Relative size of linkage groups (LG) (assuming the genome size of 1300 cM), and the number of single nucleotide polymorphisms (SNPs) retained on each LG after various quality checks.

<p>The average distance and the maximum distance between adjacent SNP pairs are also shown for each LG.</p

Relationship between single nucleotide polymorphisms (SNPs) effects obtained from RR-BLUP and Bayesian LASSO for various traits.

<p>A: Fruit firmness (FF), soluble solids (SSC), and Russet; B: Weighted cortex intensity (WCI), astringency (AST), and titratable acidity (TA).</p

Distribution of linkage disequilibrium (LD), measured with <i>r</i>², among adjacent single nucleotide polymorphisms (SNPs) pairs in the training population.

<p>Distribution of linkage disequilibrium (LD), measured with <i>r</i>², among adjacent single nucleotide polymorphisms (SNPs) pairs in the training population.</p

Average predicted accuracy (correlation) and bias (regression) of Bayesian LASSO (BL) and RR-BLUP methods for various traits: fruit firmness (FF), soluble solids (SSC), russet, weighted cortex intensity (WCI), astringency (AST), titratable acidity (TA).

<p>Standard errors are shown in parentheses.</p

Estimates of SNP effects (in additive genetic standard deviation) obtained using Bayesian LASSO for various traits: Fruit firmness (FF); Soluble solids (SSC); Russet; Weighted cortex intensity (WCI); Astringency (AST); Titratable acidity (TA).

<p>Effects are shown for each linkage group (LG: 1 to 17) across the genome.</p

Relative efficiency of GEBV-based selection compared with the conventional BLUP-based selection for various traits: fruit firmness (FF), soluble solids (SSC), russet, weighted cortex intensity (WCI), astringency (AST), titratable acidity (TA).

<p>Estimates of narrow-sense heritability (<i>h</i>²) are also shown for each trait.</p>*<p>Estimated correlation was outside parameter space (>1.0), so constrained to 1.0.</p

Average linkage disequilibrium (LD) measured as <i>r</i>², for pairs of single nucleotide polymorphisms (SNPs) in increments of 10,000 bp, according to the distance between SNPs.

<p>Average linkage disequilibrium (LD) measured as <i>r</i>², for pairs of single nucleotide polymorphisms (SNPs) in increments of 10,000 bp, according to the distance between SNPs.</p

Additional file 2: Figure S1. of Genetic control of pear rootstock-induced dwarfing and precocity is linked to a chromosomal region syntenic to the apple Dw1 loci

Alignment of linkage groups from ‘Louise Bonne de Jersey’ (LBJ) and ‘Old Home’ (OH) pears with the maps of ‘Moonglow’ (Moon) and PEAR1 (Montanari et al., 2013). The markers are named using the NCBI dbSNP accessions and their positions are indicated in centiMorgan. Microsatellite markers mapped in the ‘Moonglow’ x PEAR1 population are underlined. The linkage group (LG) numbering system is consistent with the apple LG numbering. Identified QTLs are shown with blue symbols coming from OH and brown symbols from LBJ. The Dw1 flanking marker Hi01c04 (underlined and red) mapped to LG5 of OH. (PDF 306 kb

Additional file 1: Table S1. of Genetic control of pear rootstock-induced dwarfing and precocity is linked to a chromosomal region syntenic to the apple Dw1 loci

Pearson correlation (first cell) and P-value (second cell) of all the traits measured over four years in the ‘Old Home’ x ‘Louise Bonne de Jersey’ OHxLBJ segregating pear population. Branches: branches per tree; Height: total tree height; Inflorescence: inflorescences per tree; Nodes: nodes per tree; Spurs: spurs per tree; TCAtrunk: trunk cross-sectional area 20 cm above graft unit; TCAroot: TCA of rootstock; TCAsec: TCA secondary growth of the main axis; TCAtert: TCA tertiary growth of the main axis. (PDF 164 kb

The SNP selection workflow.

<p>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.</p