Associate Professor, School of Integrative Plant Science Plant Pathology and Plant-Microbe Biology Section Cornell AgriTech
Dr. Awais Khan joined Cornell University, Plant Pathology and Plant-Microbe Biology Section, as an Associate Professor in October 2016. Prior to taking this position, he was leading a global research program on genetics of adaptation and abiotic stress tolerance, at the International Potato Center (CIP), Lima, Peru. He 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.
Mechanisms of host disease resistance in apples; particularly to fire blight and apple scab
Quantitative genetics, genomics, genetic diversity, and pre-breeding
Rapid disease detection, pathogen identification, and high-throughput phenotyping tools
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, primarily apples, 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 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. One of our reA number of fungal and bacterial diseases cause huge economic losses to the apple industry globally and are a threat to sustainable orchard production. To make research relevant to the apple 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.search 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 genetic diversity and virulence of Erwinia amylovora and Venturia inaequalis causal pathogens of fire blight and apple scab, respectively.
Outreach and Extension Focus
A number of fungal and bacterial diseases cause huge economic losses to the apple industry globally and are a threat to sustainable orchard production. To make research relevant to the apple 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.
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.
- PLBRG 7900: Graduate-Level Dissertation
View full list of Awais's publications on Google Scholar
Selected Peer-reviewed Journal Publications
- Tegtmeier R, Pompili V, Singh J, Micheletti D, Silva JK, Malnoy M, Khan MA. 2020. Candidate gene mapping identifies genomic variations in the fire blight susceptibility genes HIPM and DIPM across the Malus germplasm. Scientific Reports, 10, 16317.
- Papp D, Gao L, Thapa R, Olmstead D, Khan MA. 2020. Field apple scab susceptibility of a diverse Malus germplasm collection identifies potential sources of resistance for apple breeding. CABI Agriculture and Bioscience, In Press.
- Thapa R, Zhang K, Snavely N, Belongie S, Khan MA. 2020. The Plant Pathology 2020 challenge dataset to classify foliar disease of apples. Applications in Plant Sciences, 8 (9), e11390.
- Singh J, Cobb-Smith D, Higgins E, Khan MA. 2020. Comparative evaluation of lateral flow immunoassays, LAMP, and quantitative PCR for diagnosis of fire blight in apple orchards. Journal of Plant Pathology, https://doi.org/10.1007/s42161-020-00644-w.
- Yu M, Singh J, Khan MA, Sundin GW, Zhao Y. 2020. Complete genome sequence of the fire blight pathogen Erwinia amylovora strain Ea1189. Molecular Plant-Microbe Interactions, https://doi.org/10.1094/MPMI-06-20-0158-A.
- Pereira G, Gemenet D, Mollinari M, Olukolu B, Wood J, Diaz F, Mosquera V, Gruneberg W, Khan MA, Buell R, Yencho C, Zeng ZB. 2020. Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population. Genetics, 215 (3), 579-595.
- Yang H-W, Yu M, Liu J, Khan MA, Zhao Y. 2020. Characterization of genes involved in (p)ppGpp precursor biosynthesis in Erwinia amylovora. Journal of Plant Pathology, https://doi.org/10.1007/s42161-020-00583-6.
- Papp D, Singh J, Gadoury D, Khan MA. 2020. New North American isolates of Venturia inaequalis can overcome apple scab resistance of Malus floribunda 821. Plant Disease, 104 (3), 649-655.
- Singh J, Fabrizio J, Desnoues E, Pereira Silva J, Busch W, Khan MA. 2020. Root system traits impact early fire blight susceptibility in apple (Malus× domestica). BMC Plant Biology, 19 (1), 1-14.
- Mollinari M, Olukolu B, Pereira G, Khan MA, Gemenet D, Yencho C, and Zeng ZB. 2019. Unraveling the hexaploid sweetpotato inheritance using ultra-dense multilocus mapping. G3: Genes|Genomes|Genetics, 10 (1), 281-292.
- Singh J and Khan MA. 2019. Distinct patterns of natural selection determine sub-population structure in the fire blight pathogen, Erwinia amylovora. Scientific Reports, 9 (1), 1-13.
- Gemenet D, Pereira G, Boeck D, Wood J, Mollinari M, Olukolu B, Diaz F, Mosquera V, Ssali R, David M, Kitavi M, Burgos G, Zum Felde T, Ghislain M, Carey E, Swanckaert J, Coin L, Fei Z, Hamilton J, Yada B, Yencho C, Zeng ZB, Mwanga R, Khan MA, Gruneberg W, Buell R. 2019. Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively-associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]. Theoretical and Applied Genetics, 133, 23-36.
