Biotic Interaction Session 1
SESSION CHAIR: Melissa Mitchum, Department of Plant Pathology, University of Georgia
Soybean bites back: Interspecies transfer of a receptor gene to resist lepidopteran pests
Adam Steinbrenner, Assistant Professor, Department of Biology, University of Washington
Plant defense responses to pests and pathogens require immune receptor genes to activate resistance. We recently identified Inceptin Receptor (INR), a receptor which detects In11, a ubiquitous 11-amino acid peptide in the oral secretions of Lepidopteran larvae (caterpillars). In11 elicits strong anti-herbivore direct and indirect defenses on cowpea, common bean, mung bean, and other legumes, but is inactive on all tested soybean varieties. Comparative genomic analysis revealed that the INR gene is specific to the ~28 my old tribe of Phaseoloid legumes, but is absent in the subtribe Glycininae which includes wild, perennial, and cultivated soy (Glycine sp.), suggesting recent secondary of In11 recognition in critical crop lineages. We hypothesized that restoration the missing INR immune receptor would enhance soybean responses to herbivory. Transgenic lines of Williams 82 (WT) soybean expressing INR from common bean (Phaseolus vulgaris) restored In11 responsiveness measured by rapid In11-induced release of the defense hormone ethylene. Beet armyworm (Spodoptera exigua) larvae reared on a T1 line (segregating for INR) gained 15% less weight than on a separate line lacking the transgene. We will report on ongoing experiments to measure both direct and indirect defenses to herbivory in INR-transgenic soybean lines, including analysis of In11-induced specialized metabolites and plant volatiles. INR provides a potential defense trait for recruitment of natural enemies and induction of endogenous inducible defenses, to augment Bt-based transgenic resistance to Lepidopteran pests.
Beyond the norm: New strategies using native genes for combating virulent soybean cyst nematode populations
Andrew Scaboo, Assistant Professor, Division of Plant Science and Technology, University of Missouri
Andrew M. Scaboo1, Mariola Usovsky1, Clinton G. Meinhardt1, Pawan Basnet1, Anser Mahmood1, Bishnu Dhital1, Alice Nguyen1, Vinavi A. Gamage2, Melissa G. Mitchum2
1Division of Plant Science and Technology, University of Missouri, Columbia, MO 65201, USA.
2Department of Plant Pathology and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, GA, USA.
Breeding for soybean cyst nematode (SCN) resistance that can effectively combat the widespread increase in virulent SCN populations presents a significant challenge. Here, we present our research aimed at unraveling the genetic architecture of SCN resistance conferred by native genes in known resistant germplasm. Quantitative trait loci (QTL) were mapped using PI 90763 as a parent and QTL located on chromosome 18 (rhg1-a) and chromosome 11 (rhg2) were determined to confer SCN resistance to virulent HG 1.2.5.7 populations. The rhg2 gene was then fine-mapped to a 169 Kbp region pinpointing GmSNAP11 as the strongest candidate gene. Additionally, we will present the discovery, validation, and functional characterization of a novel soybean resistance gene, GmSNAP02. We again used unique bi-parental populations to fine-map the precise genomic location, a combination of whole genome resequencing and gene fragment PCR amplifications permitted identification and confirmation of causal haplotypes, and we validated our candidate gene (GmSNAP02) using CRISPR-Cas9 genome editing and demonstrated a gain of resistance in edited plants. Lastly, we conducted a series of genome-wide association studies (GWAS) utilizing germplasm and cultivars within both the University of Missouri soybean breeding programs and the USDA Uniform Soybean Tests – Northern Region. Through these analyses, we decipher the impact of 7 major genetic loci, including three novel loci. Overall, our research offers valuable insight into the landscape of SCN resistance genes and novel loci in U.S. public soybean breeding programs and provides a framework to develop new and improved soybean cultivars with diverse genetic modes of SCN resistance.
Deploying disease resistance genes in a CRISPR edited Disease Super Locus
Jen Jaqueth, Research Scientist, Corteva Agriscience
Disease resistance is one of the top priority traits for farmers. In 2021, US farmers lost 318 million bushels of corn yield to four top fungal diseases: northern leaf blight, southern rust, gray leaf spot and anthracnose stalk rot. This need is expected to increase in the coming years, due to the changing climate that can affect disease patterns and severity of infection. Earlier this year, Corteva announced that we are using a CRISPR gene editing approach to reposition native resistance genes into a single location in the genome. This gene-edited product will harness corn’s native resistance to these four diseases giving farmers a sustainable alternative to fungicides. Most of these disease resistance genes originate from non-US maize varieties, therefore we will be offering US farmers novel sources of disease resistance. While this gene-edited plant breeding approach is initially being applied to corn diseases that most concern North American farmers, it has the potential to be scaled to other crops, incorporate other diseases or be otherwise tailored to specific geographies.
