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).