- Li X, Singh J, Qin M, Li X, Zhang X, Zhang M, Khan MA, Zhang S, Wu J. 2019. Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and GWAS in pear (Pyrus). Plant Biotechnology Journal, 17 (8), 1582-1594.
- Pereira Silva KJ, Singh J, Bednarek R, Fei Z, Khan MA. 2019. Differential gene regulatory responses to fire blight infection in two apple cultivars (Malus× domestica). Horticulture Research, 6 (1), 35.
- Singh J, Pereira Silva KJ, Fuchs M, and Khan MA. 2019. Potential role of weather, soil and plant microbial communities in rapid decline of apple trees. PloSONE, 14 (3), https://doi.org/10.1371/journal.pone.0213293.
- Wu S, Lau KH, Cao Q, Hamilton JP, Sun H, Zhou C, Eserman L, Gemenet DC, Olukolu BA, Wang H, Crisovan E, Godden G, Jiao C, Wang X, Kitavi N, Manrique-Carpintero N, Vaillancourt B, Wiegert-Rininger K, Yang X, Bao K, Schaff J, Kreuze J, Gruneberg W, Khan MA, Ghislain M, Ma D, Jiang J, Mwanga R, Leebens-Mack J, Coin L, Yencho C, Buell R, Fei Z. 2018. Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nature Communications, 9 (1), 4580.
- Lau KH, del Rosario Herrera M, Crisovan E, Wu S, Fei Z, Khan MA, Buell CR, Gemenet DC. 2018. Transcriptomic analysis of sweet potato under dehydration stress identifies candidate genes for drought tolerance. Plant Direct, 2 (10), https://doi.org/10.1002/pld3.92.
- Zhou C, Duarte T, Silvestre R, Rossel G, Mwanga RO, Khan MA, George AW, Fei Z, Yencho GC, Ellis D, Coin LJ. 2018. Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes. Gates Open Research, 5 (2).
- Villordon A, Gregorie JC, LaBonte D, Khan MA, Selvaraj M. 2018. Variation in ‘Bayou Belle’ and ‘Beauregard’ sweetpotato root length in response to experimental phosphorus deficiency and compacted layer treatments. HortScience, 53 (10), 1534-1540.
- Wu J, Wang Y, Xu J, Korban SS, Fei Z, Tao S, Ming R, Tai S, Khan MA, Postman JD, Gu C. 2018. Diversification and independent domestication of Asian and European pears. Genome Biology, 19 (1), 77.
- Desnoues E, Norelli JL, Aldwinckle HS, Wisniewski ME, Evans KM, Malnoy M, Khan MA. 2018. Identification of novel strain-specific and environment-dependent minor QTLs linked to fire blight resistance in apples. Plant Molecular Biology Reporter, 36 (2), 247-256.
- Bai J, Mao J, Yang H, Khan MA, Fan A, Liu S, Zhang J, Wang D, Gao H, and Zhang J. 2017. Sucrose non-ferment 1 related protein kinase 2 (SnRK 2) genes could mediate the stress responses in potato (Solanum tuberosum L.). BMC Genetics, 18 (1), 41.
- Ramírez DA, Yactayo W, Rens LR, Rolando JL, Palacios S, De Mendiburu F, Mares V, Barreda C, Loayza H, Monneveux P, Zotarelli L, Khan MA, Quiroz R. 2016. Defining biological thresholds associated to plant water status for monitoring water restriction effects: Stomatal conductance and photosynthesis recovery as key indicators in potato. Agricultural Water Management, 177, 369-378.
- Saravia D, Farfán E, Gutiérrez R, Mendiburu F, Schafleitner R, Bonierbale M, Khan MA. 2016. Yield and physiological response of potatoes indicate different strategies to cope with drought stress and nitrogen fertilization. American Journal of Potato Research, 93 (3), 288-295.
- Lindqvist Kreuze H, Khan MA, Salas E, Meiyalaghan S, Thomson S, Gomez R, Bonierbale M. 2015. Tuber shape and eye depth variation in a diploid family of Andean potatoes. BMC Genetics, 16 (1), 57.
- Khan MA, Olsen KM, Sovero V, Kushad MM, Korban SS. 2014. Fruit quality traits might have played crucial role in domestication of apple. The Plant Genome, 7 (3), https://doi.org/10.3835/plantgenome2014.04.0018.
- Potts SM, Khan MA, Han Y, Kushad MM, Korban SS. 2014. Identification of Quantitative Trait Loci (QTLs) for Fruit Quality Traits in Apple. Plant Molecular Biology Reporter, 32 (1), 109-116.
- Khan MA, Zhao YF, Korban SS. 2013. Identification of genetic loci associated with fire blight resistance in Malus through combined use of QTL and association mapping. Physiologia Plantarum, 148 (3), 344-53.
