Genome-wide association mapping identifies novel loci underlying fire blight resistance in apples

Authors: THAPA, RANJITA - Cornell University; SINGH, JUGPREET - Cornell University; Gutierrez, Benjamin; ARRO, JIE - US Department Of Agriculture (USDA); KHAN, AWAIS - Cornell University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/17/2020
Publication Date: 3/1/2021
Citation: Thapa, R., Singh, J., Gutierrez, B.L., Arro, J., Khan, A. 2021. Genome-wide association mapping identifies novel loci underlying fire blight resistance in apples. The Plant Genome. https://doi.org/10.1002/tpg2.20087.
DOI: https://doi.org/10.1002/tpg2.20087

Interpretive Summary: Fire blight is the most significant disease in apple, impacting the production and health of a tree. It is caused by the bacterium Erwinia amylovora. Horticultural practices, especially pesticide applications, are used to manage this disease in apple. Some apples and their wild relatives show resistance to fire blight. This type of genetic resistance is valuable because it allows for additional protection of plants should other practices become less effective or unsustainable. Additionally, fire blight resistant apples can be used in breeding to develop new cultivars with both superior fruit and disease resistance. Using historic fire blight data from the USDA Apple collection, we identified new sources of genetic resistance that will benefit future fire blight research and apple breeding.

Technical Abstract: Fire blight, caused by epiphytotic gram-negative bacteria Erwinia amylovora, is the most destructive bacterial disease of apples. Genetic mechanisms of fire blight resistance have mainly been studied using traditional bi-parental Quantitative Trait Loci (QTL) mapping approaches. Here, we use large-scale historic shoot and blossom fire blight data collected over multiple years and Genotyping-by-Sequencing (GBS) markers to identify significant marker-trait associations in a diverse set of 566 Malus× domestica accessions. There was large variation in fire blight resistance/susceptibility in these accessions. We have identified 23 and 38 QTL distributed across all 17 chromosomes of apples with significant association to shoot and blossom blight, respectively. Out of 23 and 38 significant loci for shoot and blossom blight, 4 and 19 QTL potentially colocalized with QTL previously identified as either responsible for fire blight or apple scab resistance, respectively. Furthermore, with transcriptomics data of two apple cultivars with contrasting fire blight response, we have also identified candidate genes for fire blight susceptibility underlying these QTL regions. However, further experiments are needed to confirm and validate these marker-trait associations, develop diagnostic markers and functionally characterize candidate genes before use in marker-assisted breeding or genome-editing to develop apple cultivars with decreased fire blight susceptibility.