*Nuclear retention of transcripts as regulatory mechanism of protein translation in soybean root and nodule cells
Sutton Tennant, Graduate Student Researcher, Department of Agronomy and Horticulture, University of Nebraska–Lincoln, sutennant@huskers.unl.edu
The central dogma of molecular biology follows a simple path, DNA is transcribed into transcripts in the nucleus, and transcripts are then translated into proteins in the cytosol. However, many studies reported that protein production is not solely impacted by the level of expression of genes, but by many other regulatory processes. The number of studies exploring these post-transcriptional regulatory processes in plants is sparse. Here, combining the use of single-nucleus transcriptomic and high-resolution fluorescent in situ hybridization technologies, we provide a new perspective on the role of the nuclear retention of transcripts as a central mechanism to control RNA biology and the biology of plant cells. The analysis of confocal microscopic images of transcripts at the sub-cellular resolution combined with the use of a specifically designed Image J software package, clearly revealed the differential nuclear retention of transcripts between genes, cell types, and organs of the soybean root and nodule. This work reveals the influence of the sub-compartmentalization of transcripts as another regulatory mechanisms of protein translation and a new understanding of the central dogma of molecular biology.
*Poster selected for oral presentation.
Genetic/Breeding for Output Traits
SESSION CHAIR: Felix Fritschi, Division of Plant Science and Technology, University of Missouri
Determining genetic mechanisms of maturity in North Dakota: expanding the molecular model for MG 00 and 0
Carrie Miranda, Assistant Professor, Department of Plant Sciences, Soybean Breeding Program, North Dakota State University
Production areas of soybean have grown in North Dakota to make it the number one crop in the state however state yield averages are among the lowest in the Midwest. Maturity is one of the most important agronomic traits impacting yield potential. North Dakota is characterized by having a short season length due to frost and is necessary to have early maturing soybean. The predominate maturity groups grown in North Dakota are MG 00 and 0. It is possible to “fine tune” maturity to a region/environment to maximize yield potential. The major genetic mechanisms of soybean maturity are well characterized. The genes E1, E2, and E3 have the largest effect on soybean maturity, where the functional allele of these genes condition for late maturity and the null or semi-functional alleles condition for early maturity. It has been determined that variations of the non-functional or semi-functional alleles of these three genes create the MG 00 or MG 0 phenotype. However, it is not understood which combination of alleles is most favored for breeding purposes which can potentially affect yield. In addition, since these major genes are not fully functional it can be hypothesized that there are other genes that play a major effect in this environment which may be only minor in other maturity groups with functional E genes. The goal of this research is to determine the major effect maturity alleles present in North Dakota MG 00 and 0 germplasm. This will be accomplished by exploring known maturity gene alleles in the North Dakota State University breeding program to determine which alleles are favored. In addition, these alleles will be determined over time in historical cultivars to determine if preference changed over time. These results will enrich knowledge of the maturity molecular model necessary to create an MG 00 and 0 cultivar and could possibly identify new genetic mechanisms for yield gains.
Association mapping confirms known loci and identifies new loci which control canopy temperature in Soybean
Siva K. Chamarthi1,2,5, Avjinder S. Kaler2, Hussein Abdel-Haleem3, Felix B. Fritschi1, Jeffery D. Ray4, James R. Smith4, C. Andy King2, Larry C. Purcell2, Jason D. Gillman5*
1University of Missouri, Columbia, MO; 2University of Arkansas, Fayetteville, AR; 3USDA-ARS, Maricopa, AZ; 4USDA-ARS, Stoneville, MS; 5USDA-ARS, Columbia, MO
Drought is a major global constraint for crop productivity in rain-fed areas and Improving crop tolerance to drought is of critical importance. Less than 10% of soybean acreage is irrigated and 20-70% of soybean growing regions experience significant drought in any given year. Drought incidence and severity are projected to increase due to the ongoing effects of climate change. Active transpiration under drought indicates a genotype that still has access to soil moisture. Thus, canopy temperature (CT) can be a scalable and indirect measure of transpiration and stomatal conductance with value in distinguishing differences among genotypes in response to under-water replete and water-limited conditions. The objectives of the present study were to confirm the loci associated with CT identified previously by genome-wide association mapping and to identify novel loci using a panel of 205 diverse, maturity group (MG) IV soybean accessions. These 205 accessions were planted in seven locations across two years under six irrigated and six drought environments. Within each location, CT was normalized (nCT) on a scale from 0 to 1. By conducting genome-wide association mapping (GWAM), we identified 163 significant SNPs represented by 117 loci associated with nCT. Of these loci, 69 were consistent with earlier studies and 48 were novel loci. Remarkably, two SNPs found in our new study matched previously discovered regions for nCT and slow canopy wilting, located near the Glyma04g36870 and Glyma04g37330 genes, which have annotations involved in the regulation of water transport, stomata, and temperature responses. We also identified extreme genotypes with cooler canopies and slow wilting, as well as warmer canopies with fast wilting, compared to previous studies. We identified 156 candidate genes out of 163 significant SNPs, with 15 SNPs located within genes related to plant stress responses and other drought-related traits. These confirmed genomic loci provide a valuable resource to enhance soybean drought tolerance by pyramiding favorable alleles for nCT.
