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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

2020 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: Seven new Germplasm Enhancement of Maize (GEM) lines were released and distributed to ~30 GEM cooperators for the 2020 planting season. 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 collaborators and added to the GEM website. Related to Objective 1: The 2020 spring season was cool but did not delay field preparation or the start of nursery and yield trial planting. Impact of the Covid-19 pandemic restricted the speed and efficiency of seed processing and preparation. Program plans were modified to accommodate health and safety guidelines of social distancing and in response to anticipated field labor availability. Field research nursery material was prioritized and reduced to align with labor availability and health guidelines. Primary reductions were made in the hand pollinated nursery. Use of the flowering induction shade house to make new tropical x temperate breeding crosses was canceled for 2020 in response to labor concerns. Isolated crossing block nurseries planned for Ames are critical for the generation of hybrids used to test and evaluate segregating lines. These nurseries require minimal labor during the growing season, are not easily replaced at alternate site winter locations, and were planted in May. Yield trial planting started on schedule and was completed by May 11. Approximately 17,200 yield trial plots were planted in 2020 at 16 locations with the combined effort of ARS researchers in Ames, Iowa, and ten private cooperators across the Midwestern U.S. This facilitates evaluation of GEM hybrids in a wider geographic region with more effective resource utilization. Summarized 2019 yield trial data was shared with collaborators and made available on the GEM website. Two hundred fifty-two hybrids out of 2,100 GEM entries exceeded the mean yield of the check hybrids in Midwest trials in 2019. Of the 252 hybrids that exceeded the mean, 188 were from first year trials, and 64 from second 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 will include six top performing GEM lines from the first top line test completed in 2018 and twenty-four 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. The resulting hybrids will be evaluated within each company’s yield trial system in 2021 and again in 2022. Data will be returned to ARS researchers at Ames, Iowa, and analyzed for general combining ability (GCA) and specific combining ability (SCA) analysis 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, and aflatoxin resistance with support from U.S. private cooperators in California, Iowa, Illinois, Michigan, and Nebraska; 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 2019 were shared with collaborators and added to the GEM website. Related to Objective 2: Evaluation of breeding crosses is an important objective to determine adaptability and prioritization of exotic material for development. In 2020, 100 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 116 entry set of 50% tropical breeding crosses were planted by ARS researchers in Raleigh, North Carolina, and one cooperator, for phenotypic evaluations. A final set of 174 breeding crosses produced in winter nursery was planted at the Ames, Iowa, location for evaluation. Evaluation information associated with the 116, 50% tropical breeding crosses and 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. Progenies of several breeding crosses distributed to GEM cooperators in previous seasons were returned for 2020 planting. Ten populations were advanced to the S1 (self-pollinated once) generation with over 150 ears returned for each. Another cooperator advanced 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. Summarized phenotypic observations of breeding crosses evaluated in summer of 2019 were shared among collaborators, and superior candidates identified for continued development. Sixteen of these breeding crosses were included in GEM nursery sets at the Ames, Iowa, location. Eighteen breeding crosses were distributed to ten GEM cooperators for planting in 2020 as part of their in-kind support. This number was reduced from the planned thirty breeding crosses in response to the Covid-19 response impact on labor availability and health concerns. The populations sent to seven cooperators will be self-pollinated and a sample of each selected ear will be returned to the GEM program for 2020 nurseries. The remaining three cooperators 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 2022. Lines selected based on yield trial results will be returned to the GEM program in late 2022. Tropical land races and inbred lines require the use of a photoperiod control (shade) structure to reduce day length to 12 hours or less, necessary 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 2020 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 2021. The breeding cross focus has shifted to creation of crosses of previously released GEM lines for germplasm refinement and enhancement, in order to release improved, second cycle lines desired by GEM cooperators. Additional crossing of previously generated 50% tropical populations to generate new 25% tropical breeding cross combinations is also scheduled for 2020. A collaboration with Iowa State University 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. Related to Objective 3: Twenty GEM lines released in 2015, 2016, and 2018 were deposited in the National Plant Germplasm System (NPGS). Thirty of the allelic diversity program doubled haploid BGEM lines (jointly released by Iowa State University (ISU) and ARS) were also deposited in the NPGS. Thirty-three candidate lines for BGEM release have received their final code designations and are in the process of joint release by ARS and ISU. A summary of the lines selected for release will be communicated to collaborators and announced on the GEM website later this year. 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 due to Covid-19 pandemic concerns and labor limitations. Seed increase of the new candidates has been postponed to 2021.

1. Germplasm donation received. Bayer Crop Science initiated a Discovery breeding project in 2016 focused on adapting 31 land races to the U.S. central corn belt for the purpose of donating the resulting lines to the GEM Project. Two to four accessions of each land race were selected from the NPGS collection through consultation with ARS scientists in Ames, Iowa, and each were crossed to one stiff stalk (SS) and one non-stiff stalk (NSS) 105 RM elite Bayer line. Lines were selected for early flowering and recombined. Resulting lines representing 50%, 62.5%, and 75% land race heritage were selected for flowering at Huxley, Iowa. Ears generated in this project were reviewed and selected for advancement jointly by an ARS scientist in Ames, Iowa, and Bayer corn breeders. Bayer Crop Science donated 1,990 single ear selections (935 SS, 1,055 NSS) to the GEM Project in May 2020 for research and line development. The lines have been provided with no research or breeding restrictions and will be used in the GEM breeding program to generate candidates for public release, providing additional diverse genetics and traits.

2. Genomic selection project. Modern breeding progress can be accelerated via use of genomic information and predictive modeling to select germplasm of value for breeding. Genomic prediction (genome wide selection, GWS) has been used for over a decade in the U.S. seed industry. The Germplasm Enhancement of Maize (GEM) breeding process has been based on traditional breeding methods, some doubled haploid breeding, and multiple genetic studies have been conducted on released GEM lines, but genetic marker assisted breeding has not been employed. Implementation of these tools and their evaluation could accelerate breeding progress. Through discussions in the December 2019 Technical Steering Group (TSG) meeting, one industry cooperator offered a collaborative project to utilize their large and diverse training sets, automated training workflows, streamlined lab processes, and connected databases as an extension of their in-kind support to develop GWS models and thereby increase the germplasm evaluated and advanced within the GEM breeding program. The cooperator committed to marker evaluation and analysis of 2,500 genotyping samples per year (split between the Ames, Iowa, and Raleigh, North Carolina, programs). Samples of lines previously phenotypically evaluated and associated information were submitted to start model building and initiate the process.