New Genomic Tools for Pear: High Quality Genome Assembly and High Density SNP Array

The development of genomic tools is fundamental for understanding the genetic control of various traits using association studies and for more efficient selection of new cultivars with marker-assisted breeding. We developed an improved genome assembly of the European pear (Pyrus communis) ‘Bartlett’. For whole genome sequencing we chose a double haploid accession of ‘Bartlett’, generated at INRA Angers, in order to address issues related to assembling highly heterozygous genomes. We used a hybrid strategy with PacBio and Illumina sequencing technologies to improve scaffolding into pseudo-chromosome length compared to the fragmented published Bartlett v1.0 genome assembly. We are also developing a high density SNP array from the re-sequencing of 55 pear accessions. A first set of ~600,000 SNPs were screened on a diverse set of 284 genotypes and we will use the results to select high-quality markers for the design of a second, final array of 55,000 SNPs. We will finally use this new SNP array for the genotyping of ~2000 pear accessions held at the National Clonal Germplasm Repository (NGCR) in Corvallis (OR).