A study of gene expression changes at the <Emphasis Type="Italic">Bp-2</Emphasis> locus associated with bitter pit symptom expression in apple (<Emphasis Type="Italic">Malus pumila</Emphasis>)

Bitter pit is a physiological disorder of apples that develops in the latter stages of fruit development and during storage. It is characterized by localized necrotic cells that collapse and form pits in the epidermis and outer cortex of fruit. The disorder has been associated with low calcium concentrations, and poor calcium distribution within the fruit. To date, the mechanism that leads to individual cell necrosis, while surrounding cells remain healthy, is not fully understood. In order to ascertain the underlying process of bitter pit incidence in apple fruit, a large mapping population of “Braeburn” (susceptible to bitter pit)?×?“Cameo” (resistant to bitter pit) was used to map the trait over two growing seasons. A subset of 94 genotypes from the mapping population representing the full range of phenotypes in the same ratio as the full population were selected for genotyping and functional characterization. RNA-Seq analysis on fruit samples of three resistant and three susceptible lines at seven developmental stages (21, 42, 63, 84, 105, 126, and 147 days post fertilization) identified a number of candidate genes displaying differential gene expression. A subset of candidate genes selected based on their position within the identified QTL interval on linkage group 16 were validated by RT-qPCR, and two candidate genes displaying differential gene expression were highlighted as strong candidates for the control of bitter pit symptom expression at the Bp-2 locus.