The GBS approach [11 (link)] was used to discover SNP markers. The mapping population was a set of 213 (of the 275) F1 individuals of the progeny TGdL x MB, including the 163 plants previously analysed by Beltramo et al. (2016) and 50 new individuals [29 ]. Only the plants situated at the edge of the experimental field were excluded.
Total genomic DNA was extracted from young leaves collected in the spring using a CTAB method [31 ]. Quantity and quality of extracted DNA were determined by the Qubit assay (Thermo Fisher Scientific) and by electrophoresis on 1% agarose gel and comparison against a Lambda DNA/EcoRI + HindIII marker (Thermo Fisher Scientific). In October 2014, approximately 3 μg of genomic DNA from each individual and the two parents were sent to the Genomic Diversity Facility at Cornell University—Institute of Biotechnology (USA) (http://www.biotech.cornell.edu/brc/genomic-diversity-facility ) for GBS. Briefly, GBS libraries were constructed in 96-plex by digesting genomic DNA with the restriction enzyme ApeKI, a five-base cutter (5’ GCWGC 3’), followed by ligation of a barcode adaptor and a common Illumina sequencing adaptor to the fragmented DNA. The resulting libraries were run through an Illumina Hiseq2500 flow cell for sequencing.
Total genomic DNA was extracted from young leaves collected in the spring using a CTAB method [31 ]. Quantity and quality of extracted DNA were determined by the Qubit assay (Thermo Fisher Scientific) and by electrophoresis on 1% agarose gel and comparison against a Lambda DNA/EcoRI + HindIII marker (Thermo Fisher Scientific). In October 2014, approximately 3 μg of genomic DNA from each individual and the two parents were sent to the Genomic Diversity Facility at Cornell University—Institute of Biotechnology (USA) (
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