Introduction

The Soybean Genetics & Genomics Laboratory, led by Prof. Henry T. Nguyen, conducts research in diverse aspects of soybean, including soybean genomics, abiotic stress (root system architecture, drought, flooding, and salinity tolerance) and biotic stress (nematode resistance). The majority of the Lab’s funding currently comes from the US Department of Agriculture – National Institute of Food and Agriculture (USDA-NIFA), the United Soybean Board (USB), industry and the North Central Soybean Research Program (NCSRP).

Nguyen lab collaborates internally with University of Missouri researchers and externally with other soybean scientists across the United States. Our collaboration extends to several countries worldwide for soybean improvement and comparative legume genomics.

Soybean Genomics

The Nguyen Lab is one of the leaders in the U.S. soybean community in the soybean genomics arena. Our laboratory is presently developing a soybean super-pangenome by including 120 lines from G. max, G. soja and perennials with collaborators from the SALK Institute leveraging the PacBio HiFi data and Hi-C data of selected lines for super-scaffolding. The super-pangenome will deploy the pangenome approach to identify the structural variations associated with important and agronomic traits and potentially novel genomic regions associated with these traits. This pangenome extends our efforts in the genomics resources domain as we have recently developed near-gapless genomes of Williams 82 and Lee cultivars using PacBio long reads technology and optical mapping data collaborating with researchers from Murdoch University, Chinese University of Hong Kong and Corteva AgriScience [Garg and Khan et al., 2023]. Along with this super-pangenome, we are also developing a long reads Iso-Seq based pan-transcriptome by transcriptome sequencing of the most diverse G. max and G. soja lines and selected perennials, including several tissues such as leaf, flower, seed pods, stem and roots. The pan-transcriptome is our quest to improve the gene annotations by leveraging the superior long reads technology to identify the complete genes/isoforms and splice events. We are working with Complete Genomics and Murdoch University (Australia) to develop soybean genomes using the stLFR technology. Furthermore, we are collaborating with Prof. Marc Libault (University of Missouri) to develop a single-cell pan-transcriptome for soybean with a focus on the root system.

We are currently working on a global HapMap project to develop a high-density variations map that utilizes the near-gapless Williams 82 v5 genome and genome sequencing of a USDA germplasm collection of ~1250 lines from 43 countries, with the majority from China (515), USA (206), Korea (135), Japan (132), Russia (58), Brazil (32) to identify the genetic diversity and their trait associations. We are utilizing the information from this high-density HapMap to develop an improved 6K markers array by patterning with ThermoFisher deploying the AgriSeq approach. We are also developing a structural variations map with lines with data > 20X coverage to accurately detect the SVs and their distribution between the G. max and G. soja lines and between lines from Southern and Northern US parts. Previously, we developed a soybean pangenome using the iterative mapping and de novo assembly approach and examining the gene PAV as well as SNP diversity across 1,110 soybean lines (157 wild G. soja, 723 landraces, 228 cultivars, and two unclassified lines) [Bayer, Valliyodan and Hu et al., 2022]. We previously developed and reported improved genome assemblies using the NRGene sequencing technology for Williams 82, Lee and a new G. soja line, PI 483463, an ancestral line to G. max [Valliyodan, Cannon and Bayer et al., 2019]. This study aimed to develop a third reference genome in soybeans that will help lead to an understanding of soybean evolution.

The genomic information from our studies is not just a product of our work but a collective resource for the scientific community. It provides valuable insights into soybean genome structure, genetic diversity in the germplasm and wild species lines, domestication, and evolution. This information is shared and used in genomics-assisted breeding strategies for improved yield for farmers. We are working with several breeders and the USDA scientists to answer questions about soybean diversity by resequencing a set of exotic germplasm lines that represents the majority of the soybean diversity that exists in the modern-day soybean varieties that are grown in the U.S. Sequencing soybean germplasm lines in the U.S. was part of a project, titled “Large Scale Sequencing of Germplasm to Develop Genomic Resources for Soybean Improvement”. This project was funded by the United Soybean Board (USB) and three private companies: BASF, DOW AgroSciences (Corteva) and Monsanto (Bayer CropScience). The Nguyen Lab coordinated this research, but it was a collaborative effort, and at the time, this was the first large-scale public-private partnership of this magnitude in the soybean genetic research arena. The data being generated by these projects will benefit the soybean community and allow both public and private soybean breeders and researchers resources that they can use to improve soybean varieties for U.S. farmers.

