The evaluation of different combinations of enzyme set, aligner and caller in GBS sequencing of soybean.

ABSTRACT:

Background

Genotype-by-sequencing (GBS) is a cost-effective method for large-scale genotyping, widely used across various species, particularly those with large genomes. A critical aspect of GBS lies in the selection of restriction enzymes for genome digestion and the optimization of data analysis pipelines. However, few studies have comprehensively examined the combined effects of enzyme choice and pipeline configuration.

Results

In this study, we created GBS libraries using three commonly used restriction enzyme combinations (HindIII-NlaIII, PstI-MspI, and ApeKI) and assessed multiple SNP-calling pipelines in 15 soybean varieties. We tested four aligners (BWA-MEM, Bowtie2, BBMap, and Strobealign) and seven SNP callers (Bcftools, Stacks, DeepVariant, FreeBayes, VarScan, BBC

SUBMITTER: Zamalutdinov A 

PROVIDER: S-EPMC12330036 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature