Next-generation sequencing (NGS) has revolutionized plant and animal research in many ways including new methods of high throughput genotyping. Genotyping-by-sequencing (GBS) has been demonstrated to be a robust and cost-effective genotyping method capable of producing thousands to millions of SNPs across a wide range of species. Undoubtedly, the greatest barrier to its broader use is the challenge of data analysis. Herein we describe a comprehensive comparison of seven GBS bioinformatics pipelines developed to process raw GBS sequence data into SNP genotypes. We compared five pipelines requiring a reference genome (TASSEL-GBS v1& v2, Stacks, IGST, and Fast-GBS) and two de novo pipelines that do not require a reference genome (UNEAK and Stacks). Using Illumina sequence data from a set of 24 re-sequenced soybean lines, we performed SNP calling with these pipelines and compared the GBS SNP calls with the re-sequencing data to assess their accuracy. The number of SNPs called without a reference genome was lower (13k to 24k) than with a reference genome (25k to 54k SNPs) while accuracy was high (92.3 to 98.7%) for all but one pipeline (TASSEL-GBSv1, 76.1%). Among pipelines offering a high accuracy (>95%), Fast-GBS called the greatest number of polymorphisms (close to 35,000 SNPs + Indels) and yielded the highest accuracy (98.7%). Using Ion Torrent sequence data for the same 24 lines, we compared the performance of Fast-GBS with that of TASSEL-GBSv2. It again called more polymorphisms (25.8K vs 22.9K) and these proved more accurate (95.2 vs 91.1%). Typically, SNP catalogues called from the same sequencing data using different pipelines resulted in highly overlapping SNP catalogues (79–92% overlap). In contrast, overlap between SNP catalogues obtained using the same pipeline but different sequencing technologies was less extensive (~50–70%).
BackgroundNext-generation sequencing (NGS) technologies have accelerated considerably the investigation into the composition of genomes and their functions. Genotyping-by-sequencing (GBS) is a genotyping approach that makes use of NGS to rapidly and economically scan a genome. It has been shown to allow the simultaneous discovery and genotyping of thousands to millions of SNPs across a wide range of species. For most users, the main challenge in GBS is the bioinformatics analysis of the large amount of sequence information derived from sequencing GBS libraries in view of calling alleles at SNP loci. Herein we describe a new GBS bioinformatics pipeline, Fast-GBS, designed to provide highly accurate genotyping, to require modest computing resources and to offer ease of use.ResultsFast-GBS is built upon standard bioinformatics language and file formats, is capable of handling data from different sequencing platforms, is capable of detecting different kinds of variants (SNPs, MNPs, and Indels). To illustrate its performance, we called variants in three collections of samples (soybean, barley, and potato) that cover a range of different genome sizes, levels of genome complexity, and ploidy. Within these small sets of samples, we called 35 k, 32 k and 38 k SNPs for soybean, barley and potato, respectively. To assess genotype accuracy, we compared these GBS-derived SNP genotypes with independent data sets obtained from whole-genome sequencing or SNP arrays. This analysis yielded estimated accuracies of 98.7, 95.2, and 94% for soybean, barley, and potato, respectively.ConclusionsWe conclude that Fast-GBS provides a highly efficient and reliable tool for calling SNPs from GBS data.
Genotyping-by-sequencing (GBS) represents a highly cost-effective high-throughput genotyping approach. By nature, however, GBS is subject to generating sizeable amounts of missing data and these will need to be imputed for many downstream analyses. The extent to which such missing data can be tolerated in calling SNPs has not been explored widely. In this work, we first explore the use of imputation to fill in missing genotypes in GBS datasets. Importantly, we use whole genome resequencing data to assess the accuracy of the imputed data. Using a panel of 301 soybean accessions, we show that over 62,000 SNPs could be called when tolerating up to 80% missing data, a five-fold increase over the number called when tolerating up to 20% missing data. At all levels of missing data examined (between 20% and 80%), the resulting SNP datasets were of uniformly high accuracy (96–98%). We then used imputation to combine complementary SNP datasets derived from GBS and a SNP array (SoySNP50K). We thus produced an enhanced dataset of >100,000 SNPs and the genotypes at the previously untyped loci were again imputed with a high level of accuracy (95%). Of the >4,000,000 SNPs identified through resequencing 23 accessions (among the 301 used in the GBS analysis), 1.4 million tag SNPs were used as a reference to impute this large set of SNPs on the entire panel of 301 accessions. These previously untyped loci could be imputed with around 90% accuracy. Finally, we used the 100K SNP dataset (GBS + SoySNP50K) to perform a GWAS on seed oil content within this collection of soybean accessions. Both the number of significant marker-trait associations and the peak significance levels were improved considerably using this enhanced catalog of SNPs relative to a smaller catalog resulting from GBS alone at ≤20% missing data. Our results demonstrate that imputation can be used to fill in both missing genotypes and untyped loci with very high accuracy and that this leads to more powerful genetic analyses.
Summary Here, we describe a worldwide haplotype map for soybean (GmHapMap) constructed using whole‐genome sequence data for 1007 Glycine max accessions and yielding 14.9 million variants as well as 4.3 M tag single‐nucleotide polymorphisms (SNPs). When sampling random subsets of these accessions, the number of variants and tag SNPs plateaued beyond approximately 800 and 600 accessions, respectively. This suggests extensive coverage of diversity within the cultivated soybean. GmHapMap variants were imputed onto 21 618 previously genotyped accessions with up to 96% success for common alleles. A local association analysis was performed with the imputed data using markers located in a 1‐Mb region known to contribute to seed oil content and enabled us to identify a candidate causal SNP residing in the NPC1 gene. We determined gene‐centric haplotypes (407 867 GCHs) for the 55 589 genes and showed that such haplotypes can help to identify alleles that differ in the resulting phenotype. Finally, we predicted 18 031 putative loss‐of‐function (LOF) mutations in 10 662 genes and illustrated how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for applied soybean genomics and breeding.
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