Personal Information:
Full name: Awais Khan
Position:Abiotic Stress geneticist Potato & Sweet potato
Telephone:+51 1 349 6017 ext 3130

Dr. Awais Khan is an abiotic stress geneticist for potatoes and sweet potatoes, leading the efforts to uncover the genetic basis of abiotic stress tolerance, in particular for drought and heat, for potatoes and sweet potatoes. His background is in population and quantitative genetics, comparative genomics and bioinformatics, with wide experience of genetic and genomic tools and techniques. He is particularly interested in making use of current advances in genome sequencing and bioinformatics to address issues of maintaining crop productivity under worsening climate conditions.


Originally from Azad Kashmir, Pakistan, Dr. Khan earned an M.Sc. in Plant Breeding and Genetics/Tropical & International Agriculture at the Georg-August University Göttingen, Germany, with a focus on using biochemical and molecular markers to study the genetic diversity in safflower. He then moved on to the Swiss Federal Institute of Technology (ETH) in Zurich, Switzerland, where he identified genomic regions linked to fire blight resistance in apples. He identified and tested QTLs linked to fire blight and developed markers suitable for marker-assisted selection. Next, he worked as a postdoctoral researcher in the Department of Biology, University of York, UK on the genetic control of artemisinin (an anti-malarial drug), related metabolites, and biomass traits in Artemisia annua, assembling EST sequence reads into contigs and identifying SNPs and SSRs for the development of high-throughput genotyping assays and construction of a high-density genetic map, and conducting QTL and candidate gene association mapping.

Before moving to CIP, Dr. Khan was at the University of Illinois, Urbana-Champaign where he used genomics, quantitative and population genetics, and bioinformatics to elucidate the genetic control of fruit quality and disease resistance in apples. He designed the first high-throughput assay using Illumina Bead technology for apple and set up an efficient and high throughput genotyping platform for apple and pear based on restriction site associated DNA and genotyping-by-sequencing (GBS) approach. He was also involved with the international consortium to sequence the genome of the Asian pear.

Research Interest:

Quantitative genetics, population genetics, molecular breeding, genetic response of plants to abiotic stresses particularly drought and heat stress in potatoes and sweet potatoes.

Career highlights:

Research Experience:

08/2010-10/2012        Postdoctoral Scientist

Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana-Champaign, USA.

Research Area: Quantitative genetics and comparative genomics, molecular breeding and population genetics.


01/2008-05/2010        Postdoctoral Research Associate

CNAP, Department of Biology, University of York, United Kingdom.

Research Area: Quantitative genetics and genomics, forward and reverse genetics, molecular plant breeding, and population genetics.


09/2007-12/2007        Research Assistant    

Swiss Federal Institute of Technology Zürich (ETH), Switzerland.

Research Area: Quantitative genetics of disease resistance, marker-assisted selection and marker-assisted breeding.



Ph.D.  2004-2007      Molecular Plant Pathology and Plant Breeding.

Swiss Federal Institute of Technology Zürich (ETH), Switzerland.      

Dissertation title: The genetic basis of resistance to fire blight in apples (Malus sp.).


Master’s (M.Sc.) 2001-2003 Plant Breeding and Genetics/Tropical & International Agriculture.

Georg-August University Göttingen, Germany.

Thesis title: Morphological, Chemical and Molecular Evaluation of Genetic Diversity in Safflower.

Recent Publications (Since 2010):
  • Khan MA, Zhao Y, and Korban SS. 2013. Identification of genetic loci associated with fire blight resistance in Malus through combined use of QTL and association mapping. Physiologia plantarum.
  • Shazad U, Khan MA, Jaskani M, Khan I, Korban SS. 2013.Genetic diversity and phylogenetic analysis of Moringa oleifera using simple sequence repeats (SSRs) and the chloroplast atpB gene. Accepted in Conservation Genetics.
  • Identification of differentially expressed genes related to coloration in red/green mutant pear (Pyrus communis L.). 2013. J Wu, G Zhao, YN Yang, WQ Le, MA Khan, SL Zhang, C Gu, WJ Huang. Tree Genetics & Genomes 9 (1), 75-83
  • Gu C, Liu Q, Yang Y, Zhang S, Zhao G, Wu H, Zhang S, Khan MA and Wu J. 2013. Inheritance of Hetero-Diploid Pollen S-Haplotype in Self-Compatible Tetraploid Chinese Cherry (Prunus pseudocerasus Lindl). PLoS ONE 8 (4).
  • Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, et al. 2013. The genome of pear (Pyrus bretschneideri Rehd.). Genome Research.
  • 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. PLoS ONE. 7 (11): e47864.
  • Zhang Q, Ma B, Li H, Chang Y, Han Y, Li J, Wei G, Zhao S, Khan MA, Zhou Y, Gu C, Zhang X, Han Z, Korban SS, Li S and Han Y. 2012. Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple. BMC Genomics. 13 (1): 537.
  • Wu J, Zhao G, Yang Y, Le W, Khan MA, Zhang S, Gu C, Huang W. 2012. Identification of Differentially Expressed Genes Related to Coloration in Red/Green Mutant Pear (Pyrus communis L.). Tree Genetics and Genomes (Springer).
  • Khan MA, and Korban SS. 2012. Association mapping in forest trees and fruit crops. Journal of Experimental Botany. DOI: 10.1093/jxb/ers105. *Co-corresponding author
  • 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. PLoS ONE. DOI: 10.1371/journal.pone.0030088.*Co-first author
  • 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 Mol Biol Rep. DOI: 10.1007/s11105-011-0399-x.
  • He W, King AJ, Khan MA, Cuevas JA, Ramiaramanana D and Graham IA. 2011. Genetic and biochemical analysis of diversity in toxic and non-toxic accessions of Jatropha curcas (L.) from Madagascar and Mexico. Plant Physiology and Biochemistry 49: 1183-1190.
  • 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. DOI: 10.1093/jxb/err215.
  • 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 Mol Biol Rep. DOI: 10.1007/s11105-011-0334-1.
  • Khaliq I, Khan MA and Pearce S. 2011. Ty1-Copia retrotransposons are heterogeneous and extremely high copy number and can cause genetic instability in Agave tequilana genome. Genetic Resources and Crop Evolution. DOI: 10.1007/s10722-011-9705-6.
  • Gu C, Zhang SJ, Khan MA, Yang YN and Wu HQ. 2011. Molecular analysis of eight SFB alleles and a new SFB-like gene in Prunus pseudocerasus and Prunus speciosa. Tree Genetics and Genomes 7: 891-902.
  • 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.*Co-first author
My “CIP” Work:

Leader of Abiotic Stress Genetics in Potatoes and Sweet potatoes in Global Program Genetic Crop Improvement.

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