Developing Genetically Diverse Soybean Germplasm with an Improved Seed Composition
Benjamin Fallen, Research Agronomist, USDA-ARS Soybean and Nitrogen Fixation Research Unit, Raleigh, NC
Soybean is a major source of protein and oil in animal and human diets. Almost 75% of the total soybean meal produced in the U.S. is used for feeding livestock, with poultry and swine being the two largest consumers. To meet the growing demand for soybean meal previous efforts were focused on quantity over quality, which inadvertently led to a decrease in protein content due to an inverse relationship between protein and yield. The narrow genetic base of the U.S. soybean crop limits the ability to enhance seed composition, specifically increasing the protein content. The genetic and phenotypic diversity in wild soybean makes it an excellent source for soybean improvement. The challenge when breeding with wild soybean is the undesirable agronomic traits inherited from the wild parent. We accessed the impact of wild soybean on protein content and subsequent selection for yield. Our research led to the development of more than a dozen breeding lines with a 12.5-50% soja genome shown to yield 91-104% and exhibit 103-106% seed protein compared to elite checks based on >25 environments of data. This highlights the progress being made to develop breeding lines from wild soybean, that are genetically diverse with high yields and improved seed composition. Efforts are currently underway to determine the impacts of wild soybean on protein functionality and dietary nutrition.
*Development of EPA- and Astaxanthin-Enriched Soybean Germplasm for Aquaculture Feedstocks
Hyojin Kim, Postdoctoral Researcher, Center for Plant Science Innovation, University of Nebraska–Lincoln, hkim20@unl.edu
The omega-3 long-chain polyunsaturated fatty acids (LC-PUFAs), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), and carotenoids such as astaxanthin are recognized for their health-promoting qualities. Marine fish and fish oil currently provide the main sources of EPA/DHA and astaxanthin for human consumption, but require this lipophilic compounds in their feed for aquaculture production. To provide a land-based source of these high-value feed components, we introduced the EPA and astaxanthin biosynthetic pathways in soybean by gene stacking. Our first version of aqua-soybean stacking EPA and astaxanthin biosynthetic genes showed poor seed quality such as reduced seed oil (<20% of seed weight), abnormal seed shape, low germination rate, decreased ABA level, and less EPA level (<2% of total fatty acids). From the design–build–test–learn (DBTL) cycle, the first version of aqua-soybean was crossed with high-alpha-linolenic acid soybean to improve EPA level. These crosses showed the enhanced seed quality such as high EPA level (~10% of total fatty acids) and normal seed shape, and the unexpected results such as improved germination rate. We generated only EPA soybean line or astaxanthin soybean line, separately. Our EPA soybean line accumulated up to 15% EPA of total fatty acids in seed with normal seed quality and germination rate. In addition, we developed astaxanthin-producing lines by introduction of biosynthetic genes (AaCBFD2 and AaHBFD1) with/without phytoene synthase gene (ZmPSY). Overall, our work represents a step toward viable soybean-based sources of astaxanthin-enriched fish oil for aquaculture production.
*Poster selected for oral presentation.
Proteomics/Metabolomics
SESSION CHAIRS: Doug Allen, USDA-ARS and Donald Danforth Plant Science Center, and Michaela McGinn, Smithbucklin
Can multi-omic integration lead to a better understanding of proteomic reprogramming and rebalancing? Lessons learned from Arabidopsis
Ruthie Angelovici, Associate Professor, University of Missouri
The ability of seeds to ‘reset’ the seed’s amino acid content and composition back to their original states despite large proteomic elimination is termed “proteomic re-balancing, but its molecular mechanism remains elusive. Understanding the cellular responses underlying this phenomenon is a first step to understanding how seeds exert can such high resilience to large perturbations in their proteome. Toward this goal, we performed comparative metabolic and proteomic analyses of seven “re-balanced” mutants of the three main seed storage proteins (SSPs) in Arabidopsis (cruciferins). This analysis uncovered two conserved cellular responses in the seeds: an elevation in the reactive oxygen species (ROS) scavenging system, and an adjustment of the translational machinery composition, especially ribosomal proteins. The former suggests that storage proteins are involved in regulating seed redox homeostasis, and the latter suggests that the composition of the translational apparatus is key to the plastic rebalancing response of seeds. Further in-depth analysis of the rebalanced cruciferin triple mutant during seed maturation supported the initial finding and highlighted the early onset of proteomic rebalancing. Overall, our study uncovered two unexpected players in seed protein content and composition and opened new venues for crop seed biofortification.
A single amino acid mutation in a transcriptional repressor increases oil and protein content in soybean
Kristin Haug Collet, Research Scientist, Janel Bettis, Clay Bettis, Gina Zastrow-Hayes, Shreedharan Sriram, Yang Wang, Andrew Foudree, Merideth Hay, Zhan-Bin Liu, John Everard, Bo Shen, Corteva Agriscience, Johnston, Iowa, kristin.haugcollet@corteva.com
Climate change is a growing concern, especially the increase of CO2 release from use of fossil fuels. To help reduce carbon emission, demand for renewable biofuels is increasing. This is driving an increased demand for plant oil production especially for soybean oil, which is the second largest oil source for renewable biofuel production. To discover new genes for increasing oil in soybean, we have identified high oil mutants by high throughput single seed screening. One of these high oil mutants has been fully characterized and the mutant gene has been mapped, cloned, and validated by CRISPR gene editing. The mechanism of this novel transcriptional repressor, which regulates oil accumulation in soybean, and its application in high oil soybean development will be presented.
