Source: AGRICULTURAL RESEARCH SERVICE submitted to
BREEDING CORN TO ENABLE ORGANIC SEED PRODUCTION
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1023539
Grant No.
2020-51300-32180
Cumulative Award Amt.
$1,996,512.00
Proposal No.
2020-02117
Multistate No.
(N/A)
Project Start Date
Sep 1, 2020
Project End Date
Aug 31, 2025
Grant Year
2020
Program Code
[113.A]- Organic Agriculture Research & Extension Initiative
Recipient Organization
AGRICULTURAL RESEARCH SERVICE
1815 N University
Peoria,IL 61604
Performing Department
Corn Insects and Crop Genetics
Non Technical Summary
This project builds on the germplasm, methods and technologies developed in three previous OREI projects to achieve the objective of enabling seed companies to use organic management to produce corn seed sold to organic farmers. We will do this by developing 3-way hybrids that are better-suited to organic seed production than the single-cross hybrids currently marketed by most companies. These hybrids will carry traits desired by organic producers such as high levels of the essential nutrient methioinine and the ability to exclude GMO pollen using the Ga1 pollen exlusion system. We propose to develop a new rapid cycling breeding method that combines the contemporary methods of genomic slection and doubled haploid breeding with an organic- friendly breakthrough techonology called Spontaneous Haploid Genome Doubling. This approach will allow us to produce new varieties in about one fourth the time required by current methods. A key outreach activity will be two Organic Corn Breeding Boot Camps held at our winter nursery site in Puerto Rico and attended by midwest farmer cooperators, project investigators, and student interns from the Univeristy of Puerto Rico. Attendees will work togther to produce seed and plan on-farm trials for the following summer. Interns will travel to the farmers' locations in the summer to assist with the trials. The boot camp will provide a novel opportunity for farmers and breeders to cooperate in the process of variety development and testing.
Animal Health Component
40%
Research Effort Categories
Basic
40%
Applied
40%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20215101081100%
Knowledge Area
202 - Plant Genetic Resources;

Subject Of Investigation
1510 - Corn;

