Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple (Malus × domestica)

Abstract

Apple cultivars with durable resistance are needed for sustainable management of fire blight, the most destructive bacterial disease of apples. Although studies have identified genetic resistance to fire blight in both wild species and cultivated apples, more research is needed to understand the molecular mechanisms underlying host–pathogen interaction and differential genotypic responses to fire blight infection. We have analyzed phenotypic and transcriptional responses of ‘Empire’ and ‘Gala’ apple cultivars to fire blight by infecting them with a highly aggressive E. amylovora strain. Disease progress, based on the percentage of visual shoot necrosis, started showing significant (p\u2009<\u20090.001) differences between ‘Empire’ and ‘Gala’ 4 days after infection (dai). ‘Empire’ seems to slow down bacterial progress more rapidly after this point. We further compared transcriptome profiles of ‘Empire’ and ‘Gala’ at three different time points after fire blight infection. More genes showed differential expression in ‘Gala’ at earlier stages, but the number of differentially expressed genes increased in ‘Empire’ at 3 dai. Functional classes related to defense, cell cycle, response to stress, and biotic stress were identified and a few co-expression gene networks showed particular enrichment for plant defense and abiotic stress response genes. Several of these genes also co-localized in previously identified quantitative trait locus regions for fire blight resistance on linkage groups 7 and 12, and can serve as functional candidates for future research. These results highlight different molecular mechanisms for pathogen perception and control in two apple cultivars and will contribute toward better understanding of E. amylovora-Malus pathosystem.Disease resistance: How apples fight blightDifferent apple varieties, such as ‘Gala’ and ‘Empire,’ defend themselves against fire blight in different ways, and studying how they do it may help in breeding varieties with better resistance. Fire blight is a devastating bacterial disease that can destroy entire orchard blocks in a single season. Breeding for increased resistance is one of the most efficient ways to combat it. Some apple varieties are naturally more resistant than others, but the underlying genetics are not well understood. Awais Khan at Cornell University in New York and co-workers investigated how the ‘Gala’ and ‘Empire’ varieties defend themselves in the first 72\u2009h after infection. ‘Empire’ showed stronger resistance than ‘Gala,’ with many distinct resistance mechanisms. The researchers identified several resistance genes in each variety, which may eventually be used in breeding more blight-resistant apple varieties.