Source: The Society for In Vitro Biology submitted to
NEW TECHNOLOGIES AND ADVANCES FOR THE DEVELOPMENT OF CROP SPECIES TO ADDRESS GLOBAL CLIMATE AND NUTRITION CHALLENGES
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
Reporting Frequency
Annual
Accession No.
1032035
Grant No.
2024-67013-42195
Cumulative Award Amt.
$20,000.00
Proposal No.
2023-11744
Multistate No.
(N/A)
Project Start Date
Jun 1, 2024
Project End Date
Oct 14, 2024
Grant Year
2024
Program Code
[A1141]- Plant Health and Production and Plant Products: Plant Breeding for Agricultural Production
Project Director
Schultz, M. G.
Recipient Organization
The Society for In Vitro Biology
514 Daniels Street
Raleigh,NC 27605
Performing Department
(N/A)
Non Technical Summary
The concurrent integration of biotechnologies (e.g., transgene, gene editing, double haploid technique, synthetic apomixis) into breeding programs is instrumental in increasing the rate of genetic gain necessary to keep the pace with growing food demand, changing climates and evolving pests and diseases.The deployment of heterosis in crop breeding programs represented a breakthrough; however, since offspring cannot maintain their heterosis due to genetic separation of traits, new hybrid seeds need to be produced annually, which is laborious, expensive and not feasible in a number of important crop species, including wheat and soybean. Synthetic apomixis offers a solution to the inability to preserve heterosis. A number of alternative strategies to the conventional transformation system have been established to overcome current challenges associated with plant transformation to enable DNA-independent editing (transgene-free) using preassembled Cas protein and gRNA(s) ribonucleoproteins. Genome editing in woody/ornamental plants poses a unique set of challenges distinguishing it from annual crops causing similar labor intensive and time-consuming evaluation. The conference grant's goal is to provide attendees with the most current developments of genome modification technologies made possible by improvement of gene editing tools delivery, plant transformation processes optimization and recent advances in the understanding of synthetic apomixis systems. The integration of conventional/molecular breeding techniques with genome editing approaches could address current limitations encountered during crop improvement further enabling the investigation of gene regulation networks, de novo domestication of new crops from wild relatives, the introduction of new favorable traits and the disruption of genetic linkages between traits.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2012410108120%
2012499108020%
2032410108110%
2042410108020%
2042499108120%
2014099108110%
Goals / Objectives
The concurrent integration of biotechnologies (e.g., transgene, gene editing, double haploid technique, and synthetic apomixis) into breeding programs is instrumental in increasing the rate of genetic gain necessary to keep the pace with growing food demand, changing climates and evolving pests and diseases. The deployment of heterosis (or hybrid vigor) in crop breeding programs represented a breakthrough however, since offspring cannot maintain their heterosis due to genetic separation of traits, new hybrid seeds need to be produced annually, which is laborious, expensive and not feasible in a number of important crop species, including wheat and soybean (Hochholdinger and Baldauf, 2018). Apomixis (asexual seed formation) is a natural phenomenon in 400 species (or ca. 0.1% of all angiosperm species) belonging to 293 genera (Hojsgaard et al., 2014) that results in progeny that are mostly of maternal genotype. The introduction of apomixis into non-apomictic staple crops could offer significant agronomic benefits through the production of clonal seeds reducing the cost of hybrid seed production (Liu et al., 2013). Two feasible approaches for achieving this goal have been pursued: introgression of apomictic loci from closely related apomictic species (LeBlanc et al., 2009) and engineering synthetic apomixis (Underwood and Mercier, 2022). The successful engineering of apomixis in sexual plants requires 1) omission of the meiosis (apomeiosis), 2) the development of an unfertilized egg cell (parthenogenesis) and 3) a functional endosperm. Although synthetic apomixis has been successfully achieved in rice, the frequency of formation of synthetic apomictic seeds and their genetic stability is still too low for successful implementation of this technology in global farming systems. Further understanding of gene sequences and genome structure, required to activate apomixis, is a key element to harness its potential in the development of self-reproducing hybrids and the advancements in next-generation sequencing (NGS) technologies provide an invaluable resource for a more accurate study of gene functions and interactions in apomictic genomes against sexual genomes. NGS progresses also is accelerating the development and application of genome editing technologies (ZFNs, TALENs and CRISPR-Cas systems) that in the last