CULTIVAR DEVELOPMENT: MULTI-INSTITUTIONAL DEVELOPMENT OF ELITE SWEET CORN HYBRIDS FOR THE CONVENTIONAL AND ORGANIC MARKET

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: AFRI COMPETITIVE GRANT
• Reporting Frequency: Annual
• Accession No.: 1022346
• Grant No.: 2020-67013-30903
• Cumulative Award Amt.: $300,000.00
• Proposal No.: 2019-05410
• Project Start Date: Apr 15, 2020
• Project End Date: Apr 14, 2024
• Grant Year: 2020
• Program Code: [A1141]- Plant Health and Production and Plant Products: Plant Breeding for Agricultural Production

Recipient Organization
UNIVERSITY OF FLORIDA
G022 MCCARTY HALL
GAINESVILLE,FL 32611

Performing Department
(N/A)

Non Technical Summary
Sweet corn is one of the most popular vegetables in the U.S. This specialty crop has total production value of ~$1 billion/year. While this number is similar to other vegetables such as onions, and carrots, it is significantly smaller than conventional field corn, which belongs to the same species and is valued at ~$50 billion/year. This relatively low market value for sweet corn has resulted in comparatively little investment by private companies in the development of state-of-the art breeding resources. Hence, there is an opportunity for public breeding programs to contribute in supplying elite varieties.University of Florida (UF) and University of Wisconsin (UW) have the two major public sweet corn breeding programs in the country, and a long history of cultivar development. Current efforts target inbred development due to the challenge to maintain a public breeding program large enough to breed two complementary inbreds needed to produce an elite hybrid. Here, we propose to join efforts, combine these proven elite inbreds and put forward a multi-institution breeding program to develop hybrids for fresh market. We propose to create a total of 400 UFxUW hybrids created from elite lines from each program. The hybrids will be tested in several environments for multiple years, aiming at the release of varieties for conventional and organic systems (Aim 1). A secondary component of the proposal also includes the development of novel inbred lines (Aim 2) and the establishment of genomic selection models (Aim 3) for future variety selection.

Animal Health Component

90%

Research Effort Categories

Basic

10%

Applied

90%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1480	1081	100%

Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1480 - Sweetcorn;

Field Of Science
1081 - Breeding;

Keywords

plant breeding

cultivar development

genomic selection

hybrid breeding

sweet corn

Goals / Objectives
The long-term goal of this project is to contribute to U.S. agriculture through the development of elite sweet corn germplasm. With thisgoalin mind, we propose to join forces and put forward a multi-institution hybrid breeding program for sweet corn cultivar development. To accomplish this goal, we propose to:AIM 1: Development and multi-environment evaluation of sweet corn hybrids: We will create a total of 400 hybrids by crossing elite inbreds from University of Florida with elite inbreds from University of Wisconsin. The crosses will be tested in key locations and selected for several traits of interest. A subset of these hybrids will then be tested in more locations. We expect to identify superior hybrids that can be released for conventional and organic systems.AIM 2: Double haploid production for selected hybrids: To support the continuous nature of a breeding program and increase the genetic gains in each public breeding program, the elite hybrids selected across multiple locations will be subjected to double haploid production and resulting inbreds will be tested for performance in key environments.AIM 3: Calibration of genomic selection models for hybrid prediction: We will leverage genomic resources available on the inbred lines and phenotypic resources generated in this project to create genomic selection models that predict hybrid performance. We expect that an accurate and validated model will accelerate the development of new inbreds and hybrids and support the sustainability of both programs.

Project Methods
At the core of this project, we will create a population using a North CarolinaII design to cross 20 top inbred lines from University of Wisconsin with 20 elite inbred lines from University of Florida.For the measured traits, we will estimate single-site and multi-site Best Linear Unbiased Predictions (BLUPs) of additive and non-additive effects for each hybrid in each trait using pedigree-derived variance covariance matrices. We will also estimate general combining ability of all the inbred parents and specific combining ability of each cross. We will generate a ranking for each trait as well as a ranking from a joint heritability-based selection index. Altogether, this information will be used to select the superior hybrids, which will be evaluated in more locations the following year. In addition to a conventional section program, we will also develop genomic selection models and evaluate their predictive ability and potential for future use to accelerate the breeding program.

