Dr. Shawkat Ali

Current research and/or projects

• Evaluation of fungal endophytes for protection of blueberry bushes and grapevines diseases

• Grapevine cryotherapy as a tool for virus remediation  

• Isolation and molecular identification of onion bacterial rot causing pathogens

• Improving the production and storage of high quality apple cultivars

• Molecular identification of the root pathogens in strawberry fields

• Molecular identification of blueberry fungal pathogens

• Emerging fruit tree decline

• Characterization of effectors from fire blight pathogen Erwinia amylovowa




1.   Kun-Peng Jia#, Jianing Mi#, Shawkat Ali#, Hajime Ohyanagi, Juan C. Moreno, Abdugaffor Ablazov, Aparna Balakrishna, Lamis Berqdar, Alessia Fiore, Gianfranco Diretto, Claudio Martínez, Angel R. de Lera, Takashi Gojobori, and Salim Al-Babili (2021) An alternative, zeaxanthin epoxidase-independent abscisic acid biosynthetic pathway in plants. Molecular Plant DOI: 10.1016/j.molp.2021.09.008.

2.   Pervaiz A. Abbasi, Paul D. Hildebrand, Harrison Wright, Jeff Franklin, Shawkat Ali and Willy E. Renderos (2021). Effects of temperature and wetness on components of the infection cycle of Valdensia heterodoxa in lowbush blueberry. Plant Disease  (Submitted)

3.   A. H. Wright, S. Ali, Z. Migicovsky, G. M. Douglas, S. Yurgel, A. Bunbury-Blanchette, J. Franklin, S. Adams, A. K. Walker (2021) A characterization of a cool climate organic vineyard’s microbiome. PhytoBiome e-ISSN:2471-2906.

4.   Pervaiz A. Abbasi, Paul D. Hildebrand, Shawkat Ali, Debra L. Moreau and Willy E. Renderos (2021). Effect of relative humidity, temperature, light and plant age on infection of lowbush blueberry by Sphaerulina vaccinia. Plant Disease doi: 10.1094/PDIS-12-20-2747-RE.

5.     Shawkat Ali, Sajid Rehman, Walid Ellouze and Pervaiz, A Abbasi (2021). First Report of Moldy Core of Minneiska Apples from New ZealandCaused by Alternaria arborescens. Plant Disease Note doi: 10.1094/PDIS-01-21-0025-PDN.

6.     Ahmed Abdelfattah, Shiri Freilich, Rotem Bartuv, Yeka V. Zhimo, Ajay Kumar, Antonio Biasi, Shoshana Salim, Oleg Feygenberg, Erik Burchard, Christopher Dardick, Jia Liu, Awais Khan, Achour Amiri,  Oualid Ellouze, Shawkat Ali, Davide Spadaro, Rosario Torres, Neus Teixido, Okan Ozkaya, Andreas Buehlmann, Gabriele Berg, Susan Whitehead, Michael Wisniewski, Samir Droby (2021). Global analysis of the apple fruit microbiome: Are all apples the same? Environmental Microbiology doi:10.1111/1462-2920.15469.

