Libraries construction and sequencing

Genotyping-by-sequencing libraries were constructed using standard protocols (Poland et al., 2012), with minor modifications, at the Plateforme d’Analyses Génomiques of the Institut de Biologie Intégrative et des Systèmes (IBIS, Université Laval, Québec City, Canada). Total gDNA (200 ng) was digested with both high-fidelity enzymes PstI and MspI (New England Biolabs, Ipswich, MA, USA). Three libraries were prepared in total, each one with 96 pooled individuals. One of 96 barcoded adapters was attached to the PstI cut site for each sample and a common adapter (adapter 2) was attached to the MspI cut site of all samples using T4 ligase (New England Biolabs). Each one of the 96 samples (same volume) was pooled and the mixture was size-selected using a 2% agarose gel cassette on a BluePippin instrument (Sage Science, Beverly, MA, USA), with the elution time set from 50 to 65 min. Eluted fragments were used for multiplexed polymerase chain reactions (PCR), using standard forward primer A and reverse primer C (Poland et al., 2012). Final libraries were checked for quality on a High Sensitivity BioAnalyzer chip (Agilent, Santa Clara, CA, USA) and quantified using Picogreen (Promega, Sunnyvale, CA, USA). Each library was sequenced in one lane of an Illumina HiSeq 4000 SR100 (San Diego, CA, USA) using 100-bp single-end reads at the McGill University and Génome Québec Innovation Centre (Montreal, Canada).