Transcriptome-based SNP discovery by GBS and the construction of a genetic map for Olive: Sample GEXED_GBS_GE097
The mapping population composed of 123 F1 plants was developed from the cross between ‘Gemlik’ female parent and ‘Edincik Su’ male parent. DNA samples were extracted from 20 mg lyophilized and powdered leaf tissue using the DNeasy plant kit (Qiagen, Germany) according to the manufacturer’s instruction.  DNA concentrations were measured using a Qubit fluorimeter (Invitrogen, USA), and samples were diluted to 50 ng/µl in elution buffer.  GBS analysis was carried out by following the protocol described for maize by Elshire et al. (2011). DNA samples from both parents and 123 F1 progenies were digested individually with ApeKI restriction enzyme. Illumina sequencing adaptors with unique barcode nucleotides were ligated to DNA fragments digested with ApeKI to prepare GBS sequencing libraries. Before sequencing GBS libraries, GBS libraries of 32 samples were pooled together to run in a lane of Illumina HiSeq 2000 sequencing system. DNA samples from 125 plants (123 progeny plus 2 parents) were sequenced in 4 lanes of Illumina HiSeq 2000 sequencing system with 101nt read length.  After trimming the Illumina adaptor sequences, reads belonged to both parents and each progeny were identified from the sequencing pools using barcode nucleotides and “process_radtags” program in a pipeline software package “Stacks” (Catchen et al. 2011). 