SNP informativeness in sour cherry for the eight sets of chromosomes based on whether the SNP was derived from polymorphism in sweet cherry or in one of the two sour cherry subgenomes (i.e., <i>avium</i> or <i>fruticosa</i>).

<p>The 330 sour cherry accessions evaluated are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048305#pone.0048305.s003" target="_blank">Table S3</a>.</p>a<p>Numbers of SNPs for the subgenomes of sour cherry are split (/) between <i>avium</i> and <i>fruticosa.</i></p>b<p>Numbers in parentheses are totals for RosCOS SNPs derived from sweet cherry and are included in the first number.</p

Minor allele frequency (MAF) of polymorphic cherry SNPs.

<p>MAF was determined in sweet cherry (n = 50) and sour cherry (n = 37) evaluation panels for 1825 and 2058 polymorphic SNPs, respectively.</p

SNP informativeness in sweet cherry for the eight sets of chromosomes based on whether the SNP was derived from polymorphism in sweet cherry or in one of the two sour cherry subgenomes (i.e., <i>avium</i> or <i>fruticosa</i>).

<p>The 269 sweet cherry accessions evaluated are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048305#pone.0048305.s002" target="_blank">Table S2</a>.</p>a<p>Numbers of SNPs for the subgenomes of sour cherry are split (/) between <i>avium</i> and <i>fruticosa.</i></p>b<p>Numbers in parentheses are totals for RosCOS SNPs derived from sweet cherry and are included in the first number.</p

Workflow for SNP detection, validation, and final choice in development of the RosBREED 6K cherry SNP array v1.

<p>Stage 1 filtered 1.9 million cherry SNPs anchored to the peach genome to almost 40K SNPs. More stringent filtering criteria in Stage 2, guided by a prior validation step with a small SNP subset examined for a range of potential filters, putatively enriched the quality of the remaining 32K SNP pool. Finally, the 6K array SNPs were chosen from among stage 2 SNPs by attempting to achieve even genetic spacing over species genomes and subgenomes with pre-determined proportional allocations, after preferential inclusion of certain SNPs. ADT = Illumina's Assay Design Tool. MAF = minor allele frequency.</p

Estimated physical and genetic distribution of SNPs of the RosBREED cherry 6K SNP array v1 across sweet cherry chromosomes evaluated for 269 sweet cherry accessions.

a<p>Based on the 4214 attempted sweet cherry SNPs.</p>b<p>Based on all 1825 polymorphic SNPs.</p

Estimated genetic distribution of SNPs of the RosBREED cherry 6K SNP array v1 across sour cherry chromosomes evaluated for 330 sour cherry accessions.

a<p>Based on the 1482 attempted sour cherry SNPs (752 for the <i>avium</i> subgenome and 730 for <i>fruticosa</i>).</p>b<p>Based on all 2058 polymorphic SNPs; for the <i>avium</i> subgenome, this calculation included all sweet cherry SNPs polymorphic for sour cherry.</p

Outcomes of a GoldenGate® validation assay for a set of 144 SNPs screened with 160 cherry accessions to test potential filtering parameters.

<p>Figures shown in <b>bold</b> are for those cases where the crop for which the SNPs were developed matches the crop on which the SNPs were screened.</p>a<p>Of the 96/48 SNPs examined that targeted sweet cherry/sour cherry.</p

Single nucleotide polymorphisms (SNPs) detected across the apple genome by re-sequencing 27 apple accessions.

<p>Single nucleotide polymorphisms (SNPs) detected across the apple genome by re-sequencing 27 apple accessions.</p

Apple cultivars used for low coverage re-sequencing and subsequent single nucleotide polymorphism detection.

<p>An approximate genome coverage was estimated for each accession using a genome size of 750 Mb. The source of cultivars and numbers of Illumina GA II reads obtained are indicated. ARC: Agricultural Research Council, South Africa; PFR: The New Zealand Institute for Plant & Food Research Ltd; RosBREED: U.S.-based international project.</p

Apple Infinium® II array v1 content and evaluation in the Plant & Food Research dataset. The number of attempted SNPs and clusters is indicated per linkage group (LG), as well as their density based on the apple genome assembly in kilobases (Kb) and the ‘Golden Delicious’ genetic map (cM).

<p>The Apple Infinium® array was evaluated by screening 1398 progeny in 8 segregating populations and 117 individuals from the Plant & Food Research apple germplasm collection.</p