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

Genomic resources are becoming increasingly available for Rosaceae crops, including pears. We have used next generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars to develop a set of high throughput markers useful for large‐scale genotyping in the genus Pyrus. A set of 1096 pear SNPs was chosen and combined with 7867 apple SNPs in an Infinium II® array (Illumina). The 9K Infinium II array was evaluated using a segregating population of European pear parents (‘Old Home’ x ‘Louise Bon Jersey’) and three inter‐specific families derived from Asian (P. pyrifolia and P. x bretschneiderii) and European pear. In total, 806 polymorphic pear markers were used for the construction of the first SNP‐based genetic maps for pear. In addition, 785 SNP markers derived from apple (10% of the total apple SNPs included in the array) were polymorphic, including markers with null alleles. The study is first to assess SNP transferability across the genera Malus and Pyrus. The construction of high density SNPbased and gene‐based genetic maps represents an important step in the process of identifying chromosomal regions associated with horticultural characters, such as pest and disease resistance, fruit yield and quality.