Combination of major genes for Improvement of organic specialty corn varieties (CoMGI)

COMBINATION OF MAJOR GENES FOR IMPROVEMENT OF ORGANIC SPECIALTY CORN VARIETIES (COMGI)

Sponsoring Institution

National Institute of Food and Agriculture

Project Status

ACTIVE

Funding Source

OTHER GRANTS

Reporting Frequency

Annual

Accession No.

1026699

Grant No.

2021-51300-34896

Cumulative Award Amt.

$1,438,460.00

Proposal No.

2021-02928

Multistate No.

(N/A)

Project Start Date

Sep 1, 2021

Project End Date

Aug 31, 2025

Grant Year

2021

Program Code

[113.A]- Organic Agriculture Research & Extension Initiative

Project Director
Lubberstedt, T.

Recipient Organization
IOWA STATE UNIVERSITY
2229 Lincoln Way
AMES,IA 50011

Performing Department
Agronomy

Non Technical Summary
This project addresses the need for corn varieties suited to organic production systems and organic seed production, with a focus on sweet corn and specialty corn. The long-term objective is to establish efficient procedures to exploit major genes and major effect quantitative trait loci available in maize, that are aligned with the organic philosophy and to our knowledge have not been systematically applied in any breeding program to date.This work has the potential to change the organic seed production industry to make it better aligned with the organic ideals of sustainable nutritious food production. If successful, more companies will market corn seed that is produced organically and has been developed with the needs of organic producers in mind. The cornerstone of the outreach plan is the practical assessment of the hybrids developed in this project and their uptake by organic producers. Organic farmers will be full partners in the project and assist scientists in evaluating sweet and specialty corn lines for productivity under organic conditions. Field Days will highlight specific commercial organic varieties alongside field corn hybrids adapted for regional organic conditions. This multi-state interdisciplinary project will offer a variety of programs for sharing research results and providing information, demonstrations, and training on the principles and practices of organic plant breeding and use of tools/technology derived from this research. Data will be collected from each point of contact with farmers across all sites to allow for detailed analysis of the tools necessary to encourage widespread adoption of the practices and techniques developed within this project. In addition to research responsibilities, team members have been involved extensively in diverse education and extension programs, working with a wide range of client groups. Technology transfer techniques in this project include 1) Field Days (5 per year in Yrs 2-4); 2) conference workshops (1 per year); 3) classroom presentations (at least one per year), 4) publications, including journal articles (3) an Extension publication on "Field and Sweet Corn Varieties for Organic Crop Production in the Midwest," and 5) electronic and social media: websites, webinars (one/year through e-Organic or another national carrier), podcasts (one/year posted on project websites) and an interactive blog where participants can upload questions and comments on research results. An advisory team, representing producers, seed companies, Extension, and researchers will help provide comprehensive management plans in addition to evaluating project progress and success. PIs will meet regularly with field corn and sweet corn breeders and growers in each state and will keep them informed of progress. Co-PI Tracy works closely with a number of the sweet corn seed retailers that focus on the organic market, and we will send the best hybrids to these companies for evaluation under certified organic conditions ranging from Maine to California.

Animal Health Component

70%

Research Effort Categories

Basic

Applied

70%

Developmental

30%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1510	1081	50%
201	1480	1081	50%

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

Subject Of Investigation
1510 - Corn; 1480 - Sweetcorn;

Field Of Science
1081 - Breeding;

Keywords

Goals / Objectives
Organic corn production, and the transition from conventional to organic corn production, is affected by (1) declining prices for organic products, and (2) by climate change - facilitating spread of novel pests and diseases, and respective races and isolates. For this reason, we will focus on high margin organic sweet and specialty corn breeding in this proposal, and incorporation of genetic tools to enable efficient breeding of respective varieties. The goal of this work is to develop efficient tools and strategies for the utilization of major genes affecting pest and disease resistance, quality, reproductive and other agronomic traits in organic sweet and specialty corn breeding. Specifically, this includes (i) development and application of functional markers for efficient transfer of genes between sweet, field, and specialty corn, (ii) use of breeding strategies including DH technology for efficient transfer of major genes or QTL into elite germplasm, and (iii) on farm trials for evaluation of experimental cultivars under organic farm conditions.

