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ARS Home » Midwest Area » Ames, Iowa » Plant Introduction Research » Research » Research Project #434247

Research Project: Genetic Enhancement of Maize for U.S. Food Security and Agricultural Profitability

Location: Plant Introduction Research

2022 Annual Report

Objective 1: Manage and coordinate the Midwestern component of a multi-year, multi-site, cooperative program of maize genetic resource evaluation, genetic enhancement, inbred line development, and information sharing which will broaden the genetic base for U.S. maize. Sub-objectives: 1A. Coordinate and manage in-kind support for evaluation, development, and genetic enhancement of GEM germplasm. 1B. Manage GEM field nurseries, germplasm exchange, and seed inventories to ensure that new sources of germplasm and information reach stakeholders annually. 1C. Implement database evaluation enhancements to identify GEM lines best suited for particular uses. Objective 2: Evaluate a wide diversity of temperate, subtropical, and tropical maize genetic resources for adaptation, yield, resistance to ear, stalk, and foliar diseases, tolerance to environmental extremes, and selected value-added, product quality traits. Record and disseminate evaluation data via the GEM database, GEM website, GRIN-Global and other data sources. Sub-objectives: 2A. Evaluate 50-100 maize exotic breeding crosses and new sources of exotic germplasm annually for their adaptation to Midwestern U.S.; identify favorable agronomic traits; choose and prioritize germplasm for incorporation into breeding programs. 2B. With public and private-sector cooperators, evaluate maize germplasm for globally important leaf and stalk rot diseases, reduced ear mold and mycotoxin production, abiotic stress tolerance, host plant resistance to corn rootworm (CRW), multiple pest resistance for above ground insects, and key value-added traits such as highly digestible starch and resistant starch. Objective 3: Breed and release maize populations and inbred lines with 25% subtropical-tropical/75% temperate pedigrees which contribute to U.S. maize more diverse genetic resistance to diseases, tolerance to environmental extremes, higher yield, unique product qualities, other valuable new traits, or which enable maize trait analysis and allelic diversity research. Sub-objectives: 3A. Develop and release a novel set of “adapted” maize races resulting from the allelic diversity (AD) project as tools for gene discovery and genomic research. 3B. Develop and release germplasm with key traits, such as reduced mycotoxin level and biotic stress resistance. Disseminate germplasm information. 3C. Evaluate released lines to determine exotic genome contributions and identify unique disease and insect resistance genes.

Obj 1: Extensive collaborations with the private, public and international sectors will be initiated to broaden the germplasm base and develop useful germplasm. ARS will serve as liaison for collaborators and the Technical Steering Group (TSG), selects germplasm, facilitates germplasm acquisition and stakeholder interactions, arranges for in-kind-support, information sharing, technology transfer in the form of new germplasm and associated information, and establishes and manages nurseries and yield trials. Multiple sites will serve nurseries, observations, crossing blocks, yield trials, and stress resistance evaluations. Companies participating in the collaboration will provide proprietary genetic resource crosses and information to facilitate their utilization. Input on sources of germplasm and their attributes, potential new collaborators, and research initiatives will be solicited from project participants and the TSG. Improved website reporting of agronomic and abiotic stress resistance information will be done. Obj 2: Approximately 50-100 breeding crosses will be evaluated in multiple environments and ~30 selected annually for development in Ames or collaborator nurseries. Exotic maize breeding crosses and new sources of exotic germplasm will be evaluated for important leaf and stalk rot diseases, reduced ear mold and mycotoxin production, abiotic stress tolerance, and host plant resistance to corn rootworm and above ground insects. Trait evaluations will be conducted in favorable selection environments for traits of interest. Breeding material will be evaluated for value added traits related to grain quality. Evaluation data will be stored in the GEM database. Research findings are shared via the public GEM website and scientific publications. Obj 3: Germplasm will be developed primarily from 25% tropical/75% temperate breeding crosses. Breeding crosses will also be developed from tropical landrace accesses or modern tropical inbreds crossed with elite temperate germplasm resources, from GEM x GEM releases, and other models to maximize useful exotic germplasm contributions. Agronomic performance testing will be done in house and collaboratively. A dual line development track will release 1) conventionally derived lines which have been tested and selected for agronomic and/or stress tolerance traits, and 2) lines developed purely for the purpose of capturing allelic diversity (AD) from exotic donor genomes that do not undergo selection for agronomic or other traits. The AD project lines are to represent all of the nearly 300 landraces, with an average of 25% of their genome derived from exotic introgressions and 75% from a recurrent, US-adapted parent. Following release, lines will be genotyped and molecular marker information provided to help identify useful genetics for disease and insect resistance genes. Two years post-release, conventionally derived lines will be deposited in the National Plant Germplasm System. Incorporation of the AD lines into the NPGS collection depends on their value, as determined by the research community. Research findings will guide criteria for their inclusion; many will be incorporated over time.

