Identifying early response genes against apple Marssonina blotch via comparative gene expression analysis between resistant and susceptible cultivars

Apple Marssonina blotch, caused by the fungus Diplocarpon mali (D. mali), is a severe disease in the world. This disease causes early defoliation and reduces fruit quality and tree growth. Considering the importance of defense mechanisms that begin with early reactions, we tried to identify the genes showing early response against D. mali among flavonoid biosynthesis, antioxidants, transcription factors, and pathogenesis-related (PR) genes. We artificially inoculated D. mali suspensions on detached leaves of resistant and susceptible ‘Jiguan’ and ‘Mutsu’ apples as cultivars, respectively. Gene expression was examined at 0, 3, 6, 12, 24, 48, and 72 h post inoculation (hpi) and 7, 10, and 13 days post inoculation (dpi) and divided into early (0–12 hpi), middle (24–72 hpi), and late (7–13 dpi) stages. In ‘Jiguan’ inoculated leaves, up-regulated genes were mainly involved in the flavonoid pathway and antioxidant activity, which most likely have played an antifungal role against D. mali by maintaining free radicals and decreasing oxidative damage in plant cells. In particular, most flavonoid biosynthetic genes are significantly induced in the early stage, implying that they are early response genes. On the contrary, all PR genes were rapidly induced in inoculated ‘Mutsu’ leaves, especially when symptoms were clearly visible. These results provide insight into the genetic factors that contribute to suppressing or limiting D. mali infection at an early stage.