Bourlaye Fofana, Ph.D.

Image Bourlaye Fofana
Research Scientist

Plant Molecular Physiology and Genomics

Current research and/or projects

Current Projects

1. 2019-2023  J-002269 – Evaluate effects of  manure application in combination  with cover on  plant endophytes using metagenomics, PEI Living Labs project - Using living laboratory approach to develop and transfer innovative soil and water quality BMPs in Prince Edward Island, $102,700

2. 2019- 2022  J-002235 – Quality attributes in small fruit crops - Improvement of quality attributes in strawberry, raspberry and blackberry using metabolomic and genomic approaches, $40,000

3. 2019-2023  J-002214 – Lupuloides hops development - Evaluating phytochemical and agronomic traits of native hops (Humulus lupulus ssp lupuloides) for Eastern Canadian production systems, $33,360

4. 2018-2021    J-001776 – Cover Crops, Disease & Soil Biodiversity - Impact of cover cropping on soil microbial biodiversity, disease and pathogen load. Adam Forster (Lead), $100,000

5. 2018-2023  J-002035 – ASC-05 Diverse FC Cluster Activity 4A - ASC-05 Diverse FC Cluster Activity 4A: Genomics and molecular markers to identify resistance genes in flax, $80,000

Recently completed  projects 

6. 2015-2019  J-000991 – Integrated research-development-technology-transfer approach to enhance productivity and sustainability of potato production in Canada, $340,000

7. 2015-2018  J-001005 –Developing eastern hop (Humulus lupulus var. lupuloides) germplasm resources for improved quality traits and disease resistance, $36,000

8. 2013-2017  J-000916 – Understanding the bio-insecticidal properties of buckwheat for wireworm control and the benefits associated with growing it as a rotation crop/Understanding the microbial diversity in the buckwheat rhizosphere when compared to other rotation crops and to understand the potential interactions between the plant, the soil microbiomes and wireworm.. $ 121,300

9. 2013-2016.  J-000076 – Development of a proof-of-concept for the generation and use of mutagenized dihaploid potato lines for accelerated breeding of potato cultivars low in glycoalkaloid content and acrylamide in processed product, $121,000

10 2009-2014 – Flax Total Utilization Flax GENomics (TUFGEN) project/. Flax lignan biosynthesis, bioavailability and bioactivity, $308,750.

11. 2009-2011 – Rosehip – Innovative Canadian bioActives and Nutraceuticals  (ICAN)-rosehip project”/Rosehip genomic and germplasm characterization aspects, $316,569; Dr. Fofana : $194,269 (RBPI #1636).


Research and/or project statements

Dr. Fofana’s research program is focused on the development and characterization of pre-breeding germplasm, development of bioprocesses and genomic resources from plant and microbial bioresources for high-quality oilseed and horticultural crops, and valued bioproducts for breeders, biologists, food and non-food, and health and wellness industry. He uses molecular physiology, genomics and metagenomics as tools to achieve his objectives including:

  • Crop remodeling

  • Metabolite re-engineering

  • Seed quality

  • Biofuels feedstock engineering

  • Pre-postharvest quality

  • Germplasm development

Professional activities / interests

Editorial Functions

  • Technical Editor, Horticulture section, Canadian Journal of Plant Science  2019-present

  • Associate Editor, Botany  2018-present

  • Associate Editor, Canadian Journal of Plant Science  2016-present

  • Invited reviewer for many journals

Education and awards


2006   Certification in Higher Education Teaching (CHET)- University of Manitoba, Winnipeg

1999    Ph.D. Plant Molecular Biology and Genetics -Gembloux Agricultural University, Belgium

1995    M.Sc. Plant Molecular Biology and Genetics -Gembloux Agricultural University,Belgium

1993    AEA Plant Breeding - National University of Ivory Coast, Abidjan, Ivory Coast

1992    Msc Genetics – National - University of Ivory Coast, Abidjan, Ivory Coast

1991,   Bsc Biology and Natural Science - University of Ivory Coast, Abidjan, Ivory Coast



Research Fellowship, Natural Sciences and Engineering Research Council Canada, 2002-2005

Research Award, Belgian State Secretary for Cooperation Development Price, 1998

Travel Scholarship, Belgian National Funds for Scientific Research, 1998

Graduate Foreign Scholarship, Ivorian Government, Ministry of Higher Education & Scientific Research, 1993 – 1999.

International experience and/or work

Advisor, Volunteer  - CESO-SACO: work assignements to Burkina Faso and Ivory Coast, 2017, 2018.