Orchestrating seed metabolism to enhance synthesis of novel oils
Linah Alkotami1, Dexter White1, Maliheh Esfahanian2, Brice Jarvis2, Andrew Paulson3, Somnath Koley4, Kathleen M. Schuler1, Jianhui Zhang5, Chaofu Lu5, Doug K. Allen4,6, Young-Jin Lee3, John Sedbrook2, Timothy P. Durrett1
1Department of Biochemistry and Molecular Biophysics, Kansas State University 2School of Biological Sciences, Illinois State University 3Department of Chemistry, Iowa State University 4Donald Danforth Plant Science Center, 5Plant Sciences & Plant Pathology Department, Montana State University 6Agricultural Research Service, U.S. Department of Agriculture
Acetyl-triacylglycerols (acetyl-TAG) are TAG that possess an sn-3 acetate group instead of a long chain fatty acid. This unusual structure confers useful properties to acetyl-TAG, including reduced kinematic viscosity and improved cold temperature performance. Acetyl-TAG are synthesized in nature in the endosperm of many Euonymus seeds by unique diacylglycerol acetyltransferases (DAcTs). Isolation and expression of DAcT enzymes from different Euonymus species has resulted in the synthesis of acetyl-TAG in a number of oil seed crops, including soybean. This talk will discuss different approaches that have been used to increase the amount of acetyl-TAG synthesized in transgenic seeds. For example, the isolation of a higher activity DAcT enzyme from E. fortunei enabled increased acetyl-TAG levels. In addition, targeting of competing endogenous enzymes, using RNA interference or CRISPR-based genome editing, further enhanced the levels of acetyl-TAG synthesized. The combined effect of these different strategies has resulted in oil seeds that accumulate over 95 mol% acetyl-TAG, higher than the levels naturally found in Euonymus seeds. Despite the almost complete replacement of the type of TAG synthesized, properties of the transgenic seeds such as seed fatty acid content or seed weight were comparable to those of wild-type seeds, though a slight delay in germination was observed. Imaging of lipid accumulation in these ultra-high acetyl-TAG seeds has revealed the location of residual endogenous TAG, offering future strategies for the development of seeds that synthesize pure acetyl-TAG.
*Increasing Sulfur Content in Soybean Seed Protein
Trish Tully, Postdoctoral Associate, Donald Danforth Plant Science Center
TLA Tully1, D Duressa3, V Veena1, TP Durrett3, DK Allen1,2
1.Donald Danforth Plant Science Center, St. Louis, MO, 63132 2.United States Department of Agriculture, Agricultural Research Science, St. Louis, MO, 63132 3.Kanas State University, Manhattan, KS, 66506
Protein is one of the most valuable biomass components of soybean seeds and accounts for ~40% of seed biomass. However, soy protein is not optimal for animal meal-based diets as it is deficient in sulfur containing amino acids (cys + met). In the past, attempts to increase sulfur content in soy protein have been focused on the protein level, including heterologous protein expression and overexpression of endogenous storage proteins with high sulfur content. Unfortunately, these approaches have had limited success. Here we illustrate the first steps in increasing sulfur content of soy protein at the metabolic level. In wildtype soybean, low molecular weight thiols downstream of cysteine (γEC and hGSH) accumulate over the course of development. This sequesters sulfur in non-proteogenic compounds rather than in the protein found in meal. To increase cysteine availability for protein synthesis, we have generated RNAi-knockdown lines targeting CGL; the enzyme responsible for diverting cysteine towards γEC and hGSH biosynthesis. RNAi-knockdown lines show decreased expression of all CGL homologues with seeds that are morphologically similar to wildtype. Observed levels of free amino acids and sulfur intermediates show an increase in free cysteine and a decrease in both γEC and hGSH in CGL-knockdown lines relative to wildtype. CGL-knockdown lines also show an increase in total protein as well as an increase in protein-bound cysteine relative to wildtype. Further work will combine the CGL-knockdown lines with protease-knockdown lines; combining a push and a protect to result in a hypothesized greater increase in both total protein and protein-bound cysteine.
*Poster selected for oral presentation.