two decades have emerged as a promising platform for gene knockouts, targeted gene insertions, precise base substitutions, and multiplexing (Pixley et al. 2022, Abdallah et al. 2021). Genome editing (GE) technologies have already been successfully demonstrated to improve traits such as disease and herbicide resistance, nutritional and other quality characteristics in commercial crops (https://www.eu-sage.eu/genome-search). Production of gene edited plants generally involves 3 steps 1) delivery of gene editing reagents via transformation of plant cells, 2) in vitro culture, and 3) regeneration of edited plants. Most of the current transformation protocols rely on inefficient reagent delivery systems and low-throughput tissue culture- processes optimized for a limited number of experimental genotypes. Given these limitations, there is an immense need to develop broadly applicable and innovative plant delivery and transformation protocols. This is even more necessary in woody and ornamental species due to the physical barriers associated with the structure of the plants. Present delivery techniques predominantly rely on Agrobacterium-mediated transformation and particle bombardment. This method offers several benefits, including cost-effectiveness, ease of use, and the potential to deliver multiple T-DNAs into plant cells. A number of alternative strategies to the conventional transformation system, (i.e., Agrobacterium and particle bombardment) have been established to overcome current challenges associated with plant transformation and regeneration (Laforest et al, 2022) and also to enable DNA-independent editing (transgene-free) using preassembled Cas protein and gRNA(s) ribonucleoproteins (RNPs).Genome editing in woody and ornamental plants poses a unique set of challenges that distinguishes it from the editing of annual crops primarily due to their complex biology and extended growth period (Min et al., 2022). Woody and ornamental plants often have large and complex genomes with numerous repetitive sequences, non-coding regions, and structural variations making more challenging the identification and targeting of specific genes for editing (Yin, et al., 2021). Furthermore, many woody and ornamental plants are highly heterozygous, meaning they have two different alleles for a given gene and some are polyploid, possessing multiple copies of each chromosome. Due to their long juvenile phases the evaluation of the outcomes of both traditional and new breeding technologies is time consuming and labor intense.The specific objectives for the proposal are to:To keep the attendees of the 2024 World Congress on In Vitro Biology updated with the latest advancements in genome modification technologies. This includes improvements in the delivery of gene editing tools, optimization of plant transformation processes, and recent progress in understanding synthetic apomixis systems To educate participants about the recent progress in developing efficient apomictic systems for agriculture, bridging the gap between research and practical applications To share the latest advancements in the development of plant transformation methods, including those involving Agrobacterium.To demonstrate, through shared experiences, how both traditional and new breeding technologies can be utilized to enhance ornamental species.Furthermore, to enhance outreach to support minority and underserved students and scientists, we will offer reduced cost registration and virtual opportunities to access the content.
Project Methods
The 2024 World Congress on In Vitro Biology will offer symposia with the goal to share the most current information on available gene editing technologies and plant interactions in association with traditional plant breeding programs. These topics can address harnessing apomixis to enable the efficient creation of self-reproducing hybrids capable of maintaining heterosis, creating better alternatives to low efficiency of Agrobacterium mediated transformation, and new breeding technologies which offer effective solutions to overcome obstacles. We have invited speakers from public and private programs across the world to share their perspective, experience, and knowledge in plant gene and editing delivery, plant breeding techniques, accelerated crop development, and synthetic apoximis. Speakers will cover several areas including opportunities and challenges for realizing synthetic apomixis in crops, dna-free delivery, plant-microbial ecosystems enhancing plant functions such as biotic/abiotic stresses, engineering agrobacterium to improve plant transformation and regeneration, simultaneous transformation and editing of multiple lines in soybean and maize, non-integrating wuschel2-assited transformation and gene editing of recalcitrant maize, bioengineering and molecular breeding of native woody ornamentals and ornamentals, building new genetic model systems in the sunflower family, and cytogenics. Speakers will address how these approaches generate impactful applications in agriculture and fundamental plant biology research.

