Comprehensive description of genomewide nucleotide and structural variation in short-season soya bean

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DOI

https://doi.org/10.1111/pbi.12825

Language of the publication
English
Date
2017-11-03
Type
Article
Author(s)
  • Torkamaneh, Davoud
  • Laroche, Jérôme
  • Tardivel, Aurélie
  • O'Donoughue, Louise
  • Cober, Elroy
  • Rajcan, Istvan
  • Belzile, François
Publisher
Blackwell Publishing Ltd

Abstract

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 soya beans 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 data set 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 data sets derived from lower density genotyping tools (150 K 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 ~92 K 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 soya bean 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.

Subject

  • Beans,
  • Genetics

Keywords

  • Soybean,
  • Plant genomes,
  • Computational Biology,
  • Genome-Wide Association Study,
  • Genotype,
  • Haplotypes,
  • High-throughput nucleotide sequencing,
  • Single nucleotide polymorphisms

Rights

Pagination

749-759

Peer review

Yes

Identifiers

ISSN
1467-7644
1467-7652

Article

Journal title
Plant Biotechnology Journal
Journal volume
16
Journal issue
3
Accepted date
2017-08-14
Submitted date
2017-05-19

Citation(s)

Torkamaneh, D., Laroche, J., Tardivel, A., O'Donoughue, L., Cober, E., Rajcan, I., & Belzile, F. (2017). Comprehensive description of genomewide nucleotide and structural variation in short-season soya bean. Plant Biotechnology Journal, 16(3), 749-759. https://doi.org/10.1111/pbi.12825

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Collection(s)

Crops and horticulture

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