Genomics/Transcriptomics
SESSION CHAIR: Jason Nichols, Principal Scientist, Syngenta Crop Protection, LLC, jason.nichols@syngenta.com
Advancing Soybean Genomics for Enhanced Haplotype-Based Trait Mapping
Aamir W. Khan1, Heng Ye1, Henry T. Nguyen1,*
1Division of Plant Science and Technology, University of Missouri, Columbia, MO, USA. nguyenhenry@missouri.edu
Soybean is a major source of protein and oil worldwide. Understanding soybean domestication, genome architecture and identifying major trait linked loci accelerates genomics-assisted trait mapping efforts. Complete, gapless genomes assemblies are a prerequisite for investigating the full architecture of complex regions like centromeres or telomeres and for covering the complete gene-space of the genome for a species. Here, we report long reads enabled near-gapless genome assemblies for Williams 82 and Lee soybean cultivars. A total of ten chromosomes in Williams 82 and eight in Lee were entirely reconstructed in single contigs without any gap. Comparison of improved genome assemblies for both Wm82 and Lee with their previous versions show improvements in current genomes by filling gaps and correcting the inversions and complex rearrangements on different chromosomes. Gene annotations of these genome assemblies resulted in identification of genes in gap filled regions. We used the near gapless Williams 82 genome as a reference to map the sequence data of 514 soybean accessions from USDA genebank including 268 landraces, 216 cultivars, 30 breeders’ lines representing different maturity groups to develop a global variation map of 6.6 million single-nucleotide polymorphisms (SNPs) and 1.35 million insertions-deletions (InDels). This variation map serves as a resource for identifying haplotypes linked with distinct phenotypes and for genome wide association studies utilizing higher marker density. The genome-wide deleterious mutations limiting fitness were identified. Resources from this study will aid haplotype-based trait mapping in soybean and the identified deleterious mutations could be potential targets for gene-editing.
Soybean has a lot to Offer
Gary Stacey – Curator’s Distinguished Professor, Divisions of Plant Science and Biochemistry, University of Missouri, staceyg@missouri.edu
As I travel around and meet various scientists, I often hear comments about how soybean is so difficult to work with, cannot be transformed, lacks important resources for study, etc. I find that even folks in the soybean community share some of these same complaints. However, in my experience, there are very few things that cannot be done with soybean and the practical use of soybean rivals and, in some cases, surpasses that of the ‘so-called models’. Genetics/ molecular biology had its start with bacteriophage, progressing through use of E. coli, yeast, C. elegans, mice, and now we see a great deal of research conducted directly with humans. Likewise, plant molecular biology began with algae, progressing via Arabidopsis, other models (e.g., Medicago) and now can be broadly applied to crop plants. In my seminar, I will illustrate how we use soybean in much the same way one would use Arabidopsis to address both discovery and application. I will also outline the various resources that exist now for the study of soybean, which may not be fully apparent to the soybean community writ large. It is important that the community be aware of these resources and that they communicate broadly the utility of soybean for research. For example, one important goal is to recruit and expand the soybean community by informing young scientists that soybean, indeed, has a lot to offer.
*Tabula Glycine: The Glycine max single-cell resolution transcriptome atlas
Sergio Alan Cervantes-Perez, Postdoctoral Research Associate, Department of Agronomy and Horticulture, University of Nebraska–Lincoln, alan.cervantes@unl.edu
Soybean (Glycine max), one of the most important crops in the world, is an essential source of protein and oil with high nutritional value for human and animal consumption. It also has the capability to establish symbiotic interactions with nitrogen-fixing soil bacteria. Synthetic biology offers an opportunity to improve important soybean agronomic traits. However, the development of well-sounded synthetic biology strategies requires a deep understanding of the gene expression and their associated regulatory mechanisms in each cell/cell type composing the plant. Here, we present “Tabula Glycine” the Glycine max single-cell resolution transcriptome atlas. This atlas is composed of ~133,000 nuclei isolated from 11 organs using the single-nuclei RNA-sequencing approach. Our analysis revealed 172 different groups of nuclei clustered based on their transcriptomic profile. Using spatial transcriptomic technology and comparative genomic approaches, we functionally annotated ~80% of the clusters composing the Tabula Glycine. Focusing on the transcriptional patterns of the soybean transcription factor (TFs) genes, we observed that their activity is sufficient to define a cell type, supporting the idea that TFs genes are key regulators of cell identity. Among the soybean epidermal cells, the “root hair cell” cluster is characterized by its unique transcriptome, likely a reflection of its biological specialization and polar elongation. Notably, we found 93 TFs co-expressed in the soybean root hair including orthologs to Arabidopsis TFs controlling root hair cell development and to Medicago TFs controlling the early stages of infection by rhizobia. The Tabula Glycine is a high-resolution functional genomic resource for the soybean community.
*Poster selected for oral presentation.