  1. Kun-Peng Jia, Jianing Mi, Abdugaffor Ablazov, Shawkat Ali, Yu Yang, Aparna Balakrishna, Lamis Berqdar, Qitong Feng, Ikram Blilou and Salim Al-Babili (2021). iso-Anchorene is an endogenous metabolite that inhibits primary root growth in Arabidopsis. The Plant Journal, 107, 54–66 https://doi.org/10.1111/tpj.15271.
  1. Shawkat Ali, Pervaiz A Abbasi, Paul Hildebrand and Willy Renderos (2021). Characterization of Sphaerulina vaccinii sp. nov. as the cause of leaf spot and stem canker in lowbush blueberry and its epidemiology. Journal of Phytopathology. https://doi.org/10.1094/PHYTO-04-20-0143-R.
  1. Ana Priscilla Montenegro Alonso, Shawkat Ali, Xiao Song, Rob Linning and Guus Bakkeren (2020) UhAVR1, an HR-triggering avirulence effector of Ustilago hordei, is secreted viathe ER-Golgi pathway to the cytosol of barley coleoptile cells and contributes to virulence early in infection. J. Fungi, 6, 178; doi:10.3390/jof6030178.
  1. Michael Parcey, Steven Gayder, Vivian Morley-Senkler, Guus Bakkeren, José Ramón Úrbez-Torres, Shawkat Ali, Alan J Castle, Antonet M Svircev (2020). Comparative genomic analysis of Erwinia amylovora reveals novel insights in phylogenetic arrangement, plasmid diversity, and streptomycin resistance,  Genomics, 112, Issue 5, 3762-3772, Doi.org/1016/j.ygeno.2020.04.001.
  2. Sudarsana Poojari, Debra L. Moreau, Dieter Kahl, Mark Ritchie, Shawkat Ali & José Ramon Úrbez-Torres (2020). Disease incidence and genetic variability of economically important grapevine viruses in Nova Scotia, Can. J. Plant Pathol. 42:4, 584-594,DOI: 10.1080/07060661.2020.1730443.
  1. Shawkat Ali, Willy Renderos, Eric Bevis, Joan Hebb & Pervaiz A. Abbasi (2020) Diaporthe eres causes stem cankers and death of young apple rootstocks in Canada, Canadian Journal of Plant Pathology, 42:2, 218-227, DOI: 10.1080/07060661.2019.1653377.
  1. Pervaiz A. Abbasi, Shawkat Ali, Gordon Braun, Eric Bevis & Sherry Fillmore (2019). Reducing apple scab and frogeye or black rot infections with salicylic acid or its analogue on field-established apple trees. Can. J. Plant Pathol. 41:3, 345-354, DOI: 10.1080/07060661.2019.1610070.
  1. Alshareef NO, Wang JY, Ali S, Al-Babili S, Tester M and Schmöckel SM. (2019). Overexpression of the NAC transcription factor JUNGBRUNNEN1 (JUB1) increases salinity tolerance in tomato. Plant Physiol Biochem. 2019 Jul;140:113-121. doi: 10.1016/j.plaphy.2019.04.038.
  1. Syed Haleem Shah, Yoseline Angel, Rasmus Houborg, Shawkat Ali and Matthew McCabe (2019). A Random Forest Machine Learning Approach for the Retrieval of Leaf Chlorophyll Content in Wheat. Remote Sens. 2019, 11(8), 920; Doi.org/10.3390/rs11080920.
  1. Paul A. Wiersma, Deniz Erogul, Shawkat Ali (2018). DNA fingerprinting of closely related cultivars of sweet cherry (Prunus avium). J. Amer. Soc. Hort. Sci. 143(4):282–288. Doi.org/10.21273/JASHS04454-18.
  1. Pervaiz A. Abbasi, Shawkat Ali, Willy Renderos, Hamid A. Naeem & Yousef Papadopoulos (2018). First report of Alternaria alternata causing leaf spot and blight symptoms on alfalfa in Canada. Can. J. Plant Pathol.  Doi: 10.1080/07060661.2018.1470111.
  1. Shah ZH, Rehman HM, Akhtar T, Alsamadany H, Hamooh BT, Mujtaba T, Daur I, Al Zahrani Y, Alzahrani HAS, Ali S, Yang SH and Chung G (2018).  Humic Substances: Determining Potential Molecular Regulatory Processes in Plants. Front. Plant Sci. 9:263. Doi: 10.3389/fpls.2000263.
  1. Muhammad Jamil, Boubacar A. Kountche, Imran Haider, Xiujie Guo, Valentine O. Ntui, Kun-Peng Jia, Shawkat Ali, Umar S. Hameed, Hidemitsu Nakamura, Ying Lyu, Kai Jiang, Kei Hirabayashi, Masaru Tanokura, Stefan T. Arold, Tadao Asami, and Salim Al-Babili (2017). Methyl phenlactonoates are efficient strigolactone analogs with simple structure. Journal of Experimental Botany. Doi: 10.1093/jxb/erx438.
