Skip to main content

Khan Lab: Mechanisms of Fruit Diseases and Resistance

School of Integrative Plant Science| Plant Pathology and Plant-Microbe Biology Section

Welcome to the Khan Lab!

Briefly, specific areas of research in our program are: 1) Understanding the genetic underpinnings of host resistance and susceptibility to fire blight and apple scab, 2) Designing strategies toward the accelerated development of apple cultivars with improved disease resistance, 3) Characterizing population genetics and virulence of Erwinia amylovora and Venturia inaequalis, and 4) Developing tools for rapid disease detection and pathogen identification.


A large number of fungal and bacterial diseases cause huge economic losses to the fruit industry globally and are a threat to sustainable orchard production. Our research program’s main focus is the characterization of mechanisms of disease resistance and susceptibility, and development of strategies and tools to speed up targeted improvement of disease resistance of rosaceous fruits, primarily apples. Our research focus, the rose family (Rosaceae), is culturally and commercially valuable, as many of the most popular fruits (apples, pears, peaches, plums, almonds, apricots, strawberries, cherries, loquats, and raspberries) belong to the rosaceae family.

Some of the tools that we use are quantitative genetics, QTL and association mapping, marker-assisted selection, genomics, transcriptomics, bioinformatics, and genome editing. We are also interested in developing high-throughput methods for plant resistance phenotyping.

We use quantitative genetics, QTL and association mapping, genomics, transcriptomics and bioinformatics to detect genetic regions and candidate genes controlling resistance and susceptibility to fungal and bacterial diseases of apples such as fire blight and apple scab. We also identify molecular markers tightly linked with QTLs and develop multiplexed marker assays to deploy multiple resistance alleles in commercially favored backgrounds through marker-assisted selection. Significant efforts are devoted into fine mapping and genome editing for gene discovery, validation and to develop pre-breeding lines with improved disease resistance. In addition, we also investigate the role of root traits of apple rootstocks in modulation of scion’s disease tolerance/susceptibility.

One of our research interests is to develop high-throughput resistance phenotyping methods to visualize, quantify and assess the severity of disease, and differences in response between plants in terms of symptoms and progress rate. For example, we are developing real-time imaging and analytical methods to monitor progress of fire blight infection, with concurrent sampling of transcripts and the metabolome to identify specific spatio-temporal mechanisms at genetic, cellular, and molecular levels. We also have interest in characterizing the genetic diversity and virulence of Erwinia amylovora and Venturia inaequalis, the causal pathogens of fire blight and apple scab, respectively. We also have active collaborations to develop genome-based and machine learning-based methods for rapid disease detection and pathogen identification


The aim of our extension program is to get a strong understanding of concerns, needs, and interests of stakeholders, in order to orient and develop disease resistance research to address their priorities by applying modern genetics and genomic tools. To make our research relevant to the apple industry, growers and public, our extension and outreach focus is on connecting lab and field research for direct relevance and faster uptake of outputs. We participate, present and organize sessions at winter fruit schools, field days, meetings, workshops and expos to communicate relevant scientific findings to engage growers and public for long-term impact.


An important goal of our outreach and educational efforts are to train undergraduate and graduate students as future leaders in the disciplines of plant pathology, genetics, bioinformatics and germplasm characterization, critical fields for economic competitiveness and food security in the US and globally. Please visit Research and Extension/Outreach for more details.

We welcome and support motivated summer scholars, undergraduate, graduate students, and postdoctoral scientists. If you are interested in any of the above areas, please contact us at

October 2020

Skip to toolbar