Awais Khan

Awais Khan

Associate Professor

112 Barton Lab
(315) 787-2446

I joined Cornell University, Plant Pathology and Plant-Microbe Biology Section, as an associate professor in October 2016. Prior to taking this position, I was leading a global research program on genetics of adaptation and abiotic stress tolerance, at the International Potato Center (CIP), Lima, Peru. I earned a PhD from the Swiss Federal Institute of Technology (ETH), Zurich, Switzerland on fire blight of apples, and an MSc from Georg-August University, Gottingen, Germany, with further research experience at the University of York, UK and University of Illinois, Urbana-Champaign, USA.

Research Focus

My research focus is to characterize mechanisms of disease resistance and pathogenesis, strategies and tools for accelerated and targeted improvement of disease resistance in rosaceous fruits and to develop 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 to fungal and bacterial diseases 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 varieties with improved disease resistance. 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.

Outreach and Extension Focus

A number of fungal and bacterial diseases cause huge economic losses to the fruit industry globally and are a threat to sustainable production. To make research relevant to the industry and growers, our extension focus is on connecting lab and field research to the orchards for direct relevance and faster uptake of outputs. Either through extension specialists or direct connections with growers, we organize regular lab and orchard visits and participate in winter fruit schools, and field days. The aim of 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.

Teaching Focus

Currently, I do not have a teaching responsibility. However, I have been involved in teaching and training undergraduate, and graduate students for quantitative genetics, molecular markers, and crop improvement in my previous institutions. I have a strong interest in teaching and plan to participate as guest lecturer for courses at CALS (College of Agriculture and Life Sciences) in the near future.

Selected Publications

Journal Publications