Pear, belonging to the genus Pyrus, is one of the most economically important temperate fruit crops. Pyrus is an important genus of the Rosaceae family, subfamily Maloideae, and has at least 22 different species with over 5000 accessions maintained or identified worldwide. With the release of draft whole-genome sequences for Pyrus, opportunities for pursuing studies on the evolution, domestication, and molecular breeding of pear, as well as for conducting comparative genomics analyses within the Rosaceae family, have been greatly expanded. In this review, we highlight key advances in pear genetics, genomics, and breeding driven by the availability of whole-genome sequences, including whole-genome resequencing efforts, pear domestication, and evolution. We cover updates on new resources for undertaking gene identification and molecular breeding, as well as for pursuing functional validation of genes associated with desirable economic traits. We also explore future directions for “pear-omics”.

Development of apple (Malus domestica) cultivars resistant to fire blight, a devastating bacterial disease caused by Erwinia amylovora, is a priority for apple breeding programs. Towards this goal, the inactivation of members of the HIPM and DIPM gene families with a role in fire blight susceptibility (S genes) can help achieve sustainable tolerance. We have investigated the genomic diversity of HIPM and DIPM genes in Malus germplasm collections and used a candidate gene-based association mapping approach to identify SNPs (single nucleotide polymorphisms) with significant associations to fire blight susceptibility. A total of 87 unique SNP variants were identified in HIPM and DIPM genes across 93 Malus accessions. Thirty SNPs showed significant associations (p < 0.05) with fire blight susceptibility traits, while two of these SNPs showed highly significant (p < 0.001) associations across two different years. This research has provided knowledge about genetic diversity in fire blight S genes in diverse apple accessions and identified candidate HIPM and DIPM alleles that could be used to develop apple cultivars with decreased fire blight susceptibility via marker-assisted breeding or biotechnological approaches.

Fire blight, caused by Erwinia amylovora, is a destructive bacterial disease that severely hampers apple production. To conduct QTL (Quantitative Trait Locus) studies for breeding resistant apple cultivars, phenotyping of large genetic mapping populations of apples for fire blight resistance is essential. This, however, necessitates precise, quantitative data spanning multiple years, locations, and pathogen strains. It can be time-consuming and resource-intensive to keep QTL mapping populations for apples in the field and greenhouse. This creates a bottleneck for identifying novel QTL for fire blight resistance or developing resistant cultivars. To address this challenge, we present an image-based method for rapid and accurate phenotyping fire blight resistance using apple leaf discs. This leaf disc assay demonstrates significant (p < 0.05) percent disease area (PDA) differences in fire blight inoculations among eight apple genotypes with well-known resistance levels. Furthermore, the image-based leaf disc assay consistently shows a 40–70% difference in PDA between resistant and susceptible checks. We also report high within and across trial broad sense heritability values ranging from 0.86–0.97. We demonstrate the use of K-means clustering and best linear unbiased estimators (BLUEs) to combine multiple trials. This assay offers an efficient alternative to traditional fire blight screening methods, potentially improving our understanding of the host response and accelerating the development of resistant apple cultivars.