Project Methods
The yield improvement of corn in the U.S. since the introduction of hybrid varieties in the 1940s is a remarkable success story. The four-fold increase in productivity achieved in this time period allowed the development of our modern food industry, kept food prices low, and provided the base for sustained economic expansion. This success is due in large part to the application of technology by large seed companies, essentially mechanizing and automating the process of plant breeding with selection for yield. Over the same time-span corn evolved from a genetic to a genomic model plant, with meanwhile multiple completely sequenced genomes available including a recently sequenced sweet corn genome, numerous characterized genes and novel technologies such as genome editing available to conventional corn breeding. While some technologies do not comply with organic crop production, others are compliant (such as DNA markers) and have the potential to substantially advance organic crop breeding, if properly incorporated.Organic agriculture encourages the sustainable production of nutritious food. Corn is an important component of organic production systems, but the majority of seed available to producers are modern varieties that are products of the industrial plant breeding system and are not well suited to the needs of organic producers. Rigorous use of organic compliant technologies will help to reduce the yield gap of varieties developed for the conventional versus the organic market. Moreover, they will allow us to efficiently utilize major natural genetic variation available in maize for development of more nutritious or resilient varieties, or to develop novel specialty corn types. Tremendous opportunity exists to develop new corn varieties with characteristics valued by organic producers. Such characteristics include:- High quality sweet corn with resistance to a number of pests- Novel traits allowing organic identity preservation- Novel specialty types such as waxy and white corn- Native insect resistance - conventional corn relies on transgenes for insect resistance, so conventional breeders don't select for this trait- Disease resistance - major genes to control virus and fungal diseases are available within maize and can be utilized more efficiently based on marker-assisted selection strategiesCorn breeding has rapidly embraced new technologies (e.g., DHs and genomic selection) in order to increase the rate of gain. Companies able to achieve a high rate of gain are rewarded by capturing market share with superior products. Plant breeding programs that do not market organic varieties focus their efforts on two traits that commodity grain prices are based on, i.e., grain yield and ability to dry well in the field. This narrow focus allows breeders to make very high rates of gain. The rate of gain from breeding decreases as the square of the number of traits under selection. Because breeders of organic varieties must focus on many traits, their rate of gain is necessarily lower. Unless organic breeders develop new technologies to increase their rate of gain, organic corn varieties will continue to fall behind non-organic varieties, creating a barrier for adoption of organic practices. Conversely, consequent implementation of organic compliant breeding technologies that facilitate the improvement of many traits simultaneously will allow organic breeders to increase their rate of gain in the direction desired by organic producers, but also to rapidly incorporate natural traits in response to novel market opportunities, in response to the consequences of a changing climate such as novel pathogens, respective races, and abiotic stress tolerance.The most important trait, grain yield, is quantitatively inherited. Modern breeding programs employ genomic selection in conjunction with other methods to accelerate the breeding cycle, such as use of winter nurseries and doubled haploid (DH) technologies, to maximize genetic gains. Recently granted USDA projects support incorporation of genomic selection and DH technologies in both organic and sweet corn breeding (2020-51300-02117; SweetCAP). However, significant progress has also been made in the identification and isolation of major genes in maize, driven by advances in maize genomics. While the first reference genome sequence from maize inbred line B73 was obtained in 2009, high quality genome sequences are meanwhile available of more than 40 additional inbred lines. Consequent application of genetic and genomic resources and approaches led to isolation of multiple genes of agronomic interest. These include genes controlling bacterial, virus, and fungal disease resistance, plant architecture, kernel quality, kernel coloration, reproductive mechanisms, among others. Conventional breeding programs have different options, how to incorporate major genes in their varieties, including transgenic methods and genome editing, which are not compliant with organic regulations. In contrast, both conventional and organic maize breeding can exploit DNA marker technology to efficiently transfer important major maize genes, as well as major QTL, into elite germplasm.Development of robust markers assays can be challenging due to genomic properties of respective genes (such as duplicated sequences), genetic background effects, linkage of different genes of interest in repulsion phase, among others. Once available, such gene-derived functional markers can be employed for backcrossing, forward breeding, gene stacking, and F2 enrichment among others, which are most efficiently used in combination with DH technology. The purpose of this project is to build a platform to make agronomically important major genes and major QTL available for marker-based introgression into organic breeding materials in conjunction with DH technology not using toxic chemicals in the process, while developing advanced sweet and specialty corn inbred lines for proof of concept.

Progress 09/01/23 to 08/31/24

Outputs
Target Audience:Organic farmers, Organic organizations, Plant breeders, Seed producers, Seed processors Changes/Problems:In Madison we had extreme weather result in 2024. We did lose some experimental materials but we were able to accomplish most of our goals. What opportunities for training and professional development has the project provided?Two Ph.D. students are currently involved, Mercy Fakude (Lübberstedt) and Tae-Chun Park (Scott). Wisconsin Ph.D. student Carl Branch managed the SHGD nursery in Madison, where he made numerous backcrosses to the appropriate parents. Those backcrosses are now growing in Chile in preparation of further backcrossing and selfing. Tae-Chun Park is a 3rd year Ph.D. candidate in the Interdepartmental Plant Biology Program at Iowa State University. He was trained in developing molecular markers for major genes used in this project. In addition, the Scott group trained student interns (e.g., Hannah Clubb) in field operations and seed inventory management. Lübberstedt hosted an intern (Irvin Sosa) from University Puerto Rico Mayaguez, a Hispanic Serving Institution. Robert Turnbull and Josiah Pollock (Extension Program Specialists) were trained in on-farm experimental protocols and data analysis for this project (Delate). Wisconsin: At different times three Ph.D. Candidates we're funded partially on this work. All three defended their dissertations during the reporting period, Lexi Wilson, Kathleen McCluskey, and Carl Branch. All three have successfully gotten positions in the plant breeding related fields. How have the results been disseminated to communities of interest?Co-PI Delate is organizing the annual Iowa Organic Conference, where project participants Lubberstedt and Fakude participated in 2023, and will together with co-PI Scott participate in 2024. For 2024, a lunch session with stakeholders is planned. Lübberstedt, Scott, Tracy, and Delate as well as students have been actively participating with oral or poster presentations in various meetings and conferences in 2023 and 2024 (ASTA, CSSA, RF Baker Symposium, Maize Genetics Conference, NAPB, Iowa Organic Conference, among others). Mercy Fakude will present a poster at the 2024 CSSA meeting. Co-PI Tracy Had the opportunity to present parts of this work at the AG food and human values conference in Syracuse NY. Tracy also was able to present some of this work as an invited speaker in the organic plant breeding course a Coimbra Portugal. What do you plan to do during the next reporting period to accomplish the goals?Objective 1: Completing publication on Functional Markers. Using functional markers in development of improved sweet corn and breads and ultimately hybrids. Objective 2: Evaluation of Ga2 inducer candidates Sweet corn DH line development, carrying SHGD Continue incorporation of desirable alleles into sweet corn DH material. Investigate the extent within sweet corn germplasm of the ability to overcome pollen exclusion conferred by Ga1 and Ga2 Specialty corn: Screen for individuals with desired gene combinations. At Wisconsin we will be continuing to evaluate the doubled haploids generated through this program both in terms of performance and also in terms of spontaneous doubling. Objective 3: Delate: Trials conducted in 2024 will be repeated in 2025.