Field Of Science
1081 - Breeding;
Goals / Objectives
Corn is the second largest organic grain/seed crop in the U.S. behind wheat (Agricultural Marketing Research Center, 2018). While several seed companies sell seed that can be used in certified organic systems, essentially none of the varieties available were developed specifically for organic production systems and very few have even been evaluated in organic production environments. Further, only a small proportion of the seed sold to organic farmers is produced using certified organic practices. The goal of this work is to expand organic production by developing new varieties that are suited to seed production using certified organic practices and have characteristics desired by organic producers and to do this rapidly with a novel rapid cycling plant breeding method.
Project Methods
Rapid cycling OREI breeding pipelineRapid cycle breeding will be done by a novel combination of Genomic Selection and Doubled Haploid breeding, taking advantage of SHGD to allow recombination and seed increase to occur in the same generation. We will implement a rapid cycling breeding strategy for rapid recurrent genomic selection for DH line development and population improvement under organic conditions, starting with germplasm developed by project cooperators and carrying traits desired by organic producers including high methionine concentration and the ability to exclude foreign pollen. We will evaluate DH lines and their testcrosses under organic conditions in Iowa, Illinois, and Puerto Rico. Genotyping will be outsourced to a service provider that offers competitive technology and pricing. Finally, we will incorporate SHGD for efficient and colchicine-free DH line development.GermplasmWe will simultaneously improve two populations applying a reciprocal recurrent selection approach in which the products of the female pipeline will be used as testers for the male pipeline and vice versa. The two starting populations will be constructed from different and complementaryheterotic pools. One population will be improved as the seed parent ("female"), whereas the second population will serve as the pollen parent ("male"). The female heterotic pool will be derived from the Iowa Stiff Stalk Synthetic population combined with high methionine germplasm. We will introgress the pollen exclusion gene Ga1 and the major SHGD QTL (inbred lines carrying these genes are available) and further cross the high-methionine population with GEM and exPVP derived inbreds to broaden the genetic basis for agronomic performance and insect resistance. The goal will be to fix Ga1 and SHGD in the female population quickly and to provide sufficient genetic diversity for a sustained long term selection response. The male heterotic group will be based on population BS39 which was selected from exotic Tusón germplasm and adapted to the U.S. Corn belt. BS39 derived DH lines carrying the major SHGD QTL are already available.Improvement CyclesThe population improvement cycle will consist of two generations, carried out in the winter and summer nurseries of the one year: (1) haploid induction in breeding population, followed by (2) genotyping, selection and combination of most promising fertile haploids based on GEBVs, as well as self-pollination for DH line development. Crosses between fertile haploids will constitute the improved population which will be induced to continue the population improvement cycle.The product development cycle will be based on the selected self-pollinated fertile haploid (D0) plants. The resulting D1 lines will be self-pollinated for seed multiplication and crossed with a tester from the other pipeline for testcross seed production. Resulting hybrids will be evaluated under organic conditions for yield and yield component traits, and respective phenotypic and genotypic data will be used to update the training model for genomic selection.Genomic SelectionOur experience with variety trials conducted in organic on-farm experiments suggests that organic testing environments tend to have more experimental variation than non-organic environments. We will account for this difference by testing with greater replication than is normally used. Extending our testing efforts to a large number of environments per year (N > 10 environments) will accumulate the data we need to estimate and model Genotype × Environment interactions.We will develop genomic models to predict DH per se performance and performance in single and three-way hybrids. For our rapid cycling OREI breeding pipeline, we will adapt the general and subpopulation-specific additive ridge regression best linear unbiased prediction approach (GAS-RRBLUP). The seed parent will be a single cross hybrid (Female1 × Female2) developed from two inbred lines obtained from the female population.For this project, three-way hybrids come in two "flavors" with consequences for the applied genomic prediction protocol. Approach 1 - Female1 and Female 2 are closely related and both combine well with Male1. Approach 2 - Female1 and Female2 form a single-cross hybrid that maximizes intrapool heterosis and combines well with Male1 to produce a highly productive three-way hybrid. We will simulate traits with additive effects and additive and dominance effects, assuming different heritabilities (0.2, 0.5 or 0.9), and number of loci (3, 10, 25, or 75). Each genetic architecture will be simulated for multiple environments using the R package simplePHENOTYPES (https://bitbucket.org/fernandessb/simplephenotypes). We will test GS models for each approach (i.e., "modified single cross hybrid" vs "three-way hybrid") using available SNP marker information applying GAS-RRBLUP. Prediction accuracies for each genetic architecture will be conducted using a 5-fold cross-validation scheme. Our GS models will be used to select haploids for product development and population improvement. For population improvement selected and fertile haploids with a predetermined minimum genetic distance will be crossed to build F1 hybrids. To rapidly fix the pollen exclusion and spontaneous haploid genome doubling trait in our breeding populations, each F1 hybrid will be homozygous for the Ga1 pollen excluding locus and the major SHGD QTL. A balanced bulk of F1 hybrid seed will form the next improved cycle of the breeding populations.Doubled HaploidsThis project will require selection of millions of haploid kernels, requiring a great deal of manual labor. In order to increase the efficiency of this process, we will attempt to use single kernel evaluation by near-infrared reflectance spectroscopy (NIRS) using the skNIRS sorter for automated haploid selection. In addition to haploid selection, PI Scott will establish a calibration to identify haploids with high methionine content. Calibrations that predict methionine concentration in bulk grain exist, so it should be possible to develop a single kernel calibration.Haploid kernels selected based on NIRS will next be grown in organic nurseries to select the most vigorous haploid plants. We will induce haploid lines from existing BS39-derived inbred lines. Currently, more than 200 BS39 lines carrying SHGD are available, and have been genotyped. We will induce haploids for those 200 lines, each of which will be genetically uniform haploid lines and isogenic to the respective diploid BS39 lines. Those isogenic line pairs will be planted side-by-side in replicated trials in organic nurseries in Iowa and Illinois, to capture various agronomic traits, including seedling vigor and survival rate, plant height, etc. Since those lines have been genotyped, it will be possible to identify genome regions contributing to seedling vigor and overall inbred line performance both at the haploid and diploid level, and to incorporate these information in GS models.We will evaluate whether it is possible to reliably obtain 3 generations per year in Puerto Rico. The most important genotype to be consistently used in population improvement cycles is a haploid inducer. At the DH Facility at ISU led by co-PI Lubberstedt, more than 180 haploid inducers i have been developed, which will be evaluated for adaptation to different seasons in Puerto Rico. Primarily, adaptation traits such as resistance to local diseases and insects, tolerance to abiotic stress factors, lodging tolerance, ability to shed pollen and set seed will be monitored during the first two years of the project. The best inducer will be used for small scale haploid induction trials to produce haploids from a limited number of donor genotypes in a pilot 3-generation per year cycle, to establish protocols for working with haploid plants. If successful, larger-scale haploid inductions will be initiated from year 4 on.

