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

Torkamaneh, Davoud; Laroche, Jérôme; Tardivel, Aurélie; O'Donoughue, Louise; Cober, Elroy; Rajcan, Istvan; Belzile, François

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

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creativework.keywords - en: Soybean; Plant genomes; Computational Biology; Genome-Wide Association Study; Genotype; Haplotypes; High-throughput nucleotide sequencing; Single nucleotide polymorphisms
creativework.keywords - fr: Soja; Plantes--Génomes; Bio-informatique; Étude d'association pangénomique; Génotypes; Haplotypes; Séquençage à haut débit; Polymorphisme de nucléotide simple
dc.contributor.author: Torkamaneh, Davoud; Laroche, Jérôme; Tardivel, Aurélie; O'Donoughue, Louise; Cober, Elroy; Rajcan, Istvan; Belzile, François
dc.date.accepted: 2017-08-14
dc.date.accessioned: 2025-01-24T15:10:41Z
dc.date.available: 2025-01-24T15:10:41Z
dc.date.issued: 2017-11-03
dc.date.submitted: 2017-05-19
dc.description.abstract - en: 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.
dc.identifier.citation: 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
dc.identifier.doi: https://doi.org/10.1111/pbi.12825
dc.identifier.issn: 1467-7644; 1467-7652
dc.identifier.uri: https://open-science.canada.ca/handle/123456789/3345
dc.language.iso: en
dc.publisher - en: Blackwell Publishing Ltd
dc.rights - en: Creative Commons Attribution 4.0 International (CC BY 4.0)
dc.rights - fr: Creative Commons Attribution 4.0 International (CC BY 4.0)
dc.rights.uri - en: https://creativecommons.org/licenses/by/4.0/
dc.rights.uri - fr: https://creativecommons.org/licenses/by/4.0/deed.fr
dc.subject - en: Beans; Genetics
dc.subject - fr: Haricot; Génétique
dc.subject.en - en: Beans; Genetics
dc.subject.fr - fr: Haricot; Génétique
dc.title - en: Comprehensive description of genomewide nucleotide and structural variation in short-season soya bean
dc.type - en: Article
dc.type - fr: Article
local.article.journalissue: 3
local.article.journaltitle - en: Plant Biotechnology Journal
local.article.journalvolume: 16
local.pagination: 749-759
local.peerreview - en: Yes
local.peerreview - fr: Oui
local.requestdoi: No