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

Corresponding author: François Belzile

Next-generation sequencing (NGS) and bioinformatics tools have greatly facilitated the characterization of nucleotide variation; nonetheless (虽然如此), an exhaustive description of both SNP haplotype (单倍型) diversity and of structural variation remains elusive in most species. In this study, we sequenced a representative set of 102 short-season (短季) soya beans (大豆) 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 (趋于稳定) within this set of germplasm (种质) (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.

作者利用NGS和生物信息学工具对102个短季大豆进行了重测序，鉴定了各类型的核酸序列变异，研究了SNP单倍型多样性及结构变异。（这个翻译太难了，专业不对口啊，所以就偷了个懒。。。）

doi: 10.1111/pbi.12825