Abiotic Stress

Root System Architecture:

Root System Architecture (RSA) plays a key role in determining plant growth and productivity in a specific environment, which may vary due to soil composition, temperature, and water availability. The variability of the environment and the requirement for increased yield of soybean with less inputs, such as irrigation water and fertilizers, require improvements in the below-ground portion of soybeans.

Our laboratory is working to characterize natural genetic variations in soybean RSA and its plasticity in response to major abiotic stresses, such as drought and flooding. Important root traits are incorporated into high-yielding germplasm using molecular breeding technologies to help widen the genetic base of stress tolerance in soybean. Genes and regulatory factors controlling RSA development and plasticity can also be directly modified using gene-editing technique in the elite soybean background. In this direction, our group has pioneered in exploiting the genetic variation and discovered the root QTL/ genes associated with waterlogging stress tolerance (WLT-1) in soybean in collaboration with Prof. Julia Bailey-Serres (University of California-Riverside). Currently, we are working on a panel of genetically diverse soybean plant introductions from the USDA germplasm collection to characterize RSA and plasticity using high-throughput imaging-based rhizo-slide system and X-ray imaging system in collaboration with Chris Topp at the Donald Danforth Plant Science Center.

Drought Tolerance:

The impact water deficit has on the productivity of row crops depends on the severity, length of occurrence, and the timing during the growth cycle which drought occurs.

Our lab is focused on an integrated approach, collaborating with soybean breeders and digital phenotyping groups to utilize molecular markers, sequencing information, and modern imaging and sensing phenotyping techniques to identify genetic resources for soybean yield improvement under water-limited conditions. Our research includes field and greenhouse characterization of elite and exotic soybean germplasm and recombinant inbred populations for targeted traits such as slow canopy wilting, canopy temperature, hyperspectral indices, photosynthesis, and root system architecture to identify new sources and genes for drought tolerance improvement.

Flooding Tolerance:

Impacts of flood stress on crop yields are becoming more severe in view of recent climate change. Predicted increases of heavy precipitations will lead to higher frequencies of flooding and heavy yield losses globally. In the East Coast, North Central, and the Mississippi Delta regions, early-season flooding stress is frequent due to excessive rains in spring and early summer. As an example, the spring floods of 2019 hit the key row-crop growing regions of the United States, causing devastation in key agricultural-producing states.

Our laboratory is working to address flood tolerance in soybean at both early- and mid-season flood by identifying genetic resources and characterising the genetic and molecular mechanisms for flood tolerance. Our goal is to develop flood-tolerant germplasm and varieties through molecular breeding and gene-editing to protect yield from excess water. We deploy an integrated approach collaborating with soybean breeders in multiple states to utilize genetic resources and genomic platform to support sustainability of soybean production across the U.S.

In northern areas, temperatures fluctuate significantly in the soybean planting season, accompanied by the increasing frequency of heavy precipitations in late spring and early summer due to climate change. In the Midwest, soil temperatures (at 5 cm depth) during the late April to early May are between 5 – 7.6℃, which are not optimal for soybean seed germination and seedling establishment. The combined waterlogging and cold stresses are frequently observed in the northern plains during the regular soybean planting season. This stress usually leads to poor seedling emergence and plant establishment, and thus replanting in the later season is required, causing a significant economic loss to farmers. Our group is working with Prof. Son Tran (Texas Tech University) to characterize the genetic diversity in soybean germplasm for tolerance to the combined waterlogging and cold stresses and identify the genetic and molecular regulatory networks through genomic, genetic, and multi-omics tools.