Progress 06/01/24 to 10/14/24

Outputs
Target Audience:Since its establishment in 1946, the Society for In Vitro Biology (SIVB) has been committed to fostering the exchange of knowledge of in vitro biology of cells, tissues, and organs from both plants and animals (including humans). The membership of this professional society includes many of the leaders and pioneers of tissue culture and in vitro biology. Participants in the 2024 World Congress on In Vitro Biology were representative of over 27 countries including the USA and featured scientists working in academia, government, and industry; as well as students and postdoctoral fellows whose research bridges all aspects of in vitro biology and biotechnology for the benefit of plant, human, and animal subjects. In an ongoing effort to enhance accessibility, SIVB continued to offer much of the meeting's content in a hybrid online format, enabling scientists who faced financial or travel limitations to participate in the scientific events. SIVB firmly believes that today's students are the future of in vitro biology, and to support this belief the Society actively encourages the continued growth of emerging researchers and scientists. This commitment was reflected in the Society's outreach efforts, which included offering free registration to students worldwide for the World Congress and integrating student meetings and workshops into the scientific program. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?By presenting the latest key advancements in gene and apomixis, attendees and their laboratories will be better equipped to utilize innovative methods to accelerate their breeding programs. This will help address productivity and nutritional challenges associated with the growing global population, changing climate, and limited resources. With access to new and novel trait and delivery technologies for plants, they will gain significant benefits in their agricultural and fundamental plant biology research. How have the results been disseminated to communities of interest?Presentations were delivered live at the meeting and recorded at the same time. The recordings were shared virtually both as part of the On-Demand program (through September 30, 2024) and content of the Society's YouTube channel, allowing global participants to view and re-watch them multiple times. This capability enabled attendees to gain a deeper understanding of the research presented, enhancing their knowledge of plant breeding, and helping addressing challenges in their work. As a result, we were able to educate and support not only the 629 international scientists, researchers and students who attended the meeting in person, but also their faculty, labs, and communities who benefit from this shared knowledge. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The World Congress program provided the latest updates on crop and woody/ornamental plant improvement through genome modification technologies. These advancements were made possible by enhanced gene editing tool delivery, optimized plant transformation processes, and recent progress in understanding synthetic apomixis systems. Speakers from public and private institutions worldwide presented cutting-edge research. 1. The first session entitled "Unlocking the power of synthetic apomixis: a paradigm shift in plant breeding" convened by Todd J. Jones, Corteva Agriscience, and Heqiang Huo, University of Florida, focused on recent advances in developing efficient apomictic systems for agriculture. Apomixis can stabilize and propagate any genotype, including F1 hybrids, offering revolutionary potential for plant breeding. It allows for the creation of self-reproducing hybrids that maintain heterosis across generations, even in non-hybrid crops. In species without natural apomicts, synthetic apomixis--engineering plants to bypass meiosis, repress recombination, and induce parthenogenesis--shows promise. As of this report, the session has 135 views in the On Demand program. The presentations from this session were: Setting the Stage for Synthetic Apomixis Through Discoveries in Natural Systems presented by Peggy Ozias-Akins, University of GA. Dr. Ozias-Akins gave an update on her research about the identification and functional characterization of a gene for parthenogenesis from Pennisetum squamulatum (PsASGR-BBML). Her lab demonstrated that PsASGR-BBML can induce parthenogenesis and the production of haploid offspring in transgenic sexual pearl millet, rice and maize. Seeding the Future: Enabling Hybrid Crop Propagation Through Clonal Seeds presented by Imtiyaz Khanday, University of CA-Davis reported on a projected able to achieve high-frequency (>95% over three generations) synthetic apomixis in hybrid rice by a single step approach inducing MiMe mutations and egg cell expression of BBM1 apomictic plants maintain the phenotype of the F1 hybrid along successive generations. Hy-Gain: Harnessing Apomixis in Self-reproducing Sorghum Hybrids for Smallholder Farmers in Sub-Saharan Africa presented by Marissa Simon, Corteva Agriscience provided an update on the Hy-Gain project, funded by the Bill & Melinda Gates Foundation. The goal is to create self-reproducing hybrids in sorghum and cowpea, allowing smallholder farmers to save and grow seeds without losing yield or quality. This project involves multiple academic institutions (University of Queensland, University of GA, University of Zurich, and Langebio, Cinvestav) and Corteva. By combining Mitosis instead of Meiosis (MiMe) and spontaneous, fertilization-independent embryo development, they demonstrated a self-reproducing hybrid line in sorghum. 