Progress Report
Related to Objectives 1 and 3: Four new Germplasm Enhancement of Maize (GEM) lines were identified for 2022 release and distributed to GEM Cooperators. All lines were tested for adventitious presence (AP) of genetically engineered (GE) traits before distribution. Data associated with newly released line phenotypes, disease reactions, and yield trial evaluations were shared with cooperators in the virtual annual meeting in December. Related to Objective 1: The 2022 spring season was cool and wet resulting in serious field preparation and planting delays. On-site work restrictions associated with the Covid-19 pandemic negatively impacted the speed and efficiency of seed processing and preparation. Adjustments to seed processing automation and seed counting equipment acquired in 2020 compensated well for labor and pandemic restrictions. Process changes improved efficiency and reduced labor requirements which kept shelling and seed counting operations on schedule. The updates helped to accommodate health and safety guidelines of social distancing while also improving seed quality. Field research nursery material was prioritized and sized to align with labor availability. Use of the flowering induction shade house to make new tropical x temperate breeding crosses was canceled for 2022 in response to labor concerns. Isolated crossing nurseries critical for the generation of hybrids used to test and evaluate segregating lines were outsourced to a third-party contractor. Yield trial planting did not start until May 11. Rain and equipment related delays pushed yield trial planting completion to May 22, 2022. Approximately 11,466 yield trial plots were planted in 2022 at 14 locations with the combined effort of ARS and eight private cooperators across the Midwestern U.S. This facilitates evaluation of GEM hybrids in a wider geographic region with more effective resource utilization. Summarized 2021 yield trial data was shared with collaborators at the 2021 Cooperators Meeting held using a virtual format on December 16, 2021. One hundred twenty-five hybrids out of 1,440 GEM entries exceeded the mean yield of the check hybrids in Midwest trials in 2021. Of the 125 hybrids that exceeded the mean, all came from first year trials. Discussions with the GEM Technical Steering Group (TSG) in December of 2019, led to a new GEM top line yield trial project. Entries in this project include six top performing GEM lines from the first top line test completed in 2018 and 24 GEM lines released since 2015 identified by the Ames, Iowa and Raleigh, North Carolina programs. Seed was distributed to each of six private industry members of the TSG. The lines will be crossed to each company’s elite, proprietary tester lines in 2020 summer nurseries. A derecho event in August 2020 heavily damaged or destroyed hybrid seed production for three cooperators resulting in a program delay. Cooperators unaffected by summer storms are evaluating the resulting hybrids within their company yield trial system in 2021 and again in 2022. Hybrid evaluations across the full set of cooperators will not be possible until 2022. Data will be returned to the Ames, Iowa GEM Coordinator and analyzed for general combining ability (GCA) and specific combining ability (SCA) to provide a competitive evaluation of the top GEM lines’ yield trial performance and potential breeding value. Entries for the GEM top line testing system will be updated every two years. Participating seed industry TSG members have committed to make the top line testing system an ongoing part of their in-kind support to GEM. The data will be shared with collaborators and stakeholders at the Annual GEM Cooperators Meeting and on the GEM website. More than 200 GEM pedigrees are being evaluated for Northern Leaf Blight (NLB), Southern Leaf Blight (SLB), Gray Leaf Spot, Goss’s Wilt, Head Smut, Tar Spot, Fusarium ear rot, aflatoxin resistance, and fall armyworm resistance with support from U.S. private and public cooperators in California, Iowa, Illinois, Michigan, and Nebraska; a U.S. public cooperator in Florida; and from ARS scientists in Iowa, Missouri, Mississippi, and North Carolina. International cooperators conducted trials for globally important disease or insect pests in Africa, China, India, and Egypt. International diseases of concern include Maize Lethal Necrosis (MLN), Maize Rough Dwarf Virus (MRDV), Downy Mildew, Southern Rust, Late Wilt (Cephalosporium maydis), Heat Smut, Tar Spot, Pythium and Gibberella stalk rot, and NLB. Summarized disease evaluations from summer 2021 were shared with collaborators and will be added to the updated GEM website in late 2022. Related to Objective 2: Evaluation of breeding crosses is an important objective to determine adaptability and prioritization of exotic material for development. In 2022, 130 new 25% tropical breeding crosses were planted for evaluation using the in-kind support of three cooperators, and ARS researchers in Ames, Iowa. An additional set of 325 breeding crosses produced in winter nursery was planted at the Ames, Iowa location for evaluation. Evaluation information associated with the over 170, 25% tropical breeding crosses generated in the last year provide critical characterization of tropical land races and inbred lines, necessary to identify the best germplasm options for our temperate breeding program. Summarized phenotypic observations of breeding crosses evaluated in summer of 2021 were