Genotyping by sequencing
Genomic DNA was extracted from floral buds using Qiagen DNeasy Plant
Mini Kit (QIAGEN Strasse 1, 40724 Hilden, Germany) following the
manufacture’s instruction. Samples were sent to the Institute of Genomic
Diversity at Cornell University for genotyping by sequencing, libraries
were prepared as described in the protocol by Elshire et al. (2011).
Briefly, the DNAs from 96 individuals were digested with EcoT22I 6-base
cutter (ATGCAT) to reduce the genome complexity. A 96-plex GBS library
comprising 95 DNA samples and a negative (no DNA) were prepared by
ligating the digested DNA to unique barcode nucleotide adapters,
followed by standard PCR. The resulting 96-plex library was sequenced on
a single lane of an Illumina HiSeq 1 x 100bp.