Preparation of the library, high throughput sequencing and GBS
genotyping
Library preparation and high-throughput sequencing were performed at the
University of Wisconsin Biotechnology Center (DNA Sequencing Facility).
The preparation of the GBS genomic library was done following the
protocol detailed by Elshire et al., (2011) using the ApeKI restriction
enzyme and 44 specific barcodes. High throughput sequencing was
performed using an Illumina HiSeq 2000 (Illumina, USA) and single-strand
sequencing runs of 100 bp. The raw GBS dataset generated and analyzed
during the current study are available in the SRA repository
(https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA783610 ). Quality of
the sequenced raw data was assessed using FastQC
(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ).
SNP calling was made using Stacks v.2.2 pipeline (Catchen et al., 2013).
Values of the two main parameters (-M: number of mismatches allowed
between stacks within individuals; and -n: number of mismatches allowed
between stacks between individuals) were chosen following the
optimization procedure described in Paris et al. (2017).