3 years ago

Comprehensive Description of Genome-Wide Nucleotide and Structural Variation in Short-Season Soybean

Louise O'Donoughue, Jérôme Laroche, Elroy Cober, Aurélie Tardivel, Davoud Torkamaneh, François Belzile, Istvan Rajcan
Next-generation sequencing (NGS) and bioinformatics tools have greatly facilitated the characterization of nucleotide variation; nonetheless, an exhaustive description of both SNP haplotype diversity and of structural variation remains elusive in most species. In this study, we sequenced a representative set of 102 short-season soybeans and achieved an extensive coverage of both nucleotide diversity and structural variation (SV). We called close to 5M sequence variants (SNPs, MNPs, and Indels) and noticed that the number of unique haplotypes had plateaued within this set of germplasm (1.7M tag SNPs). This dataset proved highly accurate (98.6%) based on a comparison of called genotypes at loci shared with a SNP array. We used this catalogue of SNPs as a reference panel to impute missing genotypes at untyped loci in datasets derived from lower density genotyping tools (150K GBS-derived SNPs/530 samples). After imputation, 96.4% of the missing genotypes imputed in this fashion proved to be accurate. Using a combination of three bioinformatics pipelines, we uncovered ~92K SVs (deletions, insertions, inversions, duplications, CNVs, and translocations), and estimated that over 90% of these were accurate. Finally, we noticed that the duplication of certain genomic regions explained much of the residual heterozygosity at SNP loci in otherwise highly inbred soybean accessions. This is the first time that a comprehensive description of both SNP haplotype diversity and SV has been achieved within a regionally relevant subset of a major crop. This article is protected by copyright. All rights reserved.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1111/pbi.12825

You might also like
Never Miss Important Research

Researcher is an app designed by academics, for academics. Create a personalised feed in two minutes.
Choose from over 15,000 academics journals covering ten research areas then let Researcher deliver you papers tailored to your interests each day.

  • Download from Google Play
  • Download from App Store
  • Download from AppInChina

Researcher displays publicly available abstracts and doesn’t host any full article content. If the content is open access, we will direct clicks from the abstracts to the publisher website and display the PDF copy on our platform. Clicks to view the full text will be directed to the publisher website, where only users with subscriptions or access through their institution are able to view the full article.