The IPSC peach 9 K SNP Infinium® II array v1 was evaluated using 709 accessions divided in two independent evaluation panels, one panel from the European Union (EU) and the other from the USA (US). The EU panel comprised 232 accessions, of which 229 were peach cultivars and three were wild related Prunus species or their hybrids with peach. The US panel comprised 479 accessions that included pedigree-linked cultivars, breeding lines, and seedlings (Table S2). Overall, selected material comprised cultivars (45%), advanced selections (4%) and seedlings (51%). Accessions with pure peach and almond ancestry accounted for 82% and 2%, respectively, while 16% of genotyped material had interspecific backgrounds with almond (7%), and peach and almond wild relatives, 5% and 4%, respectively, in their pedigrees. Some US panel accessions were related Prunus species or were known interspecific hybrids: 5% had peach-related (P. davidiana and P. mira) ancestry, 10% had almond (P. dulcis), and 3% had almond-related (P. argentea and P. scoparia) ancestry. Genomic DNA extraction and quantitation were conducted as described above for the SNP validation panel for the U.S. accessions. For the EU panel, genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen) and quantitated using a Fluoroskan Ascent (Thermo Scientific, Finland) microplate reader. The IPSC array, employing exclusively Illumina Infinium® II design probes and dual color channel assays (Infinium HD Assay Ultra, Illumina), was used for genotyping, following the manufacturer's recommendations. SNP genotypes were scored with the Genotyping Module of the GenomeStudio Data Analysis software (Illumina, Inc.). A GenTrain score of >0.4 and a GenCall 10% of >0.2 were applied to remove most SNPs that did not cluster (homozygous), or had ambiguous clustering. SNPs that did not cluster for more than 50% of samples were also eliminated from further consideration. The threshold of allowed No Calls (failed genotyping) was ‘relaxed’ in anticipation of the presence of null alleles for some SNPs contributed by non-peach species.
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