Breeding/Genetics for Yield/Protection of Yield
SESSION CHAIRS: Aaron Lorenz, University of Minnesota, and Carrie Miranda, Assistant Professor, North Dakota State University
Breeding Soybean for Quantitative Disease Resistance to Phytophthora sojae
Leah McHale, Professor of Breeding & Genetics, The Ohio State University Anne Dorrance, William Rolling, Stephanie Karhoff, Cassidy Million, Christian Vargas-Garcia, Sungwoo Lee, Rouf Mian
Phytophthora root and stem rot, caused by the oomycete Phytophthora sojae, is an economically significant disease of soybean. More than 30 race-specific Resistance to P. sojae (Rps) genes have been identified and characterized. Though surveys in the North Central US have shown that, with the complexity of P. sojae field populations, none of the deployed Rps-genes confer resistance to all P. sojae isolates. In contrast to Rps genes, quantitative disease resistance (QDR) toward P. sojae is a complex trait and generally considered to be non-race specific. QDR is usually controlled by many small-effect loci throughout the genome, though there are a few notable exceptions. While the space, time, expertise, and isolate maintenance required for disease assays in phenotypic selection makes breeding for QDR towards P. sojae challenging, there is potential to improve breeding progress with traditional marker assisted selection (MAS) targeting the limited large effect QDR loci and/or genomic selection to combine small-effect QDR loci. Integrated genomic methods have implicated potential molecular mechanisms, including glutathione metabolism, auxin and jasmonic acid signaling pathways, and root architecture, in QDR to P. sojae. As we build our knowledge of the molecular basis of individual QDR loci, traditional MAS can be applied to purposely combine multiple mechanisms of QDR for optimal, durable defense.
Ten Years of the Genomes-to-Fields Maize GXE Project: Lessons and Opportunities
Natalia de Leon, Professor, Department of Agronomy, University of Wisconsin, Madison
Population growth and climate concerns demand that we increase the sustainability and efficiency of crop production. The Maize GXE project, part of the Genomes to Fields (G2F) initiative, is a multi-institutional effort focused on assessing the differential effect of environmental components on the performance of diverse maize genotypes with the goal of optimizing crop performance for specific environments. Since 2014, a research network of more than 30 principal investigators across almost 20 universities and research institutions has collected phenotypic, genotypic and environmental data for thousands of diverse maize varieties across more than 280 agriculturally relevant locations in North America. The collected information and network of collaborators have contributed to the advancement of technologies and tools that address the goal of the project and have supported scientific progress of the maize research community as a whole. This presentation will provide a description of the framework of the project and current activities and share opportunities under consideration moving forward.
Breeding for Yield in Industry
Kyle Kocak, Research Scientist, Corteva Agriscience
Modern soybean breeding programs rely on sophisticated data collection and analytical methods to drive genetic gain. These methods have changed and adapted alongside the technology that enables their use in applied settings. Ultimately plant breeders have to make decisions into which germplasm is released commercially as well as recycled for improving the genetic base. The amount of data underlying and augmenting these decisions has been growing rapidly in the past decades. This talk will highlight how data and models have helped applied plant breeders deliver genetic gain for key traits such as yield and yield stability for soybean farmers in North America.
*A Genomic Selection Pipeline for Public Soybean Breeding Programs
Vishnu Ramasubramanian, Postdoctoral Associate, University of Minnesota, vramasub@umn.edu
Genomic selection has become an important part of plant and animal breeding programs to accelerate genetic gain. We’ve implemented a GS pipeline designed for soybean public breeding programs in the US Midwest using open source tools that are currently available. Herein, we describe the steps and tools in the pipeline and discuss results for the Northern Uniform Soy Trial Population. Soybeanbase, an instance of breedbase hosted by BreedingInsight is used for the storage of both genotypic and phenotypic data. Filtering of markers and lines are done in the R environment using rTASSEL and custom R scripts. Imputation using LD – K-nearest neighbors imputation (LDKNNi) implemented in rTASSEL often showed the highest imputation accuracy in our test data. An optimized training subset selected using the STPGA package demonstrated higher accuracies in 5-fold cross-validations compared to a randomly selected subset for certain combinations of candidate and training set sizes. In this version, we’ve implemented genomic prediction models using the rrBLUP, BWGR, BGLR and SOMMER packages for single trait and multiple traits across single or multiple environments. We’ve also implemented models that include GxE interactions and environmental covariates using the SOMMER and envRtype packages. Our preliminary results indicate that modeling GxE interactions significantly improved prediction accuracies for a subset of the NUST population and including environmental covariates improved prediction accuracies only for some conditions. In the future, we plan to refine these methods and optimize the GS pipeline.
*Poster selected for oral presentation.
Biotic Interaction Session 2
SESSION CHAIR: Andrew Bent, Department of Plant Pathology, College of Agricultural & Life Sciences, University of Wisconsin–Madison
An update about SCN resistance: Peking-type and other new SCN resistant sources
Naoufal Lakhssassi, Associate Scientist, Adjunct Assistant Professor, Department of Plant Soil and Agricultural Systems, Southern Illinois University at Carbondale
Naoufal Lakhssassi1*, Sushil S. Chhapekar2*, Vikas Devkar3, Dounya Knizia1, Heng Ye2, Abdelhalim ElBaze1, Tri Vuong2, Gunvant Patil3, Henry Nguyen2, Khalid Meksem1
1Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
2Division of Plant Sciences, University of Missouri, Columbia, MO, USA.
3Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, USA.