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

Outputs
Target Audience: Nothing Reported Changes/Problems:Our main challenge is that the performance of our varieties is in most cases well below that of commercial varieties. We will continue to incorporate the best germplasm available into our breeding program. Our rapid cycling approach should allow us to improve our varieties faster than the commercial corn breeding programs can improve theirs. We should eventually catch up to them, but until we have run a few breeding cycles we will not knowhow long this will take. What opportunities for training and professional development has the project provided?We held our first Corn Breeding Boot camp in conjunction with our organic winter nursery pollination in late January in Lajas Puerto Rico. The grant funded three organic corn farmers from the Midwest to travel to Puerto Rico and work side by side with student interns from from the University of Puerto Rico and the investigators on the grant. In addition to the hands-on work experience, discussion sessions provide context that ties the field work to the larger objectives of the project and to the scientific theory behind the work. These sessions also allowed for sharing of ideas between students, farmers and scientists. Two student interns from Puerto Rico traveled to the Midwest during the following summer and assist with the field work at the university locations. They also visited the farms of the boot camp participants to learn about organic corn production in the Midwest. The boot camp provides a hands-on learning and information sharing opportunity for farmers, students and scientists interested in organic corn production. Research technicians Luisa Flores and Leidy Sarmiento managed/lead the Organic Winter Nursery performed from December 2022 to April 2023 and trained four undergraduate students from the University if Puerto Rico, Mayaguez (Elian Pabón, Marielis Santiago, Yamilette Rosado, Krinten Otero), in technical aspects of the field work required for the project. Two students from the previous season were retained (Arialie Figueroa, Thalia Ramos) to work in winter nursery activities. Also, Yamilette Rosado (Bohn's Research Program) and Thalia Ramos (Lubberstedt's Research program - ISU) spent +8 weeks performing an internship focused on corn breeding and nursery methods as part of the boot camp activities described above. Some demographic data of the winter nursery student participants, 64% has been females and 36% males; most students belong to the Agroenvironmental Sciences Department (Agronomy and Crop Protection), other departments impacted have been Ag Economics, General Agriculture, and Biology.; 100% has been undergraduates. Their GPA fluctuates from 2.60 to 3.83; 40% are in the 6thyear of their studies, 20% in their 5th; 20% in their 4thyear, and 20% in their 3rd. All of them recognize themselves as Hispanic or Latino. 60% of the participants' students are first-generation university students in their household. 80% consider themselves fluent in writing and talking in English and Spanish, while 20% consider themselves fluent in writing in English but not fluent in talking in English. 36% of the participants have graduated from the university, just 18% enrolled in graduate school in Soils and Business; 10% is working in RiceTec Inc. a winter nursery division of Hybrid Rice Seeds, 64% still performing undergrad studies. 55% of the participants in the winter nursery activities had the opportunity to participate in the summer internship experiences with the collaborators and PI of the grant. Ph.D students Shelly Kinney (Iowa State University) and Chris Mujjabi (University of Illinois - Urbana Champain) were supported by the project carried out research on their dissertations that is aligned with project objectives. Student hourly worker Hannah Clubb was trained in corn breeding methods while supporting project research. Hannah attended the 2023 National Association of Plant Breeders annual meeting in Greenville South Carolina as a Borlaug Scholar. How have the results been disseminated to communities of interest?Paul Scott gave a presentation at the University of Missouri, Columbia entitled "Breeding Corn for Organic Production Systems" November 14, 2022. 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 Paul Scott discussed this project at the Iowa Organic Association Field day, September 7, 2023, Wesley Iowa Paul Scott, Uschi Frei and Elizabeth Bovenmyerdiscussed this project at the Shriver farm field day, August 1, 2023, Jefferson, Iowa Hannah Clubb (Iowa State University undergraduate student) was interviewed by Seed World (https://www.seedworld.com/hannah-clubb-on-going-to-school-while-battling-cancer/). Park, Tae-Chun; Kinney, Shelly; Lauter, Adrienne N; Scott, Paul M,Aboobucker, Siddique I; Frei, Ursula K; Lübberstedt, Thomas, 2023, Application of DH technology and molecular markers to combine multiple major genes for improving corn quality, Poster #134 at the 65th annual Maize Genetics Conference, St. Louis Mo. Bapat, Amruta R; Moran Lauter, Adrienne N; Hufford, Matthew B; Boerman, Nicholas A; Scott, Paul M, 2023,The Ga1 locus of the genus Zea is associated with genome structures derived from multiple, independent non-homologous recombination events, Poster #249 at the 65th annual Maize Genetics Conference, St. Louis Mo. What do you plan to do during the next reporting period to accomplish the goals?In the next year we will begin testing genomic prediction models and intermate lines to develop the female population for the rapid cycle breeding program. We will continue to carry out evaluation of triple cross hybrids as well as new inbreds and F1 hybrids in organic production systems. We will continue to advance material in our breeding programs with testing to produce finished varieties.