- Wu J, Wang Z, Shi Z, Zhang S, Ming R, Z Shilin, Khan MA, Tao S, Korban SS, Wang H, Chen NJ, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen M, Wang G, Xie L, Sovero V, Sha S, Huang W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull RE, Bennetzen JL, Wang J, Zhang S. 2012. The genome of pear (Pyrus bretschneideri Rehd.). Genome Research, 23 (2), 396-408.
- Khan MA, Han Y, Zhao YF, Troggio M, Korban SS. 2012. A multi-population consensus genetic map reveals inconsistent marker order among maps likely attributed to structural variations in the apple genome. PloSONE, 7 (11), https://doi.org/10.1371/journal.pone.0047864.
- Chen Jun, Khan MA, Qiu W-M, Li J, Zhou H, Zhang Q, Guo W, Zhu T, Peng J, Sun F, Li S, Korban SS, Han Y. 2012. Diversification of genes encoding granule-bound starch synthase (GBSS) in monocots and dicots is marked by multiple genome-wide duplication events. PloSONE, 7 (1), https://doi.org/10.1371/journal.pone.0030088.
- Khan MA, Han Y, Korban SS. 2012. A high-throughput apple SNP genotyping assay using the GoldenGateTM platform. GENE (Elsevier), 494, 196-201.
- Potts SM., Han Y, Khan MA, Kushad MM, Rayburn AL and Korban SS. 2011. Genetic diversity and characterization of a core collection of Malus germplasm using simple sequence repeats (SSRs). Plant Molecular Biology Reporter, 30 (4), 827-837.
- Han Y, Zheng D, Vimolmangkang S, Khan MA, Beever JE, Korban SS. 2011. Integration of physical and genetic maps in apple confirms whole-genome and segmental duplications in the apple genome. Journal of Experimental Botany, 62 (14), 5117-5130.
- Graham IA, Besser K, Blumer S, Branigan CA, Czechowski T, Elias L, Guterman I, Harvey D, Isaac PG, Khan MA, Larson TR, Li Y, Owens S, Pawson T, Penfield T, Rae AM, Rathbone DA, Ross J, Smallwood MF, Segura V, Townsend T, Vyas D, Winzer T and Bowles D. 2010. The genetic map of Artemisia annua L. identifies multiple loci affecting yield of the antimalarial drug artemisinin, Science, 327, 328-331.
- Le Roux PM, Khan MA, Duffy B, Patocchi A, Broggini GAL and Gessler C. 2010. Quantitative trait loci mapping of fire blight resistance in the apple cultivars 'Florina' and 'NovaEasygro'. Genome, 53, 710-722.
- Khan MA, Durel C-E, Duffy B, Drouet D, Kellerhals M, Gessler C and Patocchi A. 2008. Identification and validation of QTLs linked to fire blight resistance in Malus and their applicability in marker-assisted selection. Twelfth (12th) EUCARPIA symposium on fruit breeding and genetics. Acta Horticulture (ISHS), 814, 753-758.
- Khan MA, Durel C-E, Duffy B, Drouet D, Kellerhals M, Gessler C and Patocchi A. 2007. Development of molecular markers linked to the 'Fiesta' linkage group 7 major QTL for fire blight resistance and their application for marker-assisted selection. Genome, 50, 568-577.
- Khan MA, Duffy B, Gessler C and Patocchi A. 2006. QTL mapping of fire blight resistance in apple. Molecular Breeding, 17, 299-306.
Selected Review Articles and Book Chapters
- Peil A, Emeriewen OF, Khan MA, Kostick S, Malnoy M. 2020. Status of fire blight resistance breeding in Malus. Journal of Plant Pathology, https://doi.org/10.1007/s42161-020-00581-8.
- Gemenet DC, and Khan MA. 2017. Opportunities and challenges to implementing genomic selection in clonally propagated crops. In 'Genomic Selection for Crop Improvement'. Springer, 185-198, editors R. Varshney, M. Roorkiwal and M. Sorrells.
- Rasheed A, Hao Y, Xia X, Khan MA, Xu Y, Varshney RK, He Z. 2017. Crop breeding chips and genotyping platforms: progress, challenges and perspectives. Molecular Plant, 10 (8), 1047-1064.
- Khan MA, Gemenet D, Villordon A. 2016. Root system architecture and abiotic stress tolerance: Current knowledge in root and tuber crops. Frontiers in Plant Science, 7, 1584.
- Khan MA, and Korban SS. 2012. Association mapping in forest trees and fruit crops. Journal of Experimental Botany, 63 (11), 4045-4060.