Impacts
What was accomplished under these goals? Impact statement: This proposal outlines a plant breeding approach that facilitates combination of independent genetic loci in breeding programs. This approach will impact breeding programs focused on production of organic specialty corn varieties, which often require multiple genetic loci to create a desired product. The ability to produce improved varieties faster benefits the public by making products made from the improved varieties less expensive to make, higher quality, and safer while reducing negative impacts on the environment. Objective 1: Functional marker development Functional marker development has been completed. Each group has marker assays available as needed - or receive help from other groups with genotyping as needed. Tae-Chun Park is working on a review paper on functional markers, to be submitted to Frontiers in Plant Science. At Wisconsin functional markers are being incorporated in breeding efforts. Objective 2: Use of breeding strategies including DH technology for efficient transfer of major genes or QTL into elite germplasm Ga2 haploid inducer development: In summer 2024, evaluation of individual progenies derived from different Ga2-haploid -inducer families was continued. Bulk pollen per family (18) was used to pollinate the conventional hybrid Viking 51-95UP to determine induction ability (data not available yet) and pollen of 5-6 individuals per family were used to pollinate the Ga2 and Ga1 donor, to evaluate their ability to overcome the respective crossing barrier. As expected most of the individuals were able to generate medium to decent seed set on the Ga2 donor. In addition, all of the Ga2 families derived from a haploid inducer based on the public line Mo17 were able to overcome both Ga1 and Ga2 crossing barriers. Once induction ability is determined, the best families will be selected for a final increase and testing in summer 2025, and made available for release from fall 2025 on. Development of sweet corn carrying SHGD: We continued the efforts to introgress the SHGD trait from A427 into different sweet corn backgrounds. BC2 derived haploids in the background of for example Wh17066V showed restored fertility in clearly more than 50% of the haploids, indicating, that this background per se might already have the ability to spontaneously double. New backcrosses (BC3) and BC2-derived DH lines were generated in different backgrounds. As major genes are being incorporated at Wisconsin, we have begun to test DH lines generated through program in hybrid combinations. Hybrids were evaluated in Madison in 2024 and some are very promising Development of specialty corn varieties: We continued to work with the haploids generated in materials provided by Paul Scott in summer 2024. On average 60 haploids per induced rows were established in the field after rouging out false positives, about 25% showed restored male fertility and self-pollination was attempted. About 90 DH lines could be generated, half of them with 10 kernels or more. They are returned to Paul Scott for further evaluation. The Scott group continued development of two specialty corn varieties using the DH technology described in the proposal. The first is designed to be used for production of highly digestible forage and contains the major genes o2/bm3/SHGD and Ga1 and the second is designed to produce high value waxy starch and contains the major genes y1/wx/SHGD and Ga1-S. All major genes were combined in F1 crosses which were induced last year. This year, we are selecting individual plants containing the desired gene combinations. Objective 3: On farm trials Scott: A population of high-methionine corn was grown on the farm of Travis Otto in Cherokee, Iowa. Some lodging was observed following a strong wind storm, but the plants recovered fully and all ears were harvestable. Delate: Field plot design and data collection plans for the 2023 on-farm corn variety trials were finalized via email with farmer-cooperators in February 2023. Results from the 2023 field corn season on four farms in Iowa (SW1, SW2, NC, NW) were impacted by drought. Despite the harsh weather, high yields were achieved across all farms, with no statistical yield differences between varieties. The overall average corn yield across all varieties and across all farms was 174 bu/acre. The ranking of yields was as follows: Prairie Hybrids 5141 (Deer Grove, IL) at 178 bu/acre; Blue River O.18-06UP (Albert Lea Seed, Albert Lea, MN) at 173 bu/acre; Blue River 46-02 at 165 bu/acre; Blue River 62G22 at 159 bu/acre; Blue River 54PM37 at 155 bu/acre; and Prairie Hybrids 4211 at 152 bu/acre. The USDA varieties yielded 128 bu/acre in the 19SJWE and 126 bu/acre in the 22SJWE. At the research farm site in Greenfield, IA, the organic corn yields in the longest crop rotation sequence (C-S-HR/RC-RC) averaged 187 bu/acre, compared to the conventional yields of 123 bu/acre. Corn protein levels showed no significant differences across varieties, averaging 6.4%. Corn density averaged 1.27 g/cc. Corn starch averaged 62.17% across varieties. Oil content averaged 3.58% across all varieties with no significant differences between varieties. Corn ear weight in the 2023 trial averaged 233 g/ear across the trial with no statistical differences between varieties, with the BR 54C27 numerically greater, at 248 g/ear. Kernal weight per ear averaged 207 g/ear across the trial, with PH 5141 kernel weight numerically greater, at 222 g/ear. Ear length ranged from 7.37 inches to 8.48 inches. Disease and damage ratings were relatively low across farms and varieties, averaging less than 1% of ear damage across all farms and varieties. In 2024, corn varieties that were tested across the 4 farms (NC, NW, SW1 and SW2) included PH 5141 and PH 3051 (Prairie Hybrids, Deer Grove, IL), Blue River O.18-06UP (Albert Lea Seed, Albert Lea, MN), and BR 84-04, BR 46-02 and BR 85-09 (Albert Lea Seed, Albert Lea, MN). On the SW farm, Miller Hybrids (Miller Hybrids, Kalona, IA) varieties M10-54, M11-66, and M14-81 were grown. No USDA hybrids were grown in the trial in 2024 due to seed unavailability. Corn was planted across the four sites between May 17 and June 6, 2024. Plant emergence across the four on-farm sites ranged from 27,055 plants/acre at the NC site to 34,370 plants/acre at the SW2 site. Broadleaf weed populations were managed well in 2024 across all sites with averages of 0 weed/m2 at the NW site to 5 weeds/m2 at the SW2 site. Grass weeds averaged 9/weeds/m2 across all farms, and were greatest at the SW1 farm, at 29/weeds/m2, compared to 0/weeds/m2 at the NW site.