Impacts
What was accomplished under these goals? Impact statement: Most of the corn seed available to organic farmers was not produced organically and the varieties available were not developed to meet the needs of organic corn producers. This project seeks to develop new varieties specifically designed for organic production systems by selection for breeding targets of interest to organic producers and testing in organic production environments. The products of this research will provide organic corn producers with seed options that better meet their needs. We proposed development of a rapid cycle breeding program based on modern maize breeding methods including doubled haploids and genomic selection. In this year, we collected phenotype and genotype data that will be used to train genomic selection models and created a male breeding population. On the female side, we crossed the SHGD trait into a collection of superior inbred lines that will be intermated to create the female population. We proposed to develop triple cross hybrids with superior seed production qualities. In this year, we carried out the first yield trial of a collection of triple cross hybrids. The outcome of this experiment will guide development of improved triple cross varieties.?

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: 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.
  • 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


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

Outputs
Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Shelly Kinney is a second year M.S. candidate in the Interdepartmental Genetics Program at Iowa State University. She was trained in breeding for traits that are important for organic producers, such as grain methionine concentration. Mercy Fakude is a second year Ph.D. student in the Agronomy Plant Breeding and Genetics program at Iowa State University. She was trained in genotyping for genomic prediction. Chris Mujjabi completed is M.S. degree inCrop Science at the University of Illinois. He was trained in doubled haploid technology and genomic predictions. Research technicians Luisa Flores and Leidy Sarmiento managed/lead the Organic Winter Nursery performed from December 2021 to April 2022 and trained six undergraduatestudents from the University if Puerto Rico, Mayaguez (Julio Roman, Pedro Ramos, Arialie Figueroa, Thalia Ramos, Gabriela Martinez, and Ariel Montero) in technical aspects of the field work required for the project. Two UPRM Professor (Angela Linares and Diego Viteri) and three (Julio Roman, Pedro Ramos and Arialie Figueroa) undergraduates students had the opportunity to attend to the Double Haploid Training and the National Plant Breeder Association Meeting held at Iowa State University. Also, Julio Roman, Pedro Ramos (Scott's Research Program - USDA) and Arialie Figueroa (Lubberstedt's Research program - ISU) spent +8 weeks performing aninternship focused on corn breeding and nursery methods. How have the results been disseminated to communities of interest?Paul Scott presented a seminar in Plant Biology 696, Iowa State University, "Cross Incompatibility in Corn". Ames, Iowa, September 29, 2021. Paul Scott was invited to provide information on gametophyte factors to representatives of the popcorn and seed corn industries in two meeting organized by the American Seed Trade Association, December 8, 2021. Thomas Lubbrerstedtpresented a seminar entitled "Hybrid Horizons" atthe Texas A&M plant breeingsymposiumam,Febrary 7, 2022. Thomas Lubberstedt presented at the EUCARPIA Maize & Sorghum conferencein Belgrade, Serbia,"Recent advances in maize doubled haploid technology", June 2, 2022 When in Puerto Rico to pollinate our winter nursery, Thomas Lubberstedt presenteda seminar on douple haploid technology and the science behind the technology to the staff and students involved in the winter nursery activities What do you plan to do during the next reporting period to accomplish the goals?We will intermate selected inbreds with the SHGD trait to create the male and female popuations required for our rapid cycle breeding program. We will also develop genomic selection models based on our genotype and phenotype data. In addition, we will begin to develop genomic prediction models for triple cross hybrids. We will continue to collect multi-location performance data on lines of interest in order to build more robust genomic prediction models. Next year, we will also initiate our outreach program by holding an organic corn breeding boot camp at our winter nursery site in Lajas, Puerto Rico.