Soybean cyst nematode (SCN) is the first devastating pathogen in soybeans and causes more than $1.5 billion in damages annually. Genetic variability within SCN populations plays a crucial role in the ability of the pest to adapt and overcome management practices, including planting resistant soybean varieties. Since 1960, several QTL for resistance to SCN have been identified. Advancements in molecular biology and genomic technologies have significantly facilitated the process of gene cloning and functional characterization of two key SCN resistance genes, the Rhg4 (GmSHMT08 gene) and rhg1-a (GmSNAP18 gene). PI 88788-type derived resistance cultivars were commonly and widely used due to their effectiveness against specific SCN populations. However, continuously planting of soybean cultivars that are derived from the same SCN resistance genetics, or relying on a limited set of resistant cultivars, creates selection pressure on the SCN population that shifted over time to become more virulent and better adapted to the resistant cultivars that are being used. Therefore, it is necessary to identify and characterize additional sources of SCN resistance to combat this ever-changing pest. Soybean exotic line PI 567516C carries two novel genes for SCN resistance that seem to display different resistance mechanisms other than the already known Rhg4 and rhg1 genes. We recently fine-mapped a novel SCN-resistant loci qSCN10 (O) (to a 142-kb) region containing 15 genes on Chr. 10) from soybean accession PI 567516C. Functional characterization of this novel region identified two novel genes that reduce cyst number in fully susceptible soybean line Williams-82 by 52.64% and 57.9%. Understanding the molecular basis of SCN resistance allows breeders to develop soybean cultivars with more effective and durable resistance.
Developing alternative viro-control and RNAi-based approaches to reduce white mold infection
Shin-Yi Marzano, Research Molecular Biologist, U. S. Department of Agriculture ARS, shinyi.marzano@usda.gov
Growers lack effective genetic tools to manage losses caused by Sclerotinia sclerotiorum because of a lack of resistance to the pathogen in germplasms. This necessitates the identification of alternative sources of resistance or methods for the disease control. In this talk, I will explain our efforts in developing mycoviruses as well as identifying strong candidate genes from S. sclerotiorum as the targets for the development of alternative pesticides. I will also talk about the effects of endophytic colonization of avirulent strain of S. sclerotiorum on soybean plants, which may shed light on ways to manipulate pathogen-plant interactions by involving mycoviruses capable of extracellular transmission.
Using genomics to unravel the complexities of the interaction between soybean and Phythophthora sojae
François Belzile, Yanick Asselin and Richard Bélanger, Département de phytologie, Centre de recherche et d’innovation sur les végétaux, Université Laval, Québec, Qc, G1V 0A6, Canada, Francois.Belzile@fsaa.ulaval.ca
Phytophthora sojae is arguably one of the most important pathogens of soybean worldwide. A common method of control resides in the introgression of specific resistance genes (Rps) in elite material. These Rps genes have a gene-for-gene relationship with avirulence (Avr) genes of P. sojae, which triggers defense reactions. Over the years, some Rps genes have lost their efficacy as a result of adaptation by the pathogen leading to new alleles of Avr genes whose product is no longer recognized by the product of the Rps gene. This situation compromises, for breeders and growers, the lasting reliance on genetic control. This problem is compounded by the rapid evolution of Avr genes and the fact that very few Rps genes have actually been precisely identified and cloned. Following extensive surveys of P. sojae isolates throughout soybean growing areas in Canada, we were able to define SNP haplotypes for the alleles of Avr genes associated with the most commonly deployed Rps genes, Rps1a, Rps1b, Rps1c, Rps1k, Rps3a, and Rps6. Based on this information, we have developed molecular tools that can specifically identify each haplotype of these six Avr genes found in the isolates of P. sojae recovered in soybean fields. We have further been able to identify markers that will discriminate isolates on the basis of their virulence toward the newly identified Rps11. These tools can be easily exploited by breeders and farmers to introgress and use cultivars carrying the proper Rps genes in a given environment. In parallel, we have used RenSeq to precisely define Rps regions and genes, an approach that has allowed a much clearer understanding of the 35 or so reported Rps genes along with a finer resolution of their position in the soybean genome. Once optimized, this approach should facilitate introgression of those genes by breeders.
*An integrated single-cell comparative transcriptomic and evolutionary analysis of the legume membrane microdomain-associated protein-coding genes during the nodulation process
Md Sabbir Hossain, Doctoral Student, Department of Agronomy and Horticulture, University of Nebraska–Lincoln, mhossain8@huskers.unl.edu
Legumes have the unique ability to fix atmospheric dinitrogen through a mutualistic symbiosis with rhizobia. This symbiosis starts with the infection of the legume root hair cell and ultimately leads to the development of a new root organ, the nodule. The rearrangement of the plasma membrane is a pre-requirement for rhizobial infection. For instance, membrane microdomain-associated proteins (MMAPs), including FW2.2-LIKEs (FWLs), flotillins (FLOTs), prohibitins (PHBs), and remorins (REMs), play a crucial role in the initiation and development of the infection threads, a tube-like structure that allow rhizobia to infect the plant cells. In this poster, using state-of-the-art single-cell transcriptomics technology, we evaluate the co-expression pattern of the MMAPs in each cell type composing the Glycine max and Medicago truncatula nodules. As a result, we identified two GmFWLs, one GmFLOT, two GmPHBs, and three GmREMs, and, and two MtFWLs, two MtFLOTs, three MtPHBs, and one MtREM genes preferentially expressed in the infected cells of the soybean and Medicago, respectively. Expanding our analysis to the entire soybean single-cell transcriptomic atlas, we confirmed the specific expression of these soybean MMAPs in the infected cells of the nodule. The phylogenetic analysis of the legume MMAPs revealed that most of the nodule-infected cell-specific MMAPs co-cluster together suggesting their early functional allocation to regulate the nodulation process.