Publications

Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Dermail, A., L�bberstedt, T., Suwarno, W.B., Chankaew, S., Lertrat, K., Ruanjaichon, V., Suriharn, K. (2024) Haploid Inducer by Source Germplasm by Season Interaction on Tropical Maize Using GGE Biplot and Stability Analysis. Agronomy 14, 1505.
Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Foster, T., Kloiber-Maitz, M., Gilles, L., Frei, U.K., Pfeffer, S., Chen, Y.-R., Dutta, S., Seetharam, A., Hufford, M., L�bberstedt T. (2024) Fine-mapping of a major QTL for spontaneous haploid genome doubling (qshgd1) in maize. Theor. Appl. Genet. 137:117
Type: Peer Reviewed Journal Articles Status: Published Year Published: 2024 Citation: Chen, Y.-R., Frei, U.K., L�bberstedt, T. (2024) Genomic Estimated Selection Criteria and Parental Contributions Increase Genetic Gain of Maternal Haploid Inducers in Maize. Theor. Appl. Genet. 137: 248

Progress 09/01/22 to 08/31/23

Outputs
Target Audience:Organic farmers, Organic organizations, Plant breeders, Seed producers, Seed processors Changes/Problems:U Wisconsin (Tracy) How has COVID impacted the work planned for this reporting period? COVID issues linger especially in the areas of travel for research purposes and especially hiring hourly works. Brief description of any other problems/changes/weather impacts encountered over the last reporting period. Severe drought affected most of the field operations. We were able to access irrigation and most research objectives were attained USDA-ARS (Scott) Since our initial screen for four-gene combinations in the specialty corn breeding program was not successful, we will be repeating this screen with larger numbers of individuals. What opportunities for training and professional development has the project provided?Two Ph.D. students are currently involved, Mercy Fakude (Lubberstedt) and Tae-Chun Park (Scott). Wisconsin Ph.D. student Carl Branch managed the SHGD nursery in Madison, where he made numerous backcrosses to the appropriate parents. Those backcrosses are now growing in Chile in preparation of further backcrossing and selfing. Tae-Chun Park is a second year Ph.D. candidate in the Interdepartmental Plant Biology Program at Iowa State University. He was trained in developing molecular markers for major genes used in this project. In addition, the Scott group trained student interns (e.g., Hannah Clubb) in field operations and seed inventory management. Lubberstedt hosted an intern (Thalia Ramos) from University Puerto Rico Mayaguez, a Hispanic Serving Institution. Robert Turnbull and Josiah Pollock (Extension Program Specialists) were trained in on-farm experimental protocols and data analysis for this project (Delate). How have the results been disseminated to communities of interest?Co-PI Delate is organizing the annual Iowa Organic Conference, where project participants Lubberstedt and Fakude participated in 2022, and will together with co-PI Scott participate in 2023. For 2023, a lunch session with stakeholders is planned. Co-PI Delate organized an field event in August of 2023, with participation from farmers and presentations by co-PI Scott and Dr. Frei on haploid induction and the doubled haploid process. Lubberstedt, Scott, and Fakude visited Iowa organic farmers along with other students in July of 2023 (Rossmann, Skye farms). Lubberstedt visited Beck's Hybrids in Marshalltown. Lubberstedt presented ACES and CoMGI in person at the annual OREI program meeting in Washington DC. Lubberstedt, Scott, Tracy, and Delate as well as students have been actively participating with oral or poster presentations in various meetings and conferences in 2023 (ASTA, CSSA, R.F. Baker Symposium, Maize Genetics Conference, NAPB, Iowa Organic Conference, among others). Event Paul Scott gave a presentation at the University of Missouri, Columbia entitled "Breeding Corn for Organic Production Systems" November 14, 2022. Product Press release by ARS News Service, "Scientists ratchet up key amino acid in corn" September 28, 2023, https://content.govdelivery.com/accounts/USDAARS/bulletins/372a2e6 Event Paul Scott discussed this project at the Iowa Organic Association Field day, September 7, 2023, Wesley Iowa Event Paul Scott and Ursula Frei discussed this project at the Shriver farm field day, August 1, 2023, Jefferson, Iowa, 51 participants Event Branch, Carl A. The sugary enhancer1 (se1) allele is associated with significant decreases in the amount of lutein, zeaxanthin, and tocotrienols in yellow (Y1) sugary1 (su1) kernels. Vegetable Breeding Institute Cornell University August 2023 Event Tracy, W.F. Wisconsin Sweet Corn Update. Midwest Food Products Association, Wisconsin Dells. November 2022 Event Tracy, W.F. Wisconsin Sweet Corn Update. Vegetable Breeding Institute Cornell University August 2023 Event Lubberstedt, T. Presentation of USDA ACES project at annual USDA OREI PI meeting in Washington D.C. in April 2023 Event Lubberstedt, T. Invited Presentation "Efficient breeding of resilient crops using doubled haploid technology" at R.F. Baker Symposium at ISU, Ames IA in March 2023 What do you plan to do during the next reporting period to accomplish the goals?Objective 1: Completing publication on Functional Markers. Improve molecular markers for wx, Y1, SHGD, and BM3. Objective 2: Evaluation of Ga2 inducer candidates Sweet corn DH line development, carrying SHGD Continue incorporation of desirable alleles into sweet corn DH material. Investigate the extent within sweet corn germplasm of the ability to overcome pollen exclusion conferred by Ga1 and Ga2 Specialty corn: Screen for individuals with desired gene combinations Objective 3: Continuation of on farm field trials in 2024, as described above for 2022 and 2023.