Impacts
What was accomplished under these goals? The COOP project proposes a two-generation rapid cycling breeding scheme, based on crosses between marker-selected haploid plants in the first generation and haploid induction in the second. Sufficient male and female fertility restoration in haploids with the spontaneous haploid genome doubling (SHGD) trait is a prerequisite. During the summer 2022 season, haploids generated in a background derived from the BS39 population with added SHGD ability were grown in two separate blocks. While one set was strictly self-pollinated, as many as possible cross-pollinations were attempted in the other set, using each haploid only once as a male. Seed set in cross-pollinations was with 65% of the attempted pollinations higher as in strict self-pollinations (54%), as wide anther-silking intervals were not a restricting factor in the crosses. Depending on the number of seed produced per ear, the harvested ears were divided in five groups (1: 1-9 seeds, 2: 10-19 seeds. 3: 20-30 seeds, 4: 30-79 seeds and 5: 80+ seeds). A larger percentage of the ears generated in crosses fell into the groups with less than 20 seed per ear, whereas the self-pollinated ears dominated in the groups with higher seed set, probably due to the fact, that in the crosses any plant showing silk was pollinated, independent if it had restored male fertility or not. It was obvious that plants that had restored male fertility also showed increased female fertility. The scoring for the SHGD trait evaluates the levels of restored male fertility, as this is the major bottleneck in DH production. Female fertility restoration usually is sufficient for self-pollinations and was therefore given less attention. The generated F1 between haploids will be induced during the winter, for another cycle of haploid x haploid crosses in the coming season, and a more thorough evaluation of the female side of the equation. For the marker-based selection aspects of the project, we evaluted genotyping platforms and genotyped 100 of our breeding lines with 8,000 molecular markers. We also obtained test-cross hybrid peroformance data at organic and conventional locations in Iowa and Illinois. These test-cross hybrids included a set of three-way cross hybrids designed for seed production in organic conditions.

Publications

  • Type: Journal Articles Status: Published Year Published: 2021 Citation: 1. 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.
  • 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: Journal Articles Status: Published Year Published: 2022 Citation: Sintanaparadee, P., Dermail, A., L�bberstedt, T., Lertrat, K., Chankaew, S., Suriharn, K. (2022) Seasonal variation of tropical savanna alters agronomic adaptation of Stock 6-derived inducer lines. Plants 11, 2902. https://doi.org/10.3390/plants11212902
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Fakude, M., Frei, U.K, Ganal, M.W, Bohn, M.O., Scott, M.P and Lubberstedt, T.L., 2022, Incorporating Doubled Haploid technology for more efficient organic corn breeding?, Poster presented at the National Association of Plant Breeders Annual meeting, Ames, Iowa, August 8,2022.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Bapat, A., Moran Lauter, A.N., Scott, M.P. (2022), Investigations into the genetic structure of Ga1 locus in maize, Poster presented at the National Association of Plant Breeders Annual meeting, Ames, Iowa, August 8,2022.


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

Outputs
Target Audience:We primarily reached scientists and students with interest in organic agriculture, plant breeding and genetics with our activities in this reporting period. Benefits of the work extend to farmers who grow organic corn and consumers who consume organic products based on corn such as meat, eggs, milk and corn-based food products. Changes/Problems:Covid-19 presented a serious challenge to the project, limiting our ability to carry out research and present results. By careful prioritization of research activities we were able to keep the research objectives on schedule. Our outreach plan was to host a Corn Breeding Boot Camp at our winter nursery site in Puerto Rico. Becuase of the pandemic, we were forced to cancel the boot camp activities planned for the first two years of the grant. We will hold the remaining Boot Camp activies as planned if it can be done safely according to applicalble guidelines. We will consider requesting a no-cost extension at the end of the grant to hold one of the missed Boot Camps. What opportunities for training and professional development has the project provided?Graduate students Mercy Fakude (ISU), Chris Mujjabi (UIUC), Shelly Kinney (ISU) and Amruta Bapat (ISU) participated in the research project. AB attended the 2021 virtual Maize Genetics Conference and presented a scientific poster to colleagues at the meeting. She attended the Virtual Corn Breeding Research Meeting (February 18-17, 2021) as well. The work performed for the project will be part of the dissertation research required for these student's degree programs. We also trained undergraduate researcher Hannah Clubb in technical aspects of the field work required for the project. Four virtual project meetings were held to ensure project goals are clear to all participants, to develop plans and to present data related to the project. Students received individual training from the PIs and senior project members on their specific research objectives as well. How have the results been disseminated to communities of interest?Graduate student Amruta Bapat attended the 2021 virtual Maize Genetics Conference (March 8-12, 2021) and presented a scientific poster entitled "Determining functional interactions between pectinmethylesterases encoded by the cross-incompatibility locus, Ga1" to colleagues at the meeting. Paul Scott and Thomas Lubberstedt virtually attneded the Zemun Polje research confernece (Belgrade, Serbia) and presented talks about gametophyic incompatibility systems and using doubled haploids in maize breeding, respectively. We maintained communication with interested stakeholders through informal interactions by e-mail and phone. What do you plan to do during the next reporting period to accomplish the goals?We will collect genotypic and phenotypic data required for genomic selection as required by the rapid cycle breeding program and make initial models to predict the individuals with the best predictedbreeding values. In addition, we'll advance the male and female breeding cycles using double haploid technology to generate inbred lines for the next cycle of breeding. We'll continue to evalate triple-cross hybrids and high yielding inbred lines for their potential as seed parents in organic seed production systems.

