusarium from stunted plants. Nearly 2/3 of the Pythium isolates were resistant to the fungicide mefenoxam illustrating a need for alternative fungicides to control seedling blights. WSU is screening the pathogens for highly virulent isolates of each genus on the Supersweet Jubilee Plus hybrid. 2.2 Silkfly resistance. The Florida breeding program is currently evaluating the M5 inbred line and generating new inbred lines from a Zapalote Chico sh2 (ZC-sh2) population. Trials with no insect control show silk fly resistance with both M5 and ZC-sh2 hybrids. Crosses were completed with sensitive inbred lines indicating that the silkfly resistance is a dominant or additive trait. The ZC-sh2 hybrids have significantly more resistance but excess color in the cob and silks. 2.3 Plant volatiles influencing insects. A seedling volatile collection assay was developed at the USDA-ARS to assess volatiles induced by fall armyworm. The assay collects volatiles from whole plants over an 18 h period for GC-MS analysis. Initial work with B73 field corn and P39 su1 sweet corn showed 11 major volatile differences indicating large variation in plant responses to insect herbivory. Additional assays for fall armyworm feeding choices between pairs of leaf samples and ability of plants to attract parasitic wasps have been developed. Objective 3: early season cold tolerance 3.1 Screen for seedling emergence after cold stress. The stakeholder advisory committee recommended that these assays be completed with an industry standard seed treatment. We are currently testing cold stress conditions with a few sweet corn lines to establish a standard stress condition for treated seed. WSU has a cold emergence field trial with 210 diversity panel lines. Seeds were treated with the Syngenta PHW Blend 127 and a commercial hybrid was planted throughout the trial as a check. 3.2 Engineer altered starch synthesis in sweet corn. RT-PCR validation experiments for the four candidate "late endosperm" genes from the Chen et al. (2014) endosperm transcriptome were not expressed. We found expression in mature kernels after imbibition suggesting late endosperm samples from the published study were imbibed to aid endosperm dissection prior to RNA extraction. We are currently sampling developing endosperm from Ia453-sh2 for mRNA-seq experiments to identify late expressed endosperm genes. Objective 4 seeks to improve sweet corn eating quality based on consumer preferences. 4.1 Consumer panels. We completed two consumer panels in spring 2019. This required integration of our south Florida field site with five lab groups at Florida, USDA-ARS, and Wisconsin. Five hybrids were grown for each panel, harvested, and cold-stored for 3-5 days before the panel. Samples from each variety were tested for sugars, starch, moisture, pericarp thickness, and volatiles after cooking. Results showed that sweet corn had much higher overall liking scores than typical fruits and vegetables. 4.2 Synthetic biology starch model system. We obtained the Saccharomyces cerevisiae strain that synthesizes starch using Arabidopsis enzymes (Pfister et al. 2016 eLife 5:e15552). The strain has all endogenous yeast glycogen synthesis enzymes removed and contains AGPase from E. coli. Branching enzymes, starch synthases, and isoamylases are from Arabidopsis. We are replacing these enzymes with maize genes. As a first step, we are mapping the N-termini of amyloplast localized starch synthesis enzymes from maize B73 endosperm. 4.3 Mature kernel phenotypes. Single kernel NIR calibration sets were assembled using 99 sweet corn genotypes from the Sweet CAP Diversity Panel. The calibration set consists of 54 su1 types and 45 sh2 types. Single-kernel NIR data have been collected, and we are the process of collecting analytical data: pericarp thickness, soluble sugars, phytoglycogen, and starch content. Objective 5 economic assessment and outreach. 5.1 Experimental auctions. Economic assessment questions in the consumer panels in the first panel revealed that consumers were not aware of retail prices for fresh market sweet corn. Updated questions for the second panel included background information and yielded data in-line with current prices. The second panel showed a significant increase in willingness to pay for the top two hybrids tasted as these hybrids were the only ones bought in the consumer auction. 5.2 Stakeholder outreach. See target audience narrative.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Boehlein SK, Shaw JR, Hannah LC. (2018) Enhancement of Heat Stability and Kinetic Parameters of the Maize Endosperm ADP-Glucose Pyrophosphorylase by Mutagenesis of Amino Acids in the Small Subunit With High B Factors. Front Plant Sci. 9:1849. doi:10.3389/fpls.2018.01849
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Block AK, Vaughan MM, Schmelz EA, Christensen SA. (2019) Biosynthesis and function of terpenoid defense compounds in maize (Zea mays). Planta. 249(1):21-30. doi: 10.1007/s00425-018-2999-2
  • Type: Book Chapters Status: Accepted Year Published: 2019 Citation: Gillmor, C.S., Settles, A.M., Lukowitz, W. (2019) Genetic screens to target embryo and endosperm pathways in Arabidopsis and maize. Embryogenesis (M. Bayer, ed.), Methods in Molecular Biology. In press.