shared among collaborators, and superior candidates identified for continued development. Fifty of these breeding crosses were included in the GEM 2021 winter nursery set sent to Mexico and Hawaii. Ten breeding crosses were distributed to six GEM cooperators for planting in 2022 as part of their in-kind support. Encouraging results from the advancement of breeding crosses from the S0 to S1 generation in 2021 winter nurseries resulted in an increased emphasis of this approach. Returning S1 ears were either scheduled for ear-row planting and selection in 2022 or were made into balanced bulks of the returning ears for self-pollination and selection. Selected S2 lines will be scheduled for summer 2023 nurseries for self-pollination and ear-row selection and advancement to the S3 generation. Ten S0 breeding populations were sent to six cooperators will be self-pollinated and a sample of each selected ear will be returned to the GEM program for 2023 nurseries. Three additional cooperators each received two S0 breeding populations that will self-pollinate the populations and top cross selected ears to a proprietary elite tester from their program. The top crosses will be yield tested in 2024. Lines selected based on yield trial results will be returned to the GEM program in late 2024. Progeny of several breeding crosses distributed to GEM cooperators in previous seasons were returned for 2022 planting. Eight populations were advanced to the S1 (self-pollinated once) generation with over 150 ears returned for each. Three cooperators advanced a total of five breeding crosses through their company’s breeding system. The lines generated were top crossed to their own proprietary elite germplasm and yield tested in their system. Data from these trials were provided to the GEM Program and selected top performing lines were returned for advancement to GEM Program for second year yield trials. Tropical land races and inbred lines require the use of a photoperiod control (shade) structure to reduce day length to 12 hours or less, to induce flowering in Ames, Iowa. The effort is highly labor intensive, seven days per week, for six weeks post emergence. Anticipated labor shortages and social distancing guidelines related to the Covid-19 pandemic forced us to cancel the 2021 shade structure program due to the risk of being unable to execute necessary workflows and potentially lose valuable germplasm. The photoperiod control structure program will be activated again in 2022. Additional crossing of previously generated 50% tropical populations to generate new 25% tropical breeding cross combinations is also scheduled for 2022. A collaboration with Iowa State University (ISU) has focused on using phenotypic trait performance, genotypic, and pedigree information associated with doubled haploid germplasm (BGEM lines) released by the project to differentiate between temperate and tropical conserved genome regions, and to compare the nature of well- or poorly adapted BGEM lines. Computational analysis of these with environmental data such as daylength, temperature and thermal time records have proved to be very useful in predicting adaptation. Summarized results from this study have been processed and summarized for publication. The resulting article was submitted for publication. Related to Objective 3: Seven GEM lines released in 2020 were deposited in the National Plant Germplasm System (NPGS). Thirty-three candidate lines that had received final line designation codes and prepared for BGEM 2021 release joint release with ISU were delayed pending formal ISU review. The lines are now scheduled for late 2022 release. A summary of the lines selected for release was communicated to collaborators and the formal announced will be made by late 2022. Two hundred ninety-five candidate lines for BGEM release were originally scheduled for planting, seed increase and final phenotypic notes in 2020, with planned release in early 2021, but were not planted in 2020 or 2021 due to Covid-19 pandemic concerns and labor limitations. Seed increase of the new candidates remains postponed.

1. Incorporation of genomic selection into GEM maize breeding. Genomic prediction (genome wide selection) has been used for over a decade in the U.S. seed industry to speed cultivar development. The Germplasm Enhancement of Maize (GEM) breeding process has been based on traditional breeding methods, but genomic marker assisted breeding has not been employed. Through a collaboration with a seed industry cooperator, seed samples of over 3,000 lines (representing 45 breeding populations) and associated yield trial evaluation data have been submitted for genomic evaluation and refinement of prediction models in 2021 and 2022. Genomic prediction models for the breeding populations show strong yield heritability and prediction accuracy. Heritability and prediction accuracy are lower than expected in elite modern U.S. germplasm but are accurate enough to eliminate low yielding breeding lines prior to costly yield testing. The models were used to select lines for advancement to yield trials predicted to have higher average yield potential than the original population resulting in higher yielding lines for GEM release. Use of this breeding approach increases the efficiency of the GEM line development program through elimination of low yielding segregate lines prior to conducting costly yield trials and release of higher yielding lines for GEM stakeholders.