Progress 04/15/20 to 04/14/24

Outputs
Target Audience:The primary target audiences for this project are sweet corn producers in the United States. Our results will be communicated to growers, extension agents, researchers, and to the general public through different channels, including peer reviewed publications, press releases, extension documents and social media. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?One graduate students, Two undergraduate students and one post-doc were trained in the reporting period for this project. Training included establishing the experiments, pollinating, phenotyping, analyzing data, simulating breeding programs and calibrating genomic selection models. How have the results been disseminated to communities of interest?The results have been presented in scientific conferences andpeer review publication. The results were disseminated in the International Conference of Quantitative Genetics (2024), National Association of Plant Breeders meeting (NAPB, 2023), and International Sweet Corn Development Association (ISCDA, 2023). Finally, the test-cross hybrids were showcased in the field to different sweet corn companies that collaborate with the UF and UW breeding programs. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? We have previoulsy reported the outcomes of the project and completion of aim 1. In this last term, we have completed aim 3, including the calibration of genomic selection models for the population and published the manuscripts. In 2023, testcross hybrids that were produced from the double haploid inbreds showed very good promise in multi-year, multi-environment evaluations. They will be evaluated again in 2024 in Florida and Wisconsin.

Publications

• Type: Journal Articles Status: Published Year Published: 2024 Citation: Peixoto, M. A., Coelho, I. F., Leach, K. A., Bhering, L. L., & Resende, M. F. R. (2024). Simulation-based decision-making and implementation of tools in hybrid crop breeding pipelines. Crop Science, 64, 110125.
• Type: Journal Articles Status: Submitted Year Published: 2024 Citation: Peixoto, Rodrigo Rampazo Amadeu, Leonardo Lopes Bhering, Lu�s Felipe V. Ferr�o, Patr�cio R. Munoz, M�rcio F. R. Resende Jr. SimpleMating: R-package for Prediction and Optimization of Breeding Crosses Using Genomic Selection bioRxiv 2024.05.24.595600
• Type: Journal Articles Status: Published Year Published: 2024 Citation: Peixoto MA, Leach KA, Jarquin D, Flannery P, Zystro J, Tracy WF, Bhering L and Resende MFR (2024) Utilizing genomic prediction to boost hybrid performance in a sweet corn breeding program. Front. Plant Sci. 15:1293307. doi: 10.3389/fpls.2024.1293307
• Type: Journal Articles Status: Published Year Published: 2024 Citation: Peixoto, Igor Ferreira Coelho, Kristen A Leach, Thomas L�bberstedt, Leonardo Lopes Bhering, M�rcio F R Resende, Use of simulation to optimize a sweet corn breeding program: implementing genomic selection and doubled haploid technology, G3 Genes|Genomes|Genetics, Volume 14, Issue 8, August 2024
• Type: Journal Articles Status: Submitted Year Published: 2024 Citation: Graciano R. et al. Exploring the Application of Phenomic Selection using Single-kernel Near-Infrared Spectroscopy in Corn Breeding. Submitted

Progress 04/15/22 to 04/14/23

Outputs
Target Audience:The primary target audiences for this project are sweet corn producers in the United States. Our results will be communicated to growers, extension agents, researchers, and to the general public through different channels, including peer reviewed publications, press releases, extension documents and social media. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Three graduate students, three undergraduate students and one post-doc were trained in the reporting period for this project. Training included establishing the experiments, pollinating, phenotyping, analyzing data, simulating breeding programs and calibrating genomic selection models. How have the results been disseminated to communities of interest?The results have been presented in scientific conferences and are currently being prepared for peer review publication. One student presentation about phenomic selection was awarded best M.Sc poster at the National Association of Plant Breeders (NAPB) and one oral presentation about mate-pair allocation was awarded the best talk at the Corn Breeders Meeting.The results were also presented in the Sunshine Growers Association, which includes a large group of Florida sweet corn growers. Finally, the test-cross hybrids were showcasedin the field to different sweet corn companies that collaborate with the UF and UW breeding programs. What do you plan to do during the next reporting period to accomplish the goals?The next reporting period is the final one for the project. We plan to finalize the publications and disseminate results generated in this project. Moreover, we will evaluate the TC hybrids one more year and plan to make a decision regarding variety release.