  • Type: Book Chapters Status: Accepted Year Published: 2019 Citation: Settles, A.M. (2019) EMS mutagenesis of maize pollen. Embryogenesis (M. Bayer, ed.), Methods in Molecular Biology, In press.
  • Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Zhang J., Wu S., Boehlein S.K., McCarty D.R., Myers A., Settles A.M. (2019) Maize defective kernel5 is a bacterial TamB homolog required for chloroplast envelope biogenesis. Journal of Cell Biology, Accepted pending minor revision.
  • Type: Journal Articles Status: Submitted Year Published: 2019 Citation: Gustin, J.L., Frei, U.K., Baier, J., Armstrong, P., L�bberstedt, T., Settles A.M. (2019) Maize Haploid Classification using Single Kernel Near-Infrared Spectroscopy. Applied Spectroscopy. Submitted.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Moore, V.A., Tracy, W.F. (2019) Recurrent Full-sib Family Selection for Husk Extension in Sweet Corn. Journal of the American Society for Horticultural Science. 144(1):63-69. https://doi.org/10.21273/JASHS04559-18
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: du Toit, L., Solemslie, R. (2018) Early Season Diseases and Pests of Sweet Corn in the Columbia Basin. Pacific Northwest Vegetable Association Annual Convention & Trade Show. November 14-15. Kennewick, WA
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Block, A. (2018) The impact of environmental conditions on the resistance of sweetcorn to insect pests and pathogens. International Sweet Corn Development Association Conference. November 26-27. Wisconsin Dells, WI
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Settles, A.M. (2018) Introduction to Sweet CAP. International Sweet Corn Development Association Conference. November 26-27. Wisconsin Dells, WI
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Gustin, J.L. (2018) Sweet CAP tools for seed phenotyping. International Sweet Corn Development Association Conference. November 26-27. Wisconsin Dells, WI
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Hu, Y. (2018) Efforts on sequencing the sweet corn genome. International Sweet Corn Development Association Conference. November 26-27. Wisconsin Dells, WI
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Frei, U., Boerman, N. (2018) Progress in DH technology. International Sweet Corn Development Association Conference. November 26-27. Wisconsin Dells, WI
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: du Toit, L. (2018) Early season diseases and pests of sweet corn in the Columbia Basin. International Sweet Corn Development Association Conference. November 26-27. Wisconsin Dells, WI
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Mitchell, P. (2018) Sweet corn economics: a Wisconsin update. International Sweet Corn Development Association Conference. November 26-27. Wisconsin Dells, WI
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Finegan, C., Leach, K., Boehlein, S., Resende, M. Insights into the regulation of starch biosynthesis in sweet corn endosperms. 61st Annual Maize Genetics Conference. March 14-17, St. Louis, MO
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Hu, Y., Leach, K., Baseggio, M., Swarts, K., Gore, M., Tracy, W.F., Resende, M. (2019) The whole genome assembly and population genetics of sweet corn. 61st Annual Maize Genetics Conference. March 14-17, St. Louis, MO
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Settles, A.M. (2018) Sweet CAP: Integrated technologies to improve sweet corn production and marketability. MWFPA Processing Crops Conference. November 27-29, 2018. Wisconsin Dells, WI.
  • Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Settles, A.M. (2018) Sweet CAP: Integrated technologies to improve sweet corn production and marketability. 1st Huazhong Agricultural University-University of Florida Bi-institutional Horticulture Symposium. December 8, 2018. Wuhan, China
  • Type: Other Status: Other Year Published: 2018 Citation: Settles, A.M. (2018) Sweet CAP: Integrated technologies to improve sweet corn production and marketability. Seminar at Henan Agricultural University. December 11, 2018. Zhengzhou, China