Genotyping-by-sequencing for soybean genomics

GBS was conducted following the methods and recommendations outlined by Elshire et al. (2011) (link), Sonah et al. (2013) (link), and Torkamaneh et al. (2020a (link),c) (link). The GBS library was created with ApeKI restriction enzyme digestion. A 158 million single-end reads were generated with an Ion Torrent Proton System (Thermo Fisher Scientific Inc., USA). These were processed using the Fast-GBS.v2 pipeline (Torkamaneh et al., 2020c (link)). FASTQ files were demultiplexed, trimmed, and then mapped against the soybean reference genome (Williams82 (Gmax_275_Wm82.a2.v1); Schmutz et al., 2010 (link)) with an average success rate of 94.4%. SNPs were identified from the mapped reads and filtered out if (i) they were multi-allelic, (ii) the overall read quality (QUAL) score was <20, (iii) the mapping quality (MQ) score was <30, (iv) read depth was <2, and (v) missing data >80%. Missing data imputation was performed using BEAGLE v5.1 (Browning et al., 2018 (link)) following the protocol laid out by Torkamaneh and Belzile (2015) (link).