Impacts
What was accomplished under these goals? Aim 1 - This aim was completed. The hybrids generated in this aim were used to calibrate genomic selection models. The multi-institution collaboration initiated in this project continues and new crosses between UF and UW inbreds were created in 2022. Aim 2 - We have evaluated test-cross (TC) hybrids utilizing double haploids produced in this aim crossed with commercial testers. The TC hybrids showed excellent performance in the first year of evaluation, surpassing commercial checks. They will be further evaluated in different environments and in the following years. Aim 3 - Three different manuscripts are now submitted reporting the potential to use genomic selection as a tool for sweet corn breeding. A software to use genomic data to predict the best crosses (mate-pair allocation) was developed. We expect to have all of these results published prior to the completion of the project. We have also evaluated the use of single-kernel NIR to predict related double haploid inbreds (Phenomic selection). The results indicate prediction accuracies that are, for some traits, similar to what can be accomplished via genomic selection.

Publications

• Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Graciano et al. Phenomic Selection Using Single Kernel NIRS for Predicting Complex Field Traits in Sweet Corn. NAPB, 2023.
• Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Graciano et al. Exploring the Potential of Near-Infrared Spectroscopy for Predicting Complex Field Traits in Sweet Corn. ASHS, 2023
• Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Amorim et al. Implementation of genomic selection in hybrid sweet corn breeding programs targeting long-term genetic gains. NAPB, 2023
• Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Amorim et al. An R-package for crossing optimization in breeding programs. Oral Presentation, Corn Breeders Meeting, 2023

Progress 04/15/21 to 04/14/22

Outputs
Target Audience:The primary target audiences for this project are sweet corn producers in the United States. Our results will be communicated to growers, extension agents, researchers, and to the general public through different channels, including peer reviewed publications, press releases, extension documents and social media. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Two undergraduate and five graduate students were trained in the scope of this project. Training included establishing the experiments, pollinating, phenotyping, analyzing data, simulating breeding programs and calibrating genomic selection models. How have the results been disseminated to communities of interest?The results have been presented in scientific conferences and are currently being prepared for peer review publication. The results were also presented in the Sunshine Growers Association, which includes a large groupof Florida sweet corn growers. What do you plan to do during the next reporting period to accomplish the goals?In the next reporting period, we expect to evaluate the eight hybrid selections. Decisions about variety release will be made. Furthermore, the new set of UFxUW crosses will continue to be evaluated and so will the DH inbreds generated in 2022. We also expect to publish genomic selection (GS) models and recommendations about the use of GS and DH in the breeding program.

Impacts
What was accomplished under these goals? Aim 1 - Based on BLUP evaluations from 2020, a set of 34 hybrids were selected for further evaluations. They were planted in Florida, Wisconsin and California (under organic conditions). The experiments were evaluated and hybrids were scored for plant traits, ear traits, disease resistance and flavor. Single and multi-environment BLUPs were calculated and compared to commercial checks. Based on the results, a set of 8 hybrids were selected for third year evaluation. The results indicate good adaptation and yield performance, but also a need for improved ear quality. A new group of crosses between UF and UW inbreds was generated to address these issues. Aim 2 - The double haploids produced in 2020 were planted in Idaho for inbred evaluation. They were also used to create test-cross hybrids again commercial hybrids. Inbred and hybrid performance data will be obtained in 2022. In addition to the evaluation of newly generated DH lines, a new request for DHs was submitted to Iowa State University to capture the variability between the newly established crosses reported on aim 1. The results will be evaluated in 2023. Aim 3 - Previously calibrated genomic selection models were expanded to include multi-trait models. Prediction accuracies improved. The results were presented in two different conferences by graduate students trained in the scope of this project. Furthermore, a breeding simulation software, AlphaSim (Fauxet al.2016), was used to simulate different aspects of public sweet corn breeding programs. The work evaluated the benefit of using genomic selection and double haploid breeding. Two manuscripts are currently being written to summarize and present the results.