Salinity:

Salinity is one of the abiotic stress factors that has a negative impact on the productivity of several crop plants, including soybeans. Previous studies identified GmCHX1 as a major salt tolerance gene in soybean, and two main functional variations were found in the promoter region (148/150-bp insertion) and the third exon with a retrotransposon insertion (3.78-kb). Our group identified a new and rare allele of GmCHX1 in a wild soybean line with novel variations in the STRE cis-element in the promoter region leading to a salt-inducible expression of GmCHX1, instead of consistent high-expression of GmCHX1 in the previously identified tolerant alleles. We are interested in investigating if this new allele with salt-inducible expression pattern provides an energy and cost-efficient (conditional gene expression) strategy to protect soybean yield in saline soils without yield penalty under non-stress conditions.

Overall, our laboratory has extensively evaluated a mini core set of the USDA soybean germplasm collections for natural genetic variation in different abiotic stresses including drought, waterlogging, and salt stress. We have initiated new research efforts into both cold and hot temperature stress and aim to investigate the genes and mechanisms underlying plant tolerance to a combination of abiotic stressors and develop the next-generation soybean germplasm with improved tolerance and resilience to climate change. Our abiotic research has been supported by USDA-NIFA (National Institute of Food and Agriculture) and the United Soybean Board (USB)

Biotic Stress

Soybean disease losses in the U.S. over the last 24 years demonstrated the greatest losses across states and years were from nematodes, particularly soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) and root-knot nematode (Meloidogyne incognita) as an emerging pest.

Soybean cyst (SCN), Root-knot (RKN), and Reniform (RN) nematodes are the most yield-limiting pests of soybean. SCN is the number one yield constraint pest, leading to billion-dollar losses to farmers globally. RKN is the second most major problem, particularly in the sandy or sandy loam soils in the southern U.S. and now spreading across the northern states and its growing importance in the North Central region is a concern. RN is common in cotton and can cause severe yield losses when cotton and soybeans rotate. There are different varieties or races of the nematodes making it more difficult to find resistant varieties. Another major concern is the emergence of pathotypes that can overcome resistance. It is essential to identify additional genetic sources, mechanisms, and modern tools to develop novel and sustainable approaches to combat this ever-changing pest.

Our lab pioneered the utilization of whole genome sequencing in soybean to demonstrate the SCN resistance in PI 437654 (highly resistant soybean line to all the known SCN races) is correlated with copy number variation [Patil et al, 2019]. We are employing long-read (PacBio HiFi) and deep coverage high-throughput sequencing data to identify novel haplotypes and new sources of SCN and RKN resistance among the USDA population. The focus is to characterize QTL and genes regulating the SCN and RKN resistance as well as identify the gene functions through gene-editing and omics tools.

To dissect the molecular basis of soybean cyst and root-knot nematode resistance in soybean, we employ diverse approaches of molecular breeding (fine mapping and marker-assisted selection), molecular biology (CRISPR genome editing and expression analysis), genomic technology (haplotypes and structural variations), and high-throughput plant phenotyping. Nguyen laboratory conducts research to identify novel soybean varieties that are resistant to broad-spectrum (multiple races) nematodes and understand the genetic and molecular mechanism of nematode resistance in soybeans. Our goal is to enhance the understanding of molecular aspects of plant-nematode interaction and translate this knowledge to provide new genetic resources for limiting the impact of nematodes in the northern and southern regions of the U.S. Our research identifies novel soybean accessions (PI 567516C, PI 567305 and PI 438489B) resistant to multiple nematodes including soybean cyst and root-knot nematodes. These novel accessions demonstrated unique genetic loci that are independent of known resistance loci (rhg1 and Rhg4) conferring resistance to broad-spectrum nematodes. Efforts are being undertaken not only to dissect and characterize these loci/genes through gene editing but also to develop functional markers to assist genomics-assisted breeding for nematode resistance. We are integrating the new soybean accessions (resistant to SCN and RKN) into the breeding program to develop germplasms resistant to multiple nematodes that will be a durable source of resistance to U.S. farmers.

Our lab collaborates with various soybean breeders and pathologists to evaluate diverse soybean lines from different maturity groups of USDA germplasm collection for resistance to root-knot nematodes. The nematode research program in Nguyen’s lab is supported by USDA-NIFA (National Institute of Food and Agriculture), the United Soybean Board (USB), and the Mid-South Soybean Board (MSSB).