University of Illinois Urbana-Champaign

Whole genomic structural variant calling in soybean: Analysis on 481 different soybean lines

Istanto, Dave Deandre

Content Files
ISTANTO-THESIS-2020.pdf
Supplementary Materials.zip

Permalink

https://hdl.handle.net/2142/107902

Description

Title
Whole genomic structural variant calling in soybean: Analysis on 481 different soybean lines
Author(s)
Istanto, Dave Deandre
Issue Date
2020-04-23
Director of Research (if dissertation) or Advisor (if thesis)
Hudson, Matthew
Committee Member(s)
  • Mainzer, Liudmila
  • Clough, Steven
Department of Study
Crop Sciences
Discipline
Bioinformatics
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
M.S.
Degree Level
Thesis
Date of Ingest
2020-08-26T21:54:23Z
Keyword(s)
  • Soybean
  • Transposon
  • Structural variation
  • Variant calling
Abstract
Soybean (Glycine max) is an important crop worldwide, with utilities as protein source and rotation crop. Often, soybean variant discovery is conducted using alignment methods and largely yields short variants such as SNP(s) and short indel(s). We conducted variant discovery on 481 soybean lines using both alignment and assembly methods. We used the Sentieon Haplotyper algorithm for our alignment-based variant calling and Cortex-var for our assembly-based variant discovery and found many more short variants compared to structural variants: medians 2,728,393 and 3,972 variants respectively. Additionally, we provide the user-friendly workflow script together with full-documentation for Cortex-var assembly-based variant discovery. Additionally, post variant discovery analysis was conducted with a focus on transposable element activities in the same 481 soybean lines. Structural variants were filtered for transposable element, and then the transposable elements identified were compared between elite soybean lines and Glycine soja lines, and then the transposable element activity of G. soja lines was statistically higher compared to the soybean elite lines. Consequently, it is possible to distinguish the difference between elite soybean lines, landraces, and G. soja lines through structural variant information. It was also found that some transposable elements that might be potentially disrupting genes with functions such as carbohydrate metabolism and embryo development with high activities in the leaves, pods, and pod shells.
Graduation Semester
2020-05
Type of Resource
Thesis
Permalink
http://hdl.handle.net/2142/107902
Copyright and License Information
Copyright 2020 Dave Istanto

Owning Collections

Graduate Dissertations and Theses at Illinois PRIMARY
Graduate Theses and Dissertations at Illinois
Dissertations and Theses - Crop Sciences