Table 1.
Origin of samples and re-sequencing statistics for the 14 genotypes of the discovery panel and the two double haploids.
Figure 1.
The SNP selection process was a cascade involving four steps: Detection, Quality Filtering, Illumina specific Filtering and SNP Selection, with the number of SNPs reduced after each step. The specific filtering criteria have been reported for each filtering stage, as well as the number of resulting SNPs, with the corresponding percentage survival, relative to the total number of SNP markers after the previous step. From the 20,000 selected, Illumina successfully incorporated a total of 18,019 SNP probes into the new array, 14,714 of which were newly discovered and 3,305 previously validated.
Figure 2.
SNP selection within a single focal point (FP) of chromosomes (Chrs) 1 and 9.
Genotype calls are presented for the discovery panel members: 0/1 and 1/2 indicates heterozygosity, all other codes indicate absence of polymorphism within an individual. Green, blue and orange filled cells relate to selected SNPs, having 5–8, 2–4, or just 1 heterozygous panel member/s, respectively. The physical positions at the extremities of the FP are in bold and italics (most proximal) or underlined (most distal). Within each FP, SNPs are sorted firstly by being selected or not, and secondly according to the number of heterozygous members (HET). In the Chr1-FP example, SNP-6 was not selected, as its heterozygosity pattern is identical to that of SNP-2. The single-member-heterozygote SNP-5 was included because no other more polymorphic SNP markers were available to reach the target of 11 SNPs and no nearby FPs had a specific SNP for the same panel member. In the Chr9-FP example all highly specific SNPs were ignored, as there were sufficient markers of higher heterozygosity available. The selected SNPs show a homogeneous representation of the diploid panel members.
Figure 3.
Distribution of focal points (FPs) (black lines) and IRSC SNPs (red lines) in the apple physical map v2.
All positions are in Mbps. The average distance between FPs is 311 Kbps. Only two regions longer than 1 Mbps located at the distal end of Chrs 9 and 13 are not covered by FPs and SNPs from the 8 K IRSC SNP array. Scale bars = 5 Mbps.
Figure 4.
GenomeStudio cluster plot for the 21 F1 full-sib families used for the construction of genetic maps.
Yellow dots indicate panel members that were re-sequenced and used as parents. Genotypes are called for each sample (dot) by their signal intensity (norm R) and Allele Frequency (Norm Theta) relative to canonical cluster positions (dark shading) for a given SNP marker (red = AA, purple = AB, blue = BB) a) GenomeStudio cluster plot of a newly developed robust SNP marker. b) GenomeStudio cluster plot of a failed/difficult to score SNP marker.