Key publications

  1. Solanum tuberosum Genotyping by Sequencing

    2023 - View publication details

  2. MTA Out - AGR - 20370 - Biotechnology- Plasmid construct transfer to Dr. Gefu Wang-Pruski (Dalhousie University)

    2023 - View publication details

  3. INV-20290 - Drought resistance genes in diploid potatoes

    2023 - View publication details

  4. MTA Out - AGR - 20102 - Germplasm - AAFC potato clone expressing eGFP protein transfered to Dr. Gefu Wang-Pruski (Dalhousie University)

    2023 - View publication details

  5. INV-20301 - Non browning gene-edited potatoes

    2023 - View publication details

  6. Diploid potatoes in changing climate biotic and abiotic challenges

    2023 - View publication details

  7. Potato Greening through ‘omics approaches

    2023 - View publication details

  8. Effects of soil building practices on plant endophytes associated with individual rotation crops

    2023 - View publication details

  9. Antioxidant Boosts Immunity Against Late Blight in Potatoes Weekly Scoence Stories,

    2023 - View publication details

  10. MTA - germplasm transfer to Dr. Braulio Soto-Cerda (Chili)

    2023 - View publication details

  11. Antioxidants, a booster shot for late blight prevention in potatoes

    2023 - View publication details

  12. Candidate genes for common scab (Streptomyces scabies) and drought resistance in potato as revealed by genome-wide association studies (GWAS)
    Bourlaye Fofana, Mohsin Zaidi,, and David MAIN
    Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, Prince Edward Island, C1A 4N6, Canada

    Potato scab (Streptomyces scabies) is widespread in all potato growing regions, and it significantly reduces potato quality and marketability. Drought, as an abiotic stress, is a major threat to crop productivity. Currently, the genome-wide architecture of the genetic control of these two traits are limited in potato. Here, we used a genome-wide association studies on a 384 diploid potato germplasm panel to determine the potato genomic regions and the genes potentially associated with resistance to scab and drought. Here, we show that three candidate genes located in a 0.5- 5 kb genomic region of chromosome 7 are associated with scab resistance. Furthermore, two major QTNs located on chromosome 5, explained by 16 and 32% of phenotypic variations were found associated with 25 candidate genes. The data will be presented and discussed in a context of global changing climate.

    2023 - View publication details

  13. Toward evidence that homologs of RPW8 act through salicylic acid signaling in powdery mildew resistance in flax
    Vanessa Clemis1,2, Mohsin Zaidi, Frank You3, Chunfang Zheng3, Sylvie Cloutier3, and Bourlaye Fofana1
    1Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, Prince Edward Island, C1A 4N6, Canada
    2University of Prince Edward Island, 550 University Avenue, Charlottetown, Prince Edward Island, C1A 4P3, Canada
    3Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
    Powdery mildew (PM) is an obligate biotrophic fungus (Podosphaera lini) causing high yield loss to flax (Linum usitatissimum L.). To date, no PM resistance genes have been fully functionally characterized. Using GWAS, we identified a locus harboring three flax homologs of the Arabidopsis RPW8 genes that confer broad-spectrum resistance to powdery mildew. Here, we characterized the gene expression profile of the three RPW8 candidate genes following PM inoculation. The data showed that, similar to RPW8.2 acting through the salicylic acid (SA) signaling pathway, the RPW8 homologs Lus10000835 and Lus10000836 are highly expressed in resistant flax lines compared to the suscpetible lines. In contrast, the flax RPW8 homolog Lus10009328 was highly expressed in the susceptible lines, suggesting a different signaling pathway from the other two homologs. RPW8.1 has been shown to activate ethylene signaling through aminocyclopropane-1-carboxylate oxidase gene isoform 4 (ACO4) and, this elevated ethylene negatively regulates the expression of RPW8.1, thereby attenuating its mediated-cell death and disease resistance when no disease is present to avoid unnecessary defense responses. We conclude that PM resistance induced by RPW8 in flax may mainly be activated through SA signaling pathways, and perhaps similarly to the ethylene signaling in Arabidopsis.

    2023 - View publication details

  14. Flax Genomic Workshop - Workshop organizer

    2023 - View publication details

  15. MTA AGR-19473 for incoming plant materials

    2022 - View publication details

  16. Potato greening: gaining an understanding through ‘omics approaches
    K. Dougherty1, T. F. Mitterboeck1*, M. Lague1, M. Zaidi2, B. Bizimungu1, and B. Fofana2. 1Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada E3B 4Z7 (; and 2Agriculture and Agri-Food Canada, Charlottetown, Prince Edward Island, Canada C1A 4N6.

