Molecular Genetics and Soybean Genomics Laboratory

Henry T. Nguyen, Ph.D.
Curators' Distinguished
Professor of Plant Sciences,
Division of Plant Sciences
University of Missouri
Tel: 573-882-5494
Fax: 573-882-1469
nguyenhenry@missouri.edu
Henry Nguyen

Research in the Nguyen Laboratory


Introduction

The Soybean Genetics & Genomics Laboratory, led by Dr. Henry T. Nguyen, conducts research in various aspects of soybean that includes soybean genomics, abiotic stress (drought, flooding, and salinity tolerance), biotic stress (Soybean cyst nematode (SCN), Rootknot Nematode (RKN), Reniform Nematode (RN), Phytophthora, and Sudden Death Syndrome (SDS)), and soybean seed composition.  The majority of the Lab’s funding comes from the United Soybean Board (USB), the Missouri Soybean Merchandising Council, (MSMC), and the North Central Soybean Research Program (NCSRP).

Besides working with other University of Missouri researchers, the Nguyen Lab collaborates with soybean researchers in 21 different states across the United States. There are also on-going research collaborations in 13 countries world-wide that covers six different continents.


Soybean Genomics

The Nguyen Lab is one of the leaders in the U.S. soybean community in the soybean genomics arena. Our laboratory has re-sequenced 106 wild, landraces, and elite soybean lines that represent an average of 17X depth with a 97.5% coverage rate. In the manuscript published in March, 2016, titled "Landscape of genomic diversity and trait discovery in soybean", a genome-wide association study of major traits including oil and protein content, salinity, and domestication traits resulted in the discovery of novel alleles. Genomic information from this study provides a valuable resource for understanding soybean genome structure and evolution, and can also facilitate trait dissection leading to sequencing-based molecular breeding.

A significant effort to sequence more soybean germplasm lines in the U.S. is currently underway as 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: Bayer CropScience, DOW AgroSciences, LLC, and Monsanto. The Nguyen Lab is coordinating this research. This is the first large-scale public-private partnership of this magnitude in the soybean genetic research arena. The results of this project will lay the groundwork for future soybean genetic and breeding research. In Phase I of this project, 350 of the most diverse soybean lines in the U.S. germplasm collection were selected for sequencing. The 50 most diverse soybean germplasm lines were re-sequenced at 40X coverage. The other 300 diverse soybean germplasm lines were re-sequenced at 15X coverage. In Phase II of this project, an additional 300 soybean germplasm lines are being re-sequenced at 15X coverage.

Other sequencing projects underway currently include: The De Novo sequencing of the Glycine soja line, PI 483463. This is an ancestral line to Glycine Max. This will create a third reference genome in soybean and will help lead to the understanding of soybean evolution; Sequencing of high-yielding soybean lines from several soybean breeders. By looking at genomic variations in these high yielding lines and their pedigree lines we hope to identify the genes responsible for yield traits. This information will be used in genomics-assisted breeding strategies for improved yield for farmers; and working with several breeders and the USDA to answer questions about soybean diversity, by re-sequencing a core set of G. Soja lines and a set of exotic germplasm that represents the majority of the soybean diversity that exists in the modern day soybean varieties that are grown in the U.S.

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 major role in the determination of productivity in a specific location, 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, requires improvements to the below ground portions of soybeans.

Our laboratory is working to characterize natural genetic variations occurring in soybean and their relation to yield protection under stressed environments. Identification and utilization of identified root traits are then incorporated into high yielding germplasm with developed markers to help widen the genetic base of stress tolerance in soybean. Currently we are working on a panel of genetically diverse Glycine max plant introductions from the USDA germplasm collection and Glycine soja to characterize RSA and stress tolerance under greenhouse and field conditions.

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. Drought tolerance in soybean is a complex trait to characterize and incorporate into breeding programs due to numerous factors which impact the productivity of soybean when subjected to drought.

Our lab is focusing on an integrated approach collaborating with Midwest soybean breeders to utilize molecular markers and sequencing information to improve yields under water limited conditions. Our research is focused on field and greenhouse characterization of exotic and wild soybean germplasm and recombinant inbred populations for targeted traits such as slow canopy wilting, canopy temperature, hyperspectral indices, and root system architecture to identify new sources of drought tolerance. Molecular markers associated with identified drought tolerance are then developed and used to combine multiple sources of tolerance into high yielding elite lines to provide soybean breeders with improved germplasm while increasing the genetic diversity of drought tolerance in soybean.

