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
Settles, A. 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 09/01/18 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