Publications

• Type: Journal Articles Status: Accepted Year Published: 2022 Citation: Gonzalez et al. EARCV: AN OPEN-SOURCE, COMPUTER VISION PACKAGE FOR MAIZE EAR PHENOTYPING. The Plant Phenome Journal, 2022
• Type: Journal Articles Status: Published Year Published: 2022 Citation: Marinho et al. GENOMIC SELECTION AS A TOOL FOR MAIZE CULTIVARS DEVELOPMENT. Brazilian Journal for Maize and Sorghum. https://doi.org/10.18512/rbms2022v21e1285. 2022
• Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Coelho et al. Optimizing the use of genomic selection and double haploid techonology in a sweet corn breeding program. Plant and Animal Genome International Conference. 2022.
• Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Coelho et al. Implementing double haploid technology and genomic selection into a sweet corn breeding pipeline. Maize Meeting 2022.
• Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Gonzalez et al. Computer vision for high-throughput quantitative genetics for disease resistance in sweet corn. Maize Meeting 2022.
• Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: De Amorim et al. Optimization of vegetable breeding program: a simulation study with sweet corn. Plant and Animal Genome International Conference. 2022.

Progress 04/15/20 to 04/14/21

Outputs
Target Audience: 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:Covid has limited our ability to hire and train undergraduate students. This problem has now been resolved and the training will resume on Year 2.The 2nd year evaluation of our hybrid selections in the state of New York was not possible due to Covid restrictions. These hybrids will be tested in this environment in the summer season of 2022 What opportunities for training and professional development has the project provided?Opportunities for professional development were limited due to Covid restrictions that hindered the hire and training of undergraduate students. Three graduate students from University of Florida were involved in the phenotyping and selection of the superior hybrids, as well as in the calibration of genomic selection models. How have the results been disseminated to communities of interest?A total of 3 presentations were given at professional scientific conferences by the project investigators. PI Resende has also presented the preliminary results of the project to theSunshine Sweet Corn Farmers of Florida, a sweet corn association in South Florida. What do you plan to do during the next reporting period to accomplish the goals?Experiment 1.3 - Second year evaluation of the selected 34 F1 hybrids in Florida, Wisconsin and California. Selected hybrids will be phenotyped, evaluated and selected in three environments for the second year. Experiment 2.1 - Double haploid production and evaluation to accelerate inbred development - The haploids that are currently being produced will be evaluated and used as parents to guide future crosses Experiment 3.1 - Inclusion of dominance effect and multi-site genomic selection model calibration - Different genomic selection models will be evaluated and results published.

Impacts
What was accomplished under these goals? AIM 1: Development and multi-environment evaluation of sweet corn hybrids We have created a total of 554 University of Florida x University of Wisconsin hybrids. These hybrids were created from the cross between 27 elite inbred parents from University of Wisconsin, Madison, and 24 elite inbred parents from University of Florida. A total of 420 hybrids, from the 554 created, were planted in Belle Glade, FL for evaluation in 2020. Due to limitations on seed availability, a subset of 250 hybrids were also planted in California for evaluation under organic production systems and in Wisconsin for evaluation under conventional settings. Hybrids were evaluated for plant traits, ear traits and overall performance. In Wisconsin, the hybrids were also evaluated for flavor and texture. From the data collected, we estimated genetic parameters and calculated single-site and multi-environment BLUPs (Best linear unbiased prediction). The rankings of the superior hybrids were used to select a set of 34 selections, which were tested in Belle Glade, FL in 2021 and were also sent to California and Wisconsin for 2nd year testing. AIM 2: Double haploid production for selected sweet corn hybrids Based on the hybrid's ranking and their phenotype across all three environments evaluated in 2020, we selected a set of 9 F1 hybrids that were sent to Iowa State University for Double Haploid production. Double haploids will be evaluated on year 2 of the project. AIM 3: Calibration of genomic selection models for hybrid prediction We have calibrated preliminary genomic selection models to predict the hybrid phenotypes in South Florida. Models were calibrated for the phenotypes ear height, ear length, ear width, kernel row number, leaf angle, plant height, tassel height, flowering time, number of tillers, among others. Models reached medium to high prediction accuracy, ranging from 0.38 to 0.67. The results were presented in the International Sweet Corn Development Association meeting.

Publications

• 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: 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: 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: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Resende - Deploying Genomic Selection in the University of Florida Sweet Corn breeding program. International Sweet Corn Development Association (Online)
• Type: Conference Papers and Presentations Status: Other Year Published: 2020 Citation: Resende - Genomics and phenomics applied to sweet corn breeding - University of Illinois Urbana-Champaign Seminar Series (Online)
• Type: Conference Papers and Presentations Status: Other Year Published: 2021 Citation: Resende - Optimizing and accelerating sweet corn breeding through genomics and phenomics. Florida AgExpo 2021 (Online)