Impacts
What was accomplished under these goals? Impact statement: This proposal outlines a plant breeding approach that facilitates combination of independent genetic loci in breeding programs. This approach will impact breeding programs focused on production of organic specialty corn varieties, which often require multiple genetic loci to create a desired product. The ability to produce improved varieties faster benefits the public by making products made from the improved varieties less expensive to make, higher quality, and safer while reducing negative impacts on the environment. Objective 1: Functional marker development Functional marker development has been completed. Each group has marker assays available as needed - or receive help from other groups with genotyping as needed. Tae-Chun Park is working on a review paper on functional markers, and is interacting with a distance MS in Plant Breeding student, who is preparing a Creative Component (CC) on this topic. Both publication and CC will be published in the upcoming project year. Objective 2: Use of breeding strategies including DH technology for efficient transfer of major genes or QTL into elite germplasm Development of a Ga2 haploid inducer: The Ga2 haploid inducer development was continued during the winter 2022 and summer 2023 season. Induction ability of the families was tested on a conventional hybrid (Viking 51-95UP, Albert Lee Seed, MN) and individual plants within the families were tested for their ability to overcome the Ga2 crossing barrier. We will continue with four families with the Ga2 allele present and induction abilities of 12, 13, 14, and 19% in the conventional hybrid respectively. Two of the families also showed the ability to overcome the Ga1 crossing barrier. First induction crosses in materials heterozygous for the Ga2 allele (provided by Paul Scott) were performed in summer 2023 - haploid selection has not been started yet. Development of sweet corn carrying SHGD: ISU is helping with inductions, and conducts a parallel backcross program of fertile haploids, used to create the next backcross generation. This will serve as back-up to marker-assisted backcrossing. We (Tracy and team) continued to backcross DH lines for identification and incorporation of desired alleles. We investigated issues presented by the frequency of alleles in sweet corn that can overcome the Ga1 and Ga2 crossing barriers. Development of specialty corn varieties: A challenge to developing specialty corn varieties is that some products require combining multiple unlinked genetic loci. This proposal outlines a combination of technologies that improves this process. Using the process described in the proposal, USDA-ARS is developing two types of specialty corn varieties. Corn for organic silage is being developed by combining the mutations o2, bm3, Ga1-S and SHGD. This corn will produce silage with highly digestible grain and vegetative tissues, will have added genetic purity, and will be amenable to improvement by breeding. High value corn production of high value organic specialty starches is being developed by combining the mutations y1, wx1, Ga1-S and SHGD. This corn will have white waxy kernels, with improved genetic purity, and will be amenable to improvement by breeding. These traits are valued by the organic food industry for making specialty starches and food additives. In the 2023 summer field season, we screened for fertile individuals containing all the desired mutations. This screen was not successful and will be repeated next season with larger numbers to ensure success. Objective 3: On farm trials ?In 2022, there were significant differences in corn yields between the NE farm, with excellent rainfall, compared to NC, NW and SW farms, due to the drought. The overall average corn yield across all varieties and across all farms was 185 bu/acre. There were no statistical differences among varieties when averaged across all farms, but there were numerical differences worth noting. The ranking of yields across all farms was as follows: PH 5141 (Prairie Hybrids, Dear Grove, IL) at 201 bu/acre; Blue River 62G22 (Albert Lea Seed/Blue River, Albert Lea, MN) at 191 bu/acre; PH 4211 and Viking O.18-06 at 189 bu/acre; BR 54PM37 at 182 bu/acre and Viking O.48-08 at 155 bu/acre. The USDA varieties averaged 108 bu/acre. There was quite a variation of corn moisture at harvest with the NE farm averaging 22% compared to the SW farm averaging 14%. In 2023, corn varieties that were tested across the 4 farms included: PH 5141 (Prairie Hybrids, Dear Grove, IL); Blue River 54C27 (Albert Lea Seed/Blue River, Albert Lea, MN); PH 4211 and Viking O.18-06; BR 54PM37 and Viking O.46-02. The USDA hybrids were only tested at the NC farm. Corn was planted across the four sites between May 17 and May 23, 2023. An OREI Organic Corn Variety Field Day was held on August 1, 2023, at the Shriver Farm, in Jefferson, IA, with 51 participants. As of this date, not all corn has been harvested due to wet weather. We will repeat this trial in 2024.