Water Logging Tolerance:

Impacts of flood stress on crop yields are becoming more severe in view of recent climate changes and widespread employment of irrigation systems. Predicted increases of heavy precipitations will lead to higher frequencies of flooding and heavy yield losses, as was seen across the U.S. in 2015.

Our laboratory is working to identify genetic resources and characterize mechanisms for flood tolerance, to develop flood tolerant germplasm and varieties, and to optimize management practices to protect yield from excess water. Our lab is focusing on an integrated approach collaborating with soybean breeders in multiple states to utilize genetic resource and genomic platform to support sustainability of soybean production across the U.S.

Salinity:

Salinity is one of the abiotic stress factors that has a negative impact on productivity of many crop plants, including soybeans. Our research focuses on the discovery of new sources of salt tolerance that will be utilized to develop new genetic resources. These resources will facilitate the identification of genomic variants that are applicable to next-generation breeding which will lead to the development of new soybean germplasm and varieties.



Biotic Stress


Nematode Resistance:

Soybean cyst (SCN), Root-knot (RKN), and Reniform (RN) nematodes as a whole are the most yield limiting pests of soybean. SCN is by far the number one yield limiting pest. RKN is also a major problem, particularly in the sandy or sandy loam soils in the southern U.S. RN is common in cotton and can cause severe yield losses where both cotton and soybean are in rotation. The nematodes attack and destroy soybean roots resulting in over one billion dollars in crop losses each year. There are several different varieties or races of the nematodes making it more difficult to find resistant varieties. A soybean variety might be resistant to one variety, but not another. Our laboratory is conducting research to find soybean varieties that are resistant to several or all of these nematodes.

The Nguyen Lab houses the leading public SCN phenotyping facility. The facility can screen approximately 25,000 plants per year for SCN resistance using 5 nematode populations. Besides screening soybean lines in support our the northern and southern Missouri breeding programs, screening of new genetic materials for gene discovery is on-going year round.

Diseases:

In collaboration with the Ohio State University, we are studying several fungal diseases including; Phytophthora sojae, several Pythium spp., and Fusarium graminearum. Major quantitative Trait Loci (QTL) and potential candidate genes for partial resistance to P. sojae and F. graminearum have been discovered. We are also screening for new sources of resistance and exploring the relationship that P. sojae has with flooding tolerance in soybean.

Soybean sudden death syndrome (SDS), caused by the soil borne fungus Fusarium virguliforme, is a severe threat to soybean production in the North Central region. SDS consistently ranks within the top-five yield reducing soybean diseases. In years with the greatest SDS, estimated yield losses in an excess of 75 million bushels have occurred. The pathogen is spreading across the northern states and its growing importance in the North Central region is a concern. A combination of resistant cultivars and effective management strategies is key for effective disease control.

Our lab collaborates with other soybean scientists from the USDA-ARS and several institutions, to evaluate diverse soybean lines from the USDA germplasm collection for resistance to SDS. We will be conducting genome-wide association studies (GWAS) using whole-genome sequence data to identify and analyze haplotype blocks and genes for SDS resistance.


Seed Composition


Soybean is unique among leguminous crops with seed protein content of about 40% and oil content of 21% on a dry matter basis. Soybean is also most widely grown oil seed crop in the world and represented 56% of the world's vegetable oil seed production. Additionally, meal protein and balanced carbohydrates, e.g. higher sucrose and low oligosaccharides, is the primary source of protein in livestock feed (poultry and swine). It is the key factor that determines the nutritional and economical value of soybeans.

With the development of soybean genetics and genomics resources and the state-of-art genotyping and phenotyping facilities available in our laboratory, our research has been focusing on the discovery of novel sources of high protein, modified carbohydrates, and modified fatty acids from exotic soybean germplasm and mutagenized populations. These new sources have been studied for environmental stability and utilized for the development of genetic and breeding materials. Breeder-friendly genomic tools have been developed that have greatly facilitated several new soybean germplasm and varieties.

The genetic association of genes and traits related to protein, oil, and carbohydrate content was comprehensively investigated by identifying and characterizing variations in genome structure. We have successfully developed functional genetic markers of targeted traits and cost-effective genotyping assays that have been routinely utilized in marker-assisted selection. These breeder-friendly genomic tools have greatly facilitated the development of several new soybean germplasm and varieties.

The U.S. soybean producer needs high yielding high oleic/low linolenic (HOLL) soybean varieties to provide the market with high value, highly functional soybean oil with zero trans-unsaturated fatty acids (trans fats). In collaboration with the University of Georgia, our lab conducts analyses of new HOLL soybean lines developed by different soybean breeders.