Professor Robert Stupar

These researchers have six current projects using MSI resources:

• Mutant population development/database: The researchers are currently developing a mutant collection of soybean seeds that were treated with chemicals (ENU/EMS). They will be sequencing a large number of these mutants to identify regions that contain variants (SNPs/indels/structural variants). The pilot run will consist of sequencing 70 mutant lines as well as creating a web application for other research groups to find lines carrying variants in specific genes/regions of interest.
• Comparison of mutation rates: This project is looking at change in mutation rates between standing, irradiated, and transformed genetic variation using soybean whole-genome sequencing (WGS). The group will also be looking at differences in large structural variants between these populations as well as various population genetics metrics.
• Soybean reference genome analysis: This lab is part of a new genome assembly effort for a novel soybean cultivar. While they are not doing the assembly themselves, they will be comparing the soybean reference genomes and annotations. They are also planning to add 20 WGS nanopore sequencing runs to explore structural variation in the species.
• Exploring the soybean germplasm collection: This project uses publicly available climate, soil, and genotypic data to run a mixed linear model of association. With multiple populations and 80 different environmental phenotypes available, this will result in large computational use.
• Public soybean genomes: This project uses a public dataset of ~1000 soybean genomes for further validation in the group's current mutant and mapping studies. 
• CRISPR off-targeting: The researchers recently sequenced a variety of CRISPR and non-CRISPR sets of transgenic soybean lines and are now looking to see if there is a difference in mutation rate between the CRISPR and non-CRISPR lines.