Publications

Type: Journal Articles Status: Published Year Published: 2023 Citation: Trentin, H.U., Yavuz, R., Dermail, A., Frei, U.K., Dutta, S., L�bberstedt, T. A comparison between inbred and hybrid maize haploid inducers. Plants 12:1095 https://doi.org/10.3390/plants12051095
Type: Journal Articles Status: Published Year Published: 2023 Citation: Aboobucker, S.I., Zhou, L., L�bberstedt, T. Haploid male fertility is restored by mutations in parallel spindle genes in Arabidopsis thaliana. Nature Plants 9:214-218 10.1038/s41477-022-01332-6
Type: Journal Articles Status: Published Year Published: 2023 Citation: Aboobucker, S.I., L�bberstedt, T. A genetic mechanism to restore haploid male fertility in Arabidopsis an alternative to chemical methods. Nature Plants 9:205-206 https://doi.org/10.1038/s41477-022-01335-3
Type: Journal Articles Status: Published Year Published: 2023 Citation: Dermail, A., Chankaew, S., Lertrat, K., Suwarno, W.B., L�bberstedt, T., Suriharn, K. Combining ability of tropical x temperate maize inducers for haploid induction rate, R1-nj seed set, and agronomic traits. Frontiers in Plant Science 14:1154905. doi: 10.3389/fpls.2023.1154905
Type: Journal Articles Status: Published Year Published: 2023 Citation: Dong, D., Nagasubramanian, K., Wang, R., Frei, U.K., Jubery, T.Z., L�bberstedt, T., Ganapathysubramanian, B. Self-supervised corn kernel classification and segmentation for embryo identification. Frontiers in Plant Science 14:1108355. DOI 10.3389/fpls.2023.1108355
Type: Journal Articles Status: Published Year Published: 2023 Citation: Hintch, T., Lauter, A.M., Kinney, S., L�bberstedt, T., Frei, U.K., Duangpapeng, P., Edwards, J.W., Scott, M.P. Development of maize inbred lines with elevated grain methionine concentration from a high methionine population. Crop Sci. 63: 2417-2425. https://doi.org/10.1002/csc2.20983
Type: Journal Articles Status: Published Year Published: 2023 Citation: Ledesma, A., Aguilar, F.S., Uberti, A., Hufford, M., Edwards, J., Hearne, S., L�bberstedt, T. Haplotype sharing and diversity analyses of DH Lines derived from different cycles of the Iowa Stiff Stalk Synthetic Maize Population. Frontiers in Plant Sci. 14:1226072. doi: 10.3389/fpls.2023.1226072
Type: Journal Articles Status: Published Year Published: 2023 Citation: Trentin, H.U., Krause, M., Zunjare, R., Costa Almeida, V., Rotarenco, V., Beavis, W.D., V., Frei, U.K., L�bberstedt, T. Genetic basis of maize maternal haploid induction beyond MATRILINEAL and ZmDMP. Frontiers in Plant Science 14:1218042. DOI: 10.3389/fpls.2023.1218042
Type: Journal Articles Status: Published Year Published: 2023 Citation: Sanchez, D., Santana, A.S., Morais, P., Peterlini, E., De la Fuente, G., Castellano, M., Blanco, M., L�bberstedt, T. Genome-wide association analysis of doubled haploid exotic introgression maize (Zea mays L.) lines for agronomic traits under depleted nitrogen conditions. Frontiers Plant Sci. 14:1270166. DOI: 10.3389/fpls.2023.1270166
Type: Journal Articles Status: Published Year Published: 2023 Citation: Branch, C.A. & Tracy, W.F. (2023). Divergent selection for timing of vegetative phase change. Crop Science. 2023;19
Type: Journal Articles Status: Published Year Published: 2022 Citation: Colley, M.C., Dawson, J.C., McCluskey, C., Myers, J.R., Tracy, W.F., & Lammerts van Bueren, E.T. (2022). Exploring the emergence of participatory plant breeding in countries of the global North. The Journal of Agricultural Science. https://doi.org/10.1017/S0021859621000782
Type: Journal Articles Status: Published Year Published: 2022 Citation: Colley, M.C., Tracy W.F., Lammerts van Bueren, E., Diffley, M., & Almekinders, C. (2022). How the seed of participatory plant breeding found its way in the world through adaptive management. Sustainability. 14 (2132), https:// doi.org/10.3390/su14042132
Type: Journal Articles Status: Published Year Published: 2023 Citation: Bapat, A. R., A. N. Moran Lauter, M. B. Hufford, N. A. Boerman and M. P. Scott, 2023 The Ga1 locus of the genus Zea is associated with novel genome structures derived from multiple, independent non-homologous recombination events. G3 Genes|Genomes|Genetics: jkad196. DOI: 10.1093/g3journal/jkad196
Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Delate, K. 2022. Participatory Organic Research: Methods to Enhance Farmer Researcher Partnerships, American Society of Agronomy Annula Meetings, Baltimore, MD, November 7, 2022: https://scisoc.confex.com/scisoc/2022am/meetingapp.cgi/Paper/145014
Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Fakude M, Frei UK, Foster TL, L�bberstedt T. Identification of genomic region associated with the causal QTL of SHGD trait in Ames panel by GWAS. The 64th Annual Maize Genetics Meeting. 2023
Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Fakude M, Frei UK, Foster TL, L�bberstedt T. Identification of genomic regions associated with the causal QTL of SHGD trait in Ames panel by GWAS. ASA-CSAA-SSSA. 2023

