Transcriptome analysis of watercore in Pyrus pyrifolia by comparing pairs of susceptible and resistant F1 sibs

•Watercore is a disorder characterized by watery translucent areas in Japanese pear fruit flesh.•Use of F1 sibs helped to solve its poor reproducibility problem.•F1 sibs enabled differential transcriptome analysis before symptoms become visible.•Susceptible sibs highly expressed metallothionein, invertase and hormone-related genes.•Our data provide new insights into the mechanisms of watercore development. Watercore is a physiological disorder of Japanese pear fruits, in which a watery translucent area appears in the flesh of fruits on the tree. The disorder leads to the loss of commercial value, and resistance to watercore is one of the most important features to be studied in the breeding of Japanese pear. Even in susceptible cultivars such as ‘Hosui’ (syn. ‘Housui’), the degree of watercore development varies markedly from year to year, which makes it difficult to analyze the characteristics of this phenomenon prior to visible watercore development. We used two F1 sib pairs from ‘Hosui’ × ‘Hougetsu’ and ‘Akiakari’ × ‘Taihaku’ crosses. Each pair contains a susceptible sib and a resistant sib. In these pairs, susceptible sibs developed severe watercore in all the fruits examined in each year, whereas no watercore was found even in overmature fruits of resistant sibs. To search for genes related to watercore, we used a custom pear microarray and studied differential gene expression in susceptible and resistant sibs prior to visible watercore development. We identified 115 differentially expressed genes including sugar metabolism–, hormone–, and cell wall–related genes. Some of these genes were differentially expressed only in immature fruits prior to watercore development. These genes would be useful as molecular markers to predict watercore at early developmental stages or in pear breeding programs.