Project abstract for group stuparr

Functional Genomics

These researchers have five current projects using MSI resources:

  • Mutant mapping studies: Using bulk segregate analysis, useful soybean mutant phenotypes will undergo mapping studies to restrict causative genes to a region of a chromosome. Whole-genome sequencing (WGS) will be generated and analyzed on wild-type and mutant bulks for each phenotype of interest.
  • Comparison of mutation rates: This project is looking at change in mutation rates between standing, irradiated, and transformed genetic variation using soybean WGS. The group will also be looking at differences in large structural variants between these populations as well as various population genetics metrics.
  • Creation and application of soybean co-expression networks: Using publically available soybean RNA-seq expression data, the researchers will generate expression values and build a general co-expression network. Using this network, they will then integrate it with differential expression studies for interesting phenotypes to generate a list of candidate genes.
  • 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.
  • RNA seq of F1 hybrids: This project explores the soybean transcriptome and how it is affected by parentage and copy number variation. This involves analysis of both WGS and RNA-seq data.

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