DNA was isolated from approximately 100 mg of fresh leaf blade + pseudostem tissue for 577 training set mother plants, using a high-throughput method based on that described by Whitlock et al. (2008 (link)) with modifications including a final binding, washing and eluting DNA from AcroPrep™ Advance 96 Filter Plates (Pall Corporation, Ann Arbor, MI, USA). DNA quality was checked via visualisation on ethidium bromide stained 0.8% (wt/vol) agarose/TBE gels and then quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Invitrogen, Carlsbad, CA). DNA concentrations were normalised to 20 ng/μl and subsequently used for GBS library preparation. GBS libraries were generated following the methodology of Elshire et al. (2011 (link)), with 100 ng of DNA digested using ApeKI (New England Biolabs, Ipswich, MA) and ligated to a unique barcoded adapter and a common adapter (99 ng). A total of six libraries were developed in 96-plex which included a blank and a common positive control sample. Each library was passed through a Pippin Prep™ DNA size selector (Sage Science, Beverly, MA, USA) to isolate fragments between 193 and 313 bp, which were then sequenced on two lanes of an Illumina HiSeq 2500 (Illumina, San Diego, CA, USA) at AgResearch Invermay, New Zealand.
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