  1. Thirumalaikumar Venkatesh, Devkar, Vikas Mehterov, Nikolay, Shawkat Ali, Ozgur Rengin, Turkan Ismail, Mueller-Roeber Berndt, Balazadeh Salma (2017). NAC transcription factor JUNGBRUNNEN1 enhances drought tolerance in tomato. Plant Biotechnol J. pp. 1–13. Doi: 10.1111/pbi.12776.
  1. Mohamed E. Abdelaziz, Dongjin Kim, Shawkat Ali, Nina V. Fedoroff, Salim Al-Babili (2017). Endophytic fungus Piriformospora indica enhances salt stress tolerance in Arabidopsis thaliana. Plant Science (263) 107-115.
  1. Sajid Mahmood, Daur I, Al-Solaimani SG, Ahmad S, Madkour MH, Yasir M, Hirt H, Shawkat Ali and Ali Z (2016). Plant Growth Promoting Rhizobacteria and Silicon Synergistically Enhance Salinity Tolerance of Mung Bean. Front. Plant Sci. 7: 876. Doi: 10.3389/fpls.2016.00876.
  1. Andreas Savvides, Shawkat Ali, Mark Tester, and Vasileios Fotopoulos (2016). Chemical priming against multiple abiotic stresses: mission possible? Trends in Plant Sciences 21(4):329-40. doi: 10.1016/j.tplants.
  1. Shawkat Ali, Maxime Magne, Shiyan Chen, Natasa Obradovic, Lubna Jamshaid, Xiaohong Wang, Guy Bélair and Peter Moffett (2015). Analysis of Globodera rostochiensis effectors reveals conserved functions of SPRYSEC proteins in suppressing plant immune responses Front. Plant Sci. 6:623. Doi:  10.3389/fpls.2015.00623. (Impact factor 4.4)
  1. Shawkat Ali, Maxime Magne, Shiyan Chen, Olivier Côté, Barbara Gerič Stare, Natasa Obradovic, Lubna Jamshaid, Xiaohong Wang, Guy Bélair and Peter Moffett (2015). Analysis of putative apoplastic effectors from the nematode, Globodera rostochiensis, and identification of an expansin-like protein that can induce and suppress host defenses. PLoS ONE 10 (1): e0115042. Doi: 10.1371/ journal.pone.0115042.
  1. Shawkat Ali and Guus Bakkeren (2015). Conversion of BAC Clones into Binary BAC (BIBAC) Vectors and their Delivery into Basidiomycete Fungal Cells using Agrobacterium tumefaciens. Methods in Molecular Biology. (Clifton, N.J.), vol. 1227, DOI 10.1007/978-1-4939-1652-8.
  1. Shawkat Ali, John, D Laurie, Rob Lining, José Antonio Cervantes-Chávez, Denis Gaudet and Guus Bakkeren (2014). An immunity-triggering effector from the barley smut fungus Ustilago hordei resides in an Ustilaginaceae-specific cluster bearing signs of transposable element-assisted evolution. PLoS Pathogens 10 (7): e1004223.
  1. John D. Laurie, Shawkat Ali, Rob Linning, Gertrud Mannhaupt, Philip Wong, Ulrich Güldener, Martin Münsterkötter, Richard Moore, Regine Kahmann, Guus Bakkeren and JanSchirawskie. (2012). Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of TEs. The Plant Cell. 24 (5): 1733-45.
  1. Shawkat Ali, Abdul Manan, Oirdi ME, Abdul Waheed & Bushra Mirza (2012). Agrobacterium-mediated transformation of rough lemon (Citrus jambhiri Lush.) with yeast HAL2 gene. BMC Res Notes. 5 (1): 285.
  1. Shawkat Ali & Guus Bakkeren (2011). Introduction of large DNA inserts into the barley pathogenic fungus, Ustilago hordei, via recombined binary BAC vectors and Agrobacterium-mediated transformation. Current Genetics 57 (1): 63-73.
  1. José Antonio Cervantes-Chávez, Shawkat Ali and Guus Bakkeren (2011). Response to environmental stresses, cell wall integrity and virulence are orchestrated through the calcineurin pathway in Ustilago hordei. Molecular Plant Microbe Interaction 24 (2): 219-232.
  1. Shawkat Ali & Guus Bakkeren (2011). Fungal and oomycete effectors – strategies to subdue a host. Canadian Journal of Plant Pathology, 33 (4): 425-46.
  2. Abida Yasmeen, Bushra Mirza, Samia Inayatullah, Naila Safdar, Maryam Jamil,  Shawkat Ali & M. Fayyaz Choudhry (2009). In Planta transformation of tomato. Plant Mol. Biol. Rep. 27: 20-28.
  1. Shawkat Ali & Bushra Mirza (2006). Micropropagation of rough lemon (Citrus jambhiri Lush.): Effect of explants type and hormone concentration. Acta Bot. Croat. 65 (2) 137-146.