Progress 09/01/21 to 08/31/22

Outputs
Target Audience:Organic farmers, Organic organizations, Plant breeders, Seed producers, Seed processors Changes/Problems:Scott:We expanded the gene list of the specialty corn section of the project to include the bm3 mutation, which improves the quality of silage made from corn. This adds value to the project and takes advantage of existing project resources because we have already combined this gene with o2, a gene which is a target for this project. What opportunities for training and professional development has the project provided?Two Ph.D. students are currently involved, Mercy Fakude (Lubberstedt) and Tae-Chun Park (Scott). Moreover,Henry Franzen (undergraduate student) and Josiah Pollock (Extension Program Specialist) were trained in on-farm experimental protocols and data analysis for this project (Delate).Wisconsin Ph.D. student Carl Branch managed the SPDH nursery in Madison, where he made numerous backcrosses to the appropriate parents. Those backcrosses are now growing in Chile in preparation of further backcrossing and selfing. Tae-Chun Park is a second year Ph.D. candidate in the Interdepartmental Plant Biology Program at Iowa State University. He was trained in developing molecular markers for major genes used in this project. In addition, the Scott group trained three student interns (Hannah Clubb, Pedro Ramirez and Julio Roman) in field operations and seed inventory management. Two of these interns are from University Puerto Rico Mayaguez, a Hispanic Serving Institution. In addition, seven student interns from University of Puerto Rico Mayaguez were trained in corn nursery operations at our winter nursery site in Lajas, Puerto Rico. How have the results been disseminated to communities of interest?The National Association of Plant Breeders (NAPB) meeting was hosted at ISU in 2022 (Lubberstedt and Scott were co-hosts), which allowed to present products (field tour) and outcomes (posters) to a broad audience (close to 400 participants). Field Days and conference presentations were utilized to disseminate information about the project.Organic vegetable field days were held in Madison WI in August 2022 and this project was discussed with attendees there. We continue to have buy-in from project farmers to grow the specific varieties or lines, and assist with data collection during the season. This shows great promise for their continued involvement in evaluating new lines that are developed from the ACES pipeline, which is the predecessor of CoMGI. Paul Scott presented a seminar in the Interdepartmental Plant Biology seminar series at the University of Missouri, "Breeding corn for organic production systems". Columbia, Mo, November 14, 2022 (not sure if this in the period of performance) Paul Scott presented a seminar in Plant Biology 696, Iowa State University, "Cross Incompatibility in Corn". Ames, Iowa, September 29, 2021. (not sure if this is in the period of performance) Paul Scott was invited to provide information on gametophyte factors to representatives of the popcorn and seed corn industries in two meetings organized by the American Seed Trade Association December 8, 2021. What do you plan to do during the next reporting period to accomplish the goals?Marker and plant material development will continue as planned. Delate: Hybrids from germplasm developed under the 2014 NIFA - OREI grant, and any germplasm that becomes available from this OREI grant, will be tested in organic farmer-cooperators' fields. Sweetcorn germplasm from UW's program will also be tested. We will make crosses among plants carrying two or more of the major genes that are targets in the specialty grain section of this project to create populations in which 4 desired major genes are segregating. These populations will be induced to create haploids and individuals containing all four genes will be identified.