    Potato ‘greening’ occurs when tubers are exposed to light, and results from a de novo synthesis of chlorophyll and a simultaneous formation of steroidal glycoalkaloids, which are toxic to humans and animals. Potato is the largest vegetable crop in Canada, and this greening causes substantial loss of products. Currently, there are no potato cultivars that are resistant to light–induced greening available on the market. The goal of this study is to understand the genetic components and molecular mechanisms of light-induced greening, and to use this knowledge to develop gene-editing tools to generate cultivars resistant to greening. From a core germplasm collection of over 800 mutant potato clones, two clones were observed to be tolerant to light-induced greening. These two non-greening clones, along with a greening control, underwent whole genome sequencing as well as transcriptomic sequencing after light exposure. Here, we will show our findings on single nucleotide polymorphisms (SNPs) and structural variants (SV) that differentiate the non-greening from greening clones. Deploying the non-greening trait into popular potato cultivars would be of high interest to the industry and stakeholders both for tuber appearance, quality, safety, marketability, and food waste reduction.

    2022 - View publication details

  17. Fighting against potato greening
    Louis G. Sebarese LG1, Mohsin Zaidi1, Christian Lacroix2, Fatima Mitterboek3, Benoit Bizimungu3, and Bourlaye Fofana1
    1Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, Prince Edward Island, C1A 4N6, Canada
    2University of Prince Edward Island, 550 University Avenue, Charlottetown, Prince Edward Island, C1A 4P3, Canada
    3Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, E3B 4Z7, Canada
    Potato is the largest vegetable crop in Canada, with an export value of $1.8B in 2019. As a major food source, potato nutritional quality and safety are critical for the public health. Potato greening, also known as potato sunburn, causes 2-3% loss at the farm gate and up to 17% during postharvest and retail storage. It results from a de novo synthesis of chlorophyll in the cortical parenchyma cells under the periderm after light exposure and leads to a simultaneous formation of toxic steroidal glycoalkaloids (SGAs). Whereas chlorophyll itself is not a health hazard, SGAs are toxic to humans and animals. Development of potato cultivars that are resistant to light-induced greening is a viable strategy for an economic and environmental sustainability. We will present and discuss our approach and preliminary results towards an understanding of the tuber greening phenomenon in potato.

    2022 - View publication details

  18. Mutational Genetics In Diploid Potato In The CRISPR Era
    Fofana, B.*1, A. Somalraju1, D. Main1, M. Zaidi1, B. Bizimungu2
    1Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, 440 University Avenue, Charlottetown, Prince Edward Island, C1A 4N6, Canada; 2Fredeicton Research and Development Centre, Agriculture and Agri-Food Canada, 95 Innovation Road, PO Box 20280, Fredericton, NB E3B 4Z7
    Cultivated potato (Solanum tuberosum L.) is the fourth most consumed food crop after rice wheat and maize. Cultivated potato is a clonally propagated, autotetraploid crop species with a narrow genetic diversity. Its highly heterozygous, complex genome, and tetrasomic inheritance make its genetic studies and improvement more difficult than grain crops. Recently, diploid potato breeding has regained an interest in the potato genetics community. Genetically, diploid potatoes are easy to work with, can be used as gene donors in the breeding process of cultivated potatoes, and can also be grown on their own as varieties. However, diploid breeding continuum faces many challenges including anti-nutritional factors and self-incompatibilities. Mutations are known as the key drivers for evolution and diversification in plants. In breeding and varietal selection, sources for variation are always sought as starting materials, and in the absence of desired natural variations in breeding populations, targeted or random mutagenesis is applied to induce variations. Recently, a mutagenized pre-breeding diploid potato population was developed at AAFC Charlottetown. Dr. Fofana will give an update on this genetic resource, its characterization, and its potentials in the CRISPR era.

    2022 - View publication details

  19. Mutational genetics in the CRISPR era: where do we stand at AAFC?

    2022 - View publication details

  20. Living laboratories Initiative progress report. Lightning presentation science updates. Rodd Royalty, Charlottetown, Feb 22, 2022 (Oral presentation).

    2022 - View publication details

Research facility

440 University Avenue
Charlottetown, PE C1A 4N6


  • Adjunct professor, Biology Department, UPEI, 2008 – present

  • Adjunct professor, Adjunct Professor, Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture Dalhousie University, April 2020 - Present

  • Member of the Canadian Society of plant Physiologists, October 2006-present

  • Member of the PEI Institute of Agrologists, April 2008-present

  • Member/Secretary of the Canadian Society for Horticultural Science, April 2016 - present