2. The Second session entitled "Advances in plant transformation methods to accelerate crop improvement," was convened by Raj Deepika Chauhan, Pairwise, Heqiang Huo, University of FL, Yurong Chen, Bayer US - Crop Science, and Peizhen Yang, Bayer US - Crop Science and covered recent advances in plant transformation method developments, including Agrobacterium engineering, simultaneous delivery to multiple germplasms, and recovery of transgene free gene edited plants. As of report submission, this session has received a total of 125 views in the On Demand program. The presentations from this session were: Engineering Agrobacterium to Improve Plant Transformation and Regeneration presented by Kiran Mysore, OK State University. Dr. Mysore gave an update on his strategy to increase Agrobacterium mediated transformation in wheat, alfalfa and switchgrass by engineering A. tumefaciens with a type III secretion system (T3SS) from Pseudomonas syringae to deliver proteins that suppress plant defense. Simultaneous Transformation and Editing of Multiple Lines in Soybean and Maize presented by Michelle Valentine, Bayer US - Crop Science. Dr, Valentine reported on simultaneous transformation and editing of many genotypes followed by re-identification through genotyping after plant regeneration. The system called TREDMIL (Transformation and Editing of Mixed Lines) produced transformed individuals representing 97% mixed elite genotypes in soybean; and 55% mixed maize female and male elite inbred genotypes. Non-integrating Wuschel2-assited Transformation and Gene Editing of Recalcitrant Maize B73 presented by Keunsub Lee, IA State University. Dr. Lee shared about his lab non-integrating Wus2 (NIW) T-DNA vector-assisted transformation method that uses two Agrobacterium strains: one carrying a gene-of-interest (GOI) construct and the other providing an NIW construct at a 9:1 ratio. The system was successfully deployed for both B104 and B73 to produce transgene-free gene-edited plants. 3. The third and final session entitled "Integrating new breeding technologies and traditional approaches for advancing ornamental crops" convened by Jon Mahoney, Ball Horticultural Company, and Eva Konecna, Ball Horticultural Company and showcased both traditional and new breeding technologies useful to improve ornamental species. As report submission, this session has received a total of 70 views in the On Demand program. The presentations from this session were: Bioengineering and Molecular Breeding of Native Woody Ornamentals presented by H. Dayton Wilde, University of GA. His presentation focused on Rhododendron canescens, a native azalea, aiming to develop a compact form for urban landscapes. He collected DNA from 290 R. canescens plants in Georgia, using genotyping-by-sequencing to identify genetic variation and created DNA libraries for exon capture and sequencing of genes related to plant architecture, revealing 40 high-quality SNPs to breed more compact R. canescens phenotypes. Head Start: Building New Genetic Model Systems in the Sunflower Family presented by Daniel Jones, Auburn University. Dr. Jones highlighted the need for genetic model systems to study gene functions across diverse species, including the sunflower family (Asteraceae), which has around 30,000 species. This family's success is linked to the evolution of the capitulum, a compact inflorescence. His presentation focused on how changes in developmental programs, especially stem cell maintenance, have influenced floral evolution in Asteraceae. Using comparative genomics and developmental transcriptomics, his team aims to identify and test regulatory networks involved in capitulum development. They use models like lettuce, marigold, and Bidens to study traits affecting reproductive success. Characterization of Transposon-induced Snapdragon Mutants with Improved Anthocyanin Biosynthesis and Stress Tolerance presented by Heqiang Huo, University of FL. Dr. Huo presented a study using a temperature-dependent transposon-induced mutagenesis system to create two snapdragon mutant lines with enhanced anthocyanin accumulation. One mutant had strong red pigmentation on leaves and stems, while the other had red pigmentation mainly on leaf surfaces. Genetic analysis revealed both mutants are dominant. Cytogenetics: Old-fashioned Technologies for Ornamental Crop Improvement presented by Hsuan Chen, NCSU. Dr. Chen's presentation was about Cytogenetics, a traditional breeding approach that remains important in ornamental crop improvement. It involves methods like ploidy manipulation, aneuploidization, and haploid induction to facilitate interspecific hybridization and overcome related barriers. He presented examples, including using ploidy manipulation inArachisto integrate beneficial genes from wild species. Dr. Chen presented another case involving using unreduced gametes from an interspecificHibiscushybrid to produce a polyploid aneuploid population for breeding purposes. These strategies help introduce new traits and enhance genetic diversity, making them valuable for developing improved cultivars in ornamental horticulture.

Publications

  • Type: Journal Articles Status: Awaiting Publication Year Published: 2024 Citation: In Vitro Cellular and Developmental Biology - Animal, Volume 60, Issue Proceedings, Fall 2024