Impacts
What was accomplished under these goals? (i) Functional marker development and application: Functional marker development is ongoing, with some of the markers being available. Moreover, we did meet with Eurofins, and will consider their involvement for more efficient marker development and genotyping work. (ii) Use of breeding strategies including DH technology: Development of a Ga2 haploid inducer: The current set of haploid inducer lines cannot pollinate breeding materials that have the Ga2-S locus incorporated, to prevent unintentional pollination by (transgenic) dent corn. The introgression of the Ga2-S allele started already in winter 2021 using haploid inducing lines developed in the backgrounds of B73, Mo17 and PHG83. Haploid inducer lines that have the Ga1-S allele were not able to pollinate the Ga2-S donor lines and vice versa with the exception of one Mo17 derived inducer line. Mo17 is known to be able to overcome the crossing barrier of Ga2 and opens thus for the possibility to develop an inducer line that can be used in both Ga1 and Ga2 backgrounds. During the summer 2022, BC1:F2 and BC2:F1 families were tested for their ability to pollinate the Ga2-Tester as well as the Ga1-Tester. As expected some inducer lines with Mo17 their genetic background were able to pollinate both tester. Ear to row in the selected inducer families will continue, test pollinations to determine the induction ability of the inducer lines in different genetic backgrounds are planned. (iii) On farm trials: In 2022, six commercial organic field corn varieties: BR 54PM37, BR 62G22 (Blue River, Ames, IA), Prairie Hybrids 4211, Prairie Hybrids 5141 (Prairie Hybrids, Deer Grove, IL), Viking 0.18-06, and Viking 0.48-08 (Albert Lea Seed, Albert Lea, MN) were compared on four farms in Iowa (NE, NC, SW, NW), with one farm (NC) also evaluating USDA-bred hybrids. Viking 48-08 and PH 4211 tended to have the highest plant emergence, at 32,778 plants/acre and 32,500 plants/acre, respectively, but these were statistically equivalent to all other varieties. The USDA hybrids averaged 31,666 plants/acre, with the USDA 7675 hybrid averaging 32,666 plants/acre. Regarding weed populations, often reflective of corn shading potential, the USDA 5812 hybrid had the highest number of broadleaf weeds at 6 per square meter, compared to an average of 1 weed per square meter for all commercial varieties. Viking 48-08 and PH 4211 tended to have the lowest number of broadleaf weeds, averaging 1 weed per square meter. Grass weeds were less prolific, averaging 1 weed per square meter across all varieties, with no statistical differences. The tallest varieties were BR 62G22 and Viking 48-08, at 276 cm and 261 cm, respectively, but there were no statistical differences among varieties. THE USDA varieties averaged 238 cm overall, with USDA 7681 the tallest, at 248 cm. The BR 54PM37, PH 5141, and Viking 18-06 varieties tended to produce more than 1 ear per plant, but there were no statistical differences among varieties. Insect populations (corn borer, aphids, other pests) were low in 2022, averaging damage ratings of 1 or lower, with no statistical differences among varieties. Disease incidence was also low in 2022, with no differences in ratings among varieties. USDA hybrids showed low insect or disease incidence. Yields will be correlated with pest incidence when all yields are determined.

Publications

Type: Journal Articles Status: Published Year Published: 2021 Citation: Verzegnazzi, A., Santos, I., Frei, U.K., Krause, M., 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 enables efficient doubled haploid line development in exotic maize germplasm. Theor. Appl. Genet. 134: 1423-1434 DOI: 10.1007/s00122-021-03780-8
Type: Journal Articles Status: Published Year Published: 2022 Citation: Trampe, B., Batiru, G., Pereira, A.S., G., Frei, U.K., L�bberstedt, T. (2022) QTL mapping of inducibility using genotype by sequencing in maize. Plants 11: 878 DOI 10.3390/plants11070878
Type: Book Chapters Status: Published Year Published: 2022 Citation: Muhammad-Aboobucker, S., Jubery, Z., Frei, U.K., Foster, T., Chen, Y.-R., Ganapathysubramanian, B., L�bberstedt, T. (2022) Protocols for in vivo doubled haploid (DH) technology in maize breeding: From haploid inducer to haploid genome doubling. Methods Molecular Biology, Plant Gametogenesis, Methods and Protocols (C. Lambing ed.) 2484: 213-235 https://doi.org/10.1007/978-1-0716-2253-7_16
Type: Journal Articles Status: Published Year Published: 2022 Citation: Trentin, H.U., Batiru, G., Frei, U.K., Dutta, S., L�bberstedt, T. (2022) Investigating the effect of the interaction of maize inducer and genome backgrounds on haploid induction rates. Plants 11:1527, https://doi.org/10.3390/plants11121527
Type: Journal Articles Status: Published Year Published: 2022 Citation: Santos, I., Verzegnazzi, A.L., Edwards, J., Frei, U.K., De La Fuente, G.N., Zuffo, L., Pires, L.P.M., L�bberstedt, T. (2022) Usefulness of adapted exotic maize lines developed by Doubled Haploid and Single Seed Descent methods. Theor. Appl. Genet. 135, 1829-1841, https://doi.org/10.1007/s00122-022-04075-2
Type: Book Chapters Status: Published Year Published: 2021 Citation: Boerman N.A., Lauter A.N.M., Edwards J.W., Scott M.P. (2021) Variation in degree of pollen exclusion for ga1-s unilateral cross incompatibility in temperate maize breeding populations, Agrosystems, Geosciences & Environment, John Wiley & Sons, Ltd. pp. e20220.