*Poster selected for oral presentation.
Genetic Engineering
Session Chairs – Robert Stupar, Department of Agronomy and Plant Genetics, University of Minnesota, and Wayne Parrott, Department of Crop and Soil Sciences, University of Georgia
Engineering approaches to develop hybrid soybean
Margaret Frank, Assistant Professor, School of Integrative Plant Science, Plant Biology Section, Cornell University
TBD
Understanding nutrient uptake and its potential role in water deficit conditions
Gunvant Patil, Assistant Professor, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, https://patil-lab-ttu.com/
Understanding the molecular basis of differential mineral element uptake, translocation, and accumulation in soybean is vital for developing improved cultivars. In this study, we profiled diverse soybean germplasm and identified novel QTLs associated with several mineral nutrients including Silicon (Si). Silicon (Si) is considered a beneficial element due to its ability to enhance plant growth and mitigate a variety of abiotic and biotic stresses. Outside of monocot plants, less is known about the transport and localization of Si in different crops, especially soybean. In this study, we combine association mapping, electron microscopy, and single nuclei transcriptomics and gene editing to quantify Si uptake, deposition, and characterize candidate genes for Si transport and accumulation in the soybean leaf. The snRNAseq analysis identified a potential Si efflux gene which is localized in the epidermal cells of Si-treated plants. Functional characterization using CRISPR/Cas9 of Si transport gene identified its role in water stress conditions.
Harnessing the mPing Transposable Element for Gene Discovery and Precision Genome Engineering
C. Nathan Hancock1, Peng Liu2, Zara Lacera1, Megan Collins1, and R. Keith Slotkin2
1University of South Carolina Aiken, Aiken, SC, USA, 2Donald Danforth Plant Science Center, St. Louis, MO, USA
Efficient identification and manipulation of genes influencing agronomically important traits is crucial for crop improvement. Leveraging the mPing transposable element from rice, we have developed mutagenesis resources capable of generating both knockdown and overexpression phenotypes. Experiments in soybean show that mPing-based activation tags incorporating enhancer sequences can induce upregulation of nearby genes. To enhance mutagenesis efficiency, hyperactive versions of mPing and the Pong transposase proteins responsible for mobilizing these elements are being engineered. This technology has been advanced in collaboration with Keith Slotkin’s Laboratory at the Donald Danforth Center by establishing a reliable method for sequence-specific targeting of mPing insertion in plant genomes. Linking Pong Transposase to CRISPR/Cas nucleases allows for the excised mPing elements to be inserted into the Cas targeted double stranded breaks. They have successfully used this technology to deliver enhancer elements, open reading frames, and gene expression cassettes into targeted locations in Arabidopsis and soybean genomes. In summary, these experiments demonstrate the potential of mPing-based mutagenesis for crop improvement and expanding crop genetic engineering capabilities.
*Facilitating gene discovery in soybean through mutagenesis: Identification of novel genes controlling the production of four-seeded pods
Cuong X. Nguyen1, Vikranth K. Chandrasekaran1, Manh V. Nguyen1, Gary Stacey1, Minviluz G. Stacey1
1Division of Plant Sciences, University of Missouri, vkc4kf@missouri.edu
The most important soybean agronomic trait targeted for crop improvement is increased yield, which can be achieved by increasing seed number and/or seed weight. Phenotypic screening of soybean fast neutron mutants identified a mutant line, designated MO27, that produced an increased number of four-seeded pods (4-SP), producing ~30% 4-SPs per plant compared to ~4% in wildtype. Genetic mapping and co-segregation analyses showed that the 4-SP phenotype in MO27 is controlled by the additive effects of at least two alleles located in Chr02 and Chr06. Based on the functional annotations of the deleted genes, we hypothesized that deletions of GmGATA1 on Chr. 2 and GmULT1-3 and GmULT1-5 on chr.6 are the putative causative mutations underlying the 4-SP trait. These genes encode putative transcription factors. Knock-out deletions in these genes via CRISPR/Cas9 confirmed their role in controlling the number of seeds per pod in soybean, likely through the CLAVATA3 (CLV3)-WUSCHEL (WUS) signalling pathway that coordinates stem cell proliferation with differentiation in floral meristems. Knock-out mutations of orthologous genes in Arabidopsis and tomato resulted in increased production of locules in siliques and fruits, respectively, suggesting functional conservation of GmGATA1-1 and GmULT1 in plants.
*Poster selected for oral presentation.