Impacts
What was accomplished under these goals? This year, we selected germplasm and made crosses to initaiate the rapid cycling breeding plan described in the proposal. Thisbreeding program utiliizes separate breeding populations for male and female parent lines of new hybrids to be tested for performance in organic production systems. The male populaiton is based on BS39cyc-DH lines and already contains the genes forspontaneus haploid genome doubling. The Ga1-S allele that confers exclusion of unwanted pollen was crossed into this population as well. On the female side,we crossed the required genes intogenetic backgrounds to be used in the breeding program.We developed a genotyping plan and obtained genotypes of 100 individuals from TraitGenetics to verify that the data is suitable genomic selection as will be reauired in the rapid cycling breeding program. Toward the goal of developing inbreds that are well suited to organic seed production systems,seedfor new three way hybrids and high-yielding inbred lines were produced to be evaluated for their utility as seed parents in organic seed production systems.We tested germplasm in Puerto Rico to verify we can make the crosses we need there. Breeding populations were advanced and hybrids were test in joint yield trials carried out in Illinois and Iowa. An unexpected outcome of this work was that the high insect pressure in Puerto Rico allowed selection for insect resistant varieties, including an doubled haploid inducer line that may prove valuable for use in organic enviroments which typically have increasedinsect pressure.

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., Lübberstedt, 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: 2020 Citation: Gustin, J.L., Frei, U.K., Baier, J., Armstrong, P., Lübberstedt, T., Settles, A.M. (2020) Maize haploid classification using Single Kernel Near-Infrared Spectroscopy. Plant Breeding 139:1103-1112 DOI: 10.1111/pbr.12857
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Trampe, B., Goncalves, I., Frei, U.K., Ren, J., Chen, S., Lübberstedt, T. (2020) QTL mapping of Spontaneous Haploid Genome Doubling using Genotype by Sequencing Approach in maize. Theor. Appl. Genet. 133:2131-2140
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Costa Almeida, V., Trentin, H.U., Frei, U.K., Lübberstedt, T. (2020) Genomic prediction in maternal haploid induction in maize. The Plant Genome 13:e20014 DOI: 10.1002/tpg2.20014
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: De la Fuente, G., Frei, U.K., Trampe, B., Ren, J., Bohn, M.O., Yana, N., Verzegnazzi, A., Murray, S.C., Lübberstedt, T. (2020) A diallel analysis of a maize donor population response to in vivo maternal haploid induction. II: Spontaneous Haploid Genome Doubling. Crop Sci. 60: 873-882 DOI: 10.1002/csc2.20021
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Qu, Y., Wu, P., Ren, J., Liu, Z., Tang, J., Lübberstedt, T., Chen, S., Li, H. (2020) Mapping of QTL for kernel abortion caused by in vivo haploid induction in maize (Zea mays L.). PloS One 15: e0228411
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Boerman, N.A., Frei, U.K., Lübberstedt, T. (2020) Impact of Spontaneous Haploid Genome Doubling in Maize Breeding. Plants 9: 369
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Trentin, H.U., Frei, U.K., Lübberstedt, T. (2020) Maternal haploid inducer development in maize. Plants 9: 614 doi:10.3390/plants9050614
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Ren, J., Boerman, N., Liu, R., Frei, U.K., Trampe, B., Vanous, K., Chen, S., Lübberstedt, T. (2020) QTL mapping of spontaneous haploid genome doubling. Plant Sci. 293:110337 https://doi.org/10.1016/j.plantsci.2019.110337
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Lu, Y., Moran Lauter, A., Makkena, S., Scott, M.P., Evans, M.M. 2020. Insights into the molecular control of cross-incompatibility in Zea mays. Plant Reproduction. 33: 117-128.