For my career, as Associate Professor in University of Agriculture, Faisalabad Pakistan, I have been working on CRISPR/Cas mediated genome editing for plant genetic improvement. We have been using CRISPR/Cas9 and CRISPR/Cas12a in cotton to develop resistance against Cotton Leaf Curl Virus Disease (CLCuD). We have designed single and multiplex constructs against Rep, βC1 and overlapping regions of genes of CLCuD to develop resistance. Results of these studies have been published in GM crops and Food, Plant protection science, International Journal of Molecular Sciences and Frontiers in Plant Science. Recently, I got a project on developing CRISPRi-mediated low gossypol cotton, and we have designed a CRISPRi construct to reduce gossypol specifically in cotton seeds. Similarly, I have obtained funding to develop low-phytate maize through CRISPR technology. We also have established cotton transformation in collaboration with Professor Abhaya M Dandekar, University of California, Davis, USA. This work is part of a research grant on “CRISPR/Cas9 based virus resistance in cotton” from USAid in collaboration with Professor Yinong Yang from Pennsylvania State University and Professor Abhaya M Dandekar, UC Davis, California, USA. In addition, we have been using CRISPR/Cas for the genetic improvement of plants for quality improvement and abiotic stress tolerance using Arabidopsis as a model system. Recently, one of my projects to produce double zero brassica has been shortlisted for funding as well.

Future Goals:

• CRISPR-Cas mediated gene editing for genetic improvement of cotton.
• Gene editing in maize through CRISPR-Cas.
• CRISPR-mediated gene editing in model plants (Arabidopsis and Benthamiana) for functional genomics

Projects:

1. Genes conferring tolerance to salt stress on plants and their impact on human health and longevity. Funding Agency- Global Center of Excellent (COE) Program of the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT). 300, 000 JPY. Duration 1 year (2009).
2. Utilization of plants for human health and longevity: Genes for protecting plants against environmental stresses. Funding Agency- Global Center of Excellent (COE) Program of the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT). 300, 000 JPY. Duration 1 year (2010).
3. Contribution of plants to human health and longevity: Utilization of genes for protecting plants against salt stress. Funding Agency- Global Center of Excellent (COE) Program of the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT). 300, 000 JPY. Duration 1 year (2011).
4. CRISPR/Cas9 based virus resistance in cotton. Funding Agency- US-Aid. US-Pakistan Center for Advanced Studies in Agriculture and Food Security (USPCAS-AFS) 33, 000 USD.
5. Development of RNA based next generation biopesticides to control cotton bollworms. Funding agency Higher Education Commission (HEC), Pakistan, under NRPU scheme 2016-2017. Project No.6350. Approved for funding. 4.2 Million
6. CRISPR/Cas9 based virus resistance in cotton funded by Punjab Agriculture Research Board, Pakistan. 0.907 Million
7. Development of low phytate maize through CRISPR-Cas genome editing. No. PSF-NSLP-877. 2.9 Million. Funded by Pakistan Science Foundation (PSF), Islamabad.
8. CRISPRi mediated tissue specific reduction of gossypol contents in cottonseeds: 6.25M. No. PSF/CRP/Consrm-58. Funded by Pakistan Science Foundation (PSF), Islamabad.
9. Gene editing in Aedes aegypti using CRISPR-Cas9 system to replace blood sucking females to nectar feeding males. 8.7 Million funded by HEC-NRPU, Islamabad, Pakistan. Co-PI.
10. Gene editing of cadherin receptors for Bt toxin in pink bollworm, Pectinophoragossypiella using CRISPR-Cas9 system to develop non-feeding character towards Bt cotton. 2.7 Million funded by HEC-NRPU. Role-Co-PI
11. Gene Editing of Biological Agents for Nutritional, Biochemical and Therapeutic Purpose (Establishment of National Center for Genome Editing for Crop Improvement and Human Health). 500 Million funded by Planning Commission of Pakistan. Role-Co-PI
12. Gut Microbiota mining in Pakistan and its utilization in Health and Disease, an approach towards developing Novel probiotics. 4.3 Million funded by Jiangnan University, China. Role-Co-PI
13. Multiplex CRISPR/Cas editing to develop double zero Brassica juncea (Project No. CS-445)- (7 Million) Revised after Reviewer comments. Under evaluation of ALP (Agricultural Linkage Program), Pakistan Agricultural Research Council (PARC).