Books and Book chapters

  1.  Abbasi, P.A., Braun, G., Bevis, E., Luo, H., Song, J., Fillmore, S., and Ali, S. 2020. Impact of trunk injections and foliar sprays of salicylic acid and Actigard® on apple scab and frogeye or black rot infections and changes in leaf protein profiles. Acta Hortic. 1269. ISHS 2020. DOI 10.17660/ActaHortic.2020.1269.7

Professional activities / interests

• Plant-pathogens-host relationships

• Plant-microbe association

• Role of effectors in promoting and suppressing plant diseases such as study of fungal and bacterial virulence, avirulence and pathogenicity genes

• Molecular genetics of phytopathogens and plant-associated microorganisms

• Plant tissue culture and gene transformation

• Plant abiotic stress response

Education and awards


B.Sc. (Hons) Agriculture, Gomal University, 2001

M.Phil. Biotechnology,  Quaid-i-Azam University, Islamabad, 2004.

Ph.D.  Department of Botany, University of British Columbia Vancouver Canada, 2011


FQRNT Postdoctoral Fellowship, Quebec, Canada 2013

NSERC, visiting fellowships in Canadian Government Laboratories, 2011-2013

Gold Medal, B.Sc. (Hons)

Merit-based scholarship, B.Sc. (Hons)

International experience and/or work

January 2014 to June 2017, Post-doctoral Fellow, Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal KSA.

October 2015 to November 2015, Visiting Research Scientist, Max-Plank Institute of Molecular Physiology, Potsdam, Germany.

November 2015 to December 2015, Visiting Research Scientist, Institute of Molecular Plant Sciences, University of Edinburgh UK.



Key publications

  1. Ellouze, W., Schneider, K. and Ali, S. 2021. Apples to apples: An international study of local and global apple fruit microbiomes has implications for future pathogen control strategies. Fruit & Vegetable, September 22, 2021. https://www.fruitandveggie.com/apples-to-apples/

    2021 - View publication details

  2. Montenegro Alonso, A.P., Ali, S., Song, X., Linning, R., Bakkeren, G. (2020). UhAVR1, an HR-Triggering Avirulence Effector of Ustilago hordei, Is Secreted via the ER�Golgi Pathway, Localizes to the Cytosol of Barley Cells during in Planta-Expression, and Contributes to Virulence Early in Infection. Journal of Fungi, [online] 6(3), 1-32. http://dx.doi.org/10.3390/jof6030178

    2020 - View publication details

  3. Parcey, M., Gayder, S., Morley-Senkler, V., Bakkeren, G., Úrbez-Torres, J.R., Ali, S., Castle, A.J., Svircev, A.M. (2020). Comparative genomic analysis of Erwinia amylovora reveals novel insights in phylogenetic arrangement, plasmid diversity, and streptomycin resistance. Genomics, [online] 112(5), 3762-3772. http://dx.doi.org/10.1016/j.ygeno.2020.04.001

    2020 - View publication details

  4. Ali, S., Magne, M., Chen, S., Côté, O., Stare, B.G., Obradovic, N., Jamshaid, L., Wang, X., Bélair, G., Moffett, P. (2015). Analysis of putative apoplastic effectors from the nematode, Globodera rostochiensis, and identification of an expansin-like protein that can induce and suppress host defenses. PLoS ONE, [online] 10(1), http://dx.doi.org/10.1371/journal.pone.0115042

    2015 - View publication details

  5. Ali, S., Laurie, J.D., Linning, R., Cervantes-Chávez, J.A., Gaudet, D., Bakkeren, G. (2014). An Immunity-Triggering Effector from the Barley Smut Fungus Ustilago hordei Resides in an Ustilaginaceae-Specific Cluster Bearing Signs of Transposable Element-Assisted Evolution. PLoS Pathogens, [online] 10(7), http://dx.doi.org/10.1371/journal.ppat.1004223

    2014 - View publication details

  6. Laurie, J.D., Ali, S., Linning, R., Mannhaupt, G., Wong, P., Güldener, U., Münsterkötter, M., Moore, R., Kahmann, R., Bakkeren, G., Schirawski, J. (2012). Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of transposable elements. Plant Cell, [online] 24(5), 1733-1745. http://dx.doi.org/10.1105/tpc.112.097261

    2012 - View publication details

  7. Cervantes-Chávez, J.A., Ali, S., Bakkeren, G. (2011). Response to environmental stresses, cell-wall integrity, and virulence are orchestrated through the calcineurin pathway in ustilago hordei. Molecular Plant-Microbe Interactions, [online] 24(2), 219-232. http://dx.doi.org/10.1094/MPMI-09-10-0202

    2011 - View publication details

  8. Ali, S., Bakkeren, G. (2011). Introduction of large DNA inserts into the barley pathogenic fungus, Ustilago hordei, via recombined binary BAC vectors and Agrobacterium-mediated transformation. Current Genetics, [online] 57(1), 63-73. http://dx.doi.org/10.1007/s00294-010-0324-0

    2011 - View publication details

Research facility

32 Main Street
Kentville, NS B4N 1J5