- Khan MA, Zhao Y and Korban SS. 2011. Molecular mechanisms of pathogenesis and resistance to the bacterial pathogen Erwinia amylovora, causal agent of fire blight disease in rosaceae. Plant Molecular Biology Reporter, 30 (2), 247-260.
- Khan MA and Papp D. 2020. Confirming the breakdown of apple scab resistance in Malus floribunda 821, the most important source for scab resistance breeding, in North America. New York Fruit Quarterly, 28 (1), 5-7.
- van Zoeren J and Khan MA. 2020. Using computer vision to detect foliar diseases in apples. Cornell Cooperative Extension, Lake Ontario Fruit Program. Fruit Notes, 20 (7).
- Khan MA, Cobb-Smith D, Higgins L, and Singh J. 2019. Pathogen detection assays for fire blight management in apple orchards. New York Fruit Quarterly, 27 (2), 27-30.
- Khan MA and Singh J. 2019. Rapid decline of apple trees: Looking into potential causes. New York Fruit Quarterly, 27 (2), 15-18.
- Khan MA, Desnoues E, and Clark M. 2018. Bacterial strain affects cultivar response to fire blight in apples. New York Fruit Quarterly, 26 (2), 15-20.
- Khan MA. 2018. Importance of bacterial strains in cultivar response to fire blight. Cornell Cooperative Extension, Lake Ontario Fruit Program. Fruit Notes, 18 (5).
- Khan MA and Singh J. 2018. Apple cultivars use varying mechanisms in response to fire blight infection. New York Fruit Quarterly, 26 (4).
- Khan MA and Chao T. 2017. Wild apple species as a source of fire blight resistance for sustainable productivity of apple orchards. New York Fruit Quarterly, 25 (4), 13-18.
- Merk HL, Wheeler N, Sim S, Khan MA, Harry D, Kling J, Zhang Z, Van Deynze A, Francis D. 2012. Association Analysis. eXtension Foundation. Available at: http://www.extension.org/pages/63011/association-analysis.
- Khan MA. 2012. Association mapping and TASSEL software tutorial. eXtension Foundation. Available at: http://www.extension.org/pages/62755/association-mapping-and-tassel-software-tutorial.
- Khan MA. 2011. Estimation of linkage disequilibrium (ld) decay. eXtension Foundation. Available at: http://www.extension.org/pages/61909/estimation-of-linkage-disequilibrium-ld-decay.
Selected Invited Presentations
- Genetics of host resistance, susceptibility levels, and root traits for disease management in apples. Student invited; MSU PBGB-Corteva Graduate Student Symposium; December 2019.
- Genome and phenome-based technologies for detection and disease management, Center of Biotechnology Research at Constantine, Algeria; September 2019.
- Two promising strategies to fire blight control: decreased host susceptibility levels and rootstock traits, Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, State College; September 2019.
- Significance of RSA of Vegetatively Propagated and Woody Perennial Crops for Abiotic and Biotic stress tolerance at Session “The Plant Root System: Gateway to Plant-Beneficial Rhizosphere Microbe Interactions”; APS Plant Health; Cleveland, Ohio; August 2019.
- Malus Species: Valuable Genetic Resource for Pest and Disease Resistance in Apple, International Fire blight Symposium; Traverse City, Michigan; June 2019.
- Importance of bacterial strain-specificity to improve fire blight resistance and management in apple, 9th International Rosaceae genomics Conference, Nanjing, China; June 2018.
- Improving crop stress tolerance: phenomics, genomics, and the environment, University of Illinois, Urbana-Champaign; September 2017.
- Grant will help researchers prevent apple fire blight in US - Cornell Chronicle [2020-10-05]
- Apple scab study aims for disease-resistant genes - Good Fruit Grower [2020-02-20]
- Fire blight spreads northward, threatening apple orchards - New York Times [2019-12-02]
- Awards fund innovations in digital agriculture - Cornell Chronicle [2019-06-14]
- Young apple trees are dying, and no one understands why - The Economist [2019-04-13]
- Something is rapidly killing young apple trees in North American orchards. Scientists are stumped - Science - [2019-03-21]
- Eight grants focus on innovation in China - Cornell Chronicle [2019-03-27]
15 Castle Creek Drive
112 Barton Lab
Geneva, NY 14456
mak427 [at] cornell.edu
School & Section
School of Integrative Plant Science
Plant Pathology and Plant-Microbe Biology Section
Plant Pathology and Plant-Microbe Biology
Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
- Master of Science
Georg-August University, Goettingen, Germany
Awais in the news
A team of researchers has sequenced the Honeycrisp apple genome, a boon for scientists and breeders working with this popular and economically important cultivar.
- Cornell AgriTech
- School of Integrative Plant Science
- Cornell AgriTech
- School of Integrative Plant Science
- Plant Pathology and Plant-Microbe Biology Section