RAD-Seq of Beta vulgaris subsp. vulgaris: Low and high geosmin
A single 1-cm disk of leaf tissue was submitted to the University of Wisconsin Biotechnology Center (Madison, WI) for DNA extraction and genotyping by sequencing (Elshire et al. 2011). DNA libraries were prepared by digestion with NsiI-BfaI and ligation of GBS barcodes and adapters. Paired-end reads (2 x 150 bp) were generated on one shared lane of an Illumina NovaSeq 6000 sequencer. Genomic data quality control, sequence alignment, and SNP calling was performed by the University of Wisconsin Bioinformatics Resource Center (Madison, WI). Skewer software (Jiang et al. 2014) was used to remove adapters, primers, and low-quality bases, to trim reads until achievement of Phred quality 20, and to discard excessively short reads. Demultiplexed 64 bp forward reads were aligned to B. vulgaris ssp. vulgaris reference genome EL10.2 (McGrath et al. 2020) using the Tassel v2 GBS Pipeline (Glaubitz et al. 2014) and alignment software Bowtie 2 (Langmead et al. 2012).