Journal Article

A bumper crop of SNPs in soybean through high‐density genotyping‐by‐sequencing (HD‐GBS)

Hyten, David L., Torkamaneh, Davoud, Belzile, François, Boyle, Brian, Laroche, Jérôme

2021

Overview

1 Figure. (a) Predicted distribution of fragments (100–800 bp; 100 bp bin size) derived from in silico digestion with seven different restriction enzymes or combinations thereof. (b) Quality assessment of a 96‐plex HD‐GBS library using a Bioanalyzer. (c) Distribution of PE reads per sample after demultiplexing. (d) Distribution of variants as a function of their depth of coverage following HD‐GBS. (e) Number of variants, (f) proportion of missing data and (g) cost per sample for six different genotyping platforms in soybean. After size selection and PCR amplification, the quality of the GBS library was assessed and the resulting profile (Figure 1b) indicated that the vast majority of size‐selected fragments (including sequencing adapters) ranged between 200 and 600 bp. [...]the other Skim‐Seq datasets (@0.5x and 0.2x), as expected, yielded accuracies falling between the two former categories. [...]our results demonstrate that HD‐GBS provides an extremely low‐cost method for obtaining an ultra‐dense panel of markers enabling high‐quality imputation of untyped variants from a reference panel.

• Publisher: John Wiley & Sons, Inc,John Wiley and Sons Inc
• Subject: Accuracy / Adapters / Agricultural economics / Arrays / Brief Communications / Conflicts of interest / Data analysis / Datasets / Demultiplexing / Enzymes / Fragments / Genetic testing / Genome, Plant - genetics / Genomes / Genotype / Genotyping / Genotyping Techniques / genotyping‐by‐sequencing / Glycine max - genetics / High-Throughput Nucleotide Sequencing / high‐density genotyping / imputation / Libraries / Missing data / Polymorphism, Single Nucleotide - genetics / Quality assessment / Quality control / Sequence Analysis, DNA / soybean / Soybeans / whole‐genome sequencing