Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids

Abstract

We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear ('Old Home'×'Louise Bon Jersey') and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality.

Figure 1. Pedigree diagrams for segregating populations used for SNP evaluation.

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

Figure 2. A typical example of an AB×AB SNP (ss527787957), as represented in GenomeStudio.

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.

Figure 3. Typical examples of SNPs with null allele as represented in GenomeStudio.

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.

Figure 4. Alignment of LG9 from four parental maps P128R068T003, ‘Moonglow’, P202R137T052 and ‘Old Home’.

The lines between the maps each show markers in common with two other parents.

Figure 5. Alignment of OH×LBJ LG6 with chromosome 6 of the 'Golden Delicious' genome.

Lines show the markers in common.