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

Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization

BackgroundBoth a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development. To address this gap, we designed a high-density, high-efficiency and robust single nucleotide polymorphism (SNP) array for pear, with the main objectives of conducting genetic diversity and genome-wide association studies.ResultsBy applying a two-step design process, which consisted of the construction of a first 'draft' array for the screening of a small subset of samples, we were able to identify the most robust and informative SNPs to include in the Applied Biosystems™ Axiom™ Pear 70 K Genotyping Array, currently the densest SNP array for pear. Preliminary evaluation of this 70 K array in 1416 diverse pear accessions from the USDA National Clonal Germplasm Repository (NCGR) in Corvallis, OR identified 66,616 SNPs (93% of all the tiled SNPs) as high quality and polymorphic (PolyHighResolution). We further used the Axiom Pear 70 K Genotyping Array to construct high-density linkage maps in a bi-parental population, and to make a direct comparison with available genotyping-by-sequencing (GBS) data, which suggested that the SNP array is a more robust method of screening for SNPs than restriction enzyme reduced representation sequence-based genotyping.ConclusionsThe Axiom Pear 70 K Genotyping Array, with its high efficiency in a widely diverse panel of Pyrus species and cultivars, represents a valuable resource for a multitude of molecular studies in pear. The characterization of the USDA-NCGR collection with this array will provide important information for pear geneticists and breeders, as well as for the optimization of conservation strategies for Pyrus

Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization

Background Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development. To address this gap, we designed a high-density, high-efficiency and robust single nucleotide polymorphism (SNP) array for pear, with the main objectives of conducting genetic diversity and genome-wide association studies. Results By applying a two-step design process, which consisted of the construction of a first ‘draft’ array for the screening of a small subset of samples, we were able to identify the most robust and informative SNPs to include in the Applied Biosystems™ Axiom™ Pear 70 K Genotyping Array, currently the densest SNP array for pear. Preliminary evaluation of this 70 K array in 1416 diverse pear accessions from the USDA National Clonal Germplasm Repository (NCGR) in Corvallis, OR identified 66,616 SNPs (93% of all the tiled SNPs) as high quality and polymorphic (PolyHighResolution). We further used the Axiom Pear 70 K Genotyping Array to construct high-density linkage maps in a bi-parental population, and to make a direct comparison with available genotyping-by-sequencing (GBS) data, which suggested that the SNP array is a more robust method of screening for SNPs than restriction enzyme reduced representation sequence-based genotyping. Conclusions The Axiom Pear 70 K Genotyping Array, with its high efficiency in a widely diverse panel of Pyrus species and cultivars, represents a valuable resource for a multitude of molecular studies in pear. The characterization of the USDA-NCGR collection with this array will provide important information for pear geneticists and breeders, as well as for the optimization of conservation strategies for Pyru

Alignment of LG9 from four parental maps P128R068T003, ‘Moonglow’, P202R137T052 and ‘Old Home’.

<p>The lines between the maps each show markers in common with two other parents.</p

A typical example of an AB×AB SNP (ss527787957), as represented in GenomeStudio.

<p>Parents ‘Old Home’ and ‘Louise Bon Jersey’ are indicated in yellow; the red cluster is identified as AA, the blue as BB and the purple as AB genotype. The total number of the individuals analyzed here is 297 and the segregation ratio is 1∶2:1.</p

Alignment of OH×LBJ LG6 with chromosome 6 of the 'Golden Delicious' genome.

<p>Lines show the markers in common.</p

Pedigree diagrams for segregating populations used for SNP evaluation.

<p>A) P128R068T003בMoonglow’; B) P037R048T081×P019R045T042, and C) P202R137T052×P128R068T003 and P202R137T052×P266R225T064.</p

Typical examples of SNPs with null allele as represented in GenomeStudio.

<p>A) A 00×AB SNP (ss527789894), as represented in GenomeStudio. Parents P128R068T003 and ‘Moonglow’ are indicated in yellow; the red and blue clusters are identified as A0 and B0 genotypes, respectively. The total number of the individuals analyzed is 143 and the segregation ratio is 1∶1. B) A 00×A0 SNP (ss475879014), as represented in GenomeStudio. Parents P128R068T003 and ‘Moonglow’ are indicated in yellow; the red cluster is identified as heterozygous genotypes (A0), while genotypes with missing call (in black) are identified as homozygous for the null allele (00). The total number of the individuals analyzed is 143 and the segregation ratio is 1∶1. C) A A0×B0 SNP (ss475882353), as represented in GenomeStudio. Parents P128R068T003 and ‘Moonglow’ are indicated in yellow; the red, blue and purple clusters are identified as A0, B0 and AB genotypes, respectively, while genotypes with missing call (in black) are identified as homozygous for the null allele (00). The total number of the individuals analyzed is 143 and the segregation ratio is 1∶1:1∶1.</p

Number of polymorphic and mapped apple and pear markers for each segregating population.

<p>OH×LBJ = ‘Old Home’בLouise Bon Jersey’; T003×M = P128R068T003בMoonglow’; T042×T081) = P019R045T042×P037R048T081; T052×T003 = P202R137T052×P128R068T003; T052×T065 = P202R137T052×P266R225T064.</p