Publications:

1. Sidra Ashraf, Aftab Ahmad, Amer Jamil, Bushra Sadia, Judith K. Brown, and Sultan Habibullah Khan. (2023) LbCas12a mediated suppression of Cotton leaf curl Multan virus. Frontiers in Plant Science 14: 1233295.
2. Khan, Zulqurnain, Sultan Habibullah Khan, Aftab Ahmed, Muhammad Umar Iqbal, Muhammad Salman Mubarik, Muhammad Zubair Ghouri, Furqan Ahmad et al. (2023). Genome editing in cotton: challenges and opportunities. Journal of Cotton Research 6, no. 1: 1-21.
3. Oranab, S., Ghaffar, A., Ahmad, A., Pasha, M. F. K., Munir, B., Arif, S., ... & Ahmad, H. M. (2023). Genome-wide analysis of cyclic nucleotide-gated ion channels (CNGCS) of Arabidopsis thaliana under abiotic stresses. SABRAO J. Breed. Genet, 55(1), 38-49.
4. Naeem, M., Bano, N., Manzoor, S., Ahmad, A., Munawar, N., Razak, S. I. A., ... & Hazafa, A. (2023). Pathogenetic Mechanisms of Liver-Associated Injuries, Management, and Current Challenges in COVID-19 Patients. Biomolecules, 13(1), 99.
5. Ranian, K., Zahoor, M. K., Zulhussnain, M., & Ahmad, A. (2022). CRISPR/Cas9 mediated sex-ratio distortion by sex specific gene editing in Aedes aegypti. Saudi journal of biological sciences, 29(4), 3015-3022.
6. Munawar, N., Ahmad, A., Anwar, M. A., & Muhammad, K. (2022). Modulation of Gut Microbial Diversity through Non-Pharmaceutical Approaches to Treat Schizophrenia. International Journal of Molecular Sciences, 23(5), 2625.
7. Khan, Z., Razzaq, A., Sattar, T., Ahmed, A., Khan, S. H., & Ghouri, M. Z. (2022). Understanding floral biology for CRISPR-based modification of color and fragrance in horticultural plants. F1000Research, 11(854), 854.
8. Tanveer, A., Akhtar, B., Sharif, A., Saleem, U., Rasul, A., Ahmad, A., & Jilani, K. (2022). Pathogenic role of cytokines in COVID-19, its association with contributing co-morbidities and possible therapeutic regimens. Inflammopharmacology, 30(5):1503-1516
9. Riaz, B., Kashif Zahoor, M., Malik, K., Ahmad, A., Majeed, H. N., Jabeen, F., ... & Ranian, K. (2022). Frequency of Pyrethroid Insecticide Resistance kdr Gene and Its Associated Enzyme Modulation in Housefly, Musca domestica L. Populations from Jhang, Pakistan. Frontiers in Environmental Science, 704.
10. Aslam, S., Khan, S. H., Ahmad, A., Walawage, S. L., & Dandekar, A. M. (2022). Founder transformants of cotton (Gossypium hirsutum L.) obtained through the introduction of DS-Red, Rec, Rep and CRISPR/Cas9 expressing constructs for developing base lines of recombinase mediated gene stacking. PloS one, 17(2), e0263219.
11. Ahmad, A., Munawar, N., Khan, Z., Qusmani, A. T., Khan, S. H., Jamil, A., ... & Qari, S. H. (2021). An Outlook on Global Regulatory Landscape for Genome-Edited Crops. International Journal of Molecular Sciences, 22(21), 11753. https://doi.org/10.3390/ijms222111753
12. Binyameen, B., Khan, Z., Khan, S. H., Ahmad, A., Munawar, N., Mubarik, M. S., ... & Qari, S. H. (2021). Using Multiplexed CRISPR/Cas9 for Suppression of Cotton Leaf Curl Virus. International journal of molecular sciences, 22(22), 12543. https://doi.org/10.3390/ijms222212543
13. Ahmad, A., Munawar, N., Khan, Z., Qusmani, A. T., Khan, S. H., Jamil, A., ... & Qari, S. H. (2021). An Outlook on Global Regulatory Landscape for Genome-Edited Crops. International Journal of Molecular Sciences, 22(21), 11753. https://doi.org/10.3390/ijms222111753
14. Oranab, S., Ghaffar, A., Kiran, S., Yameen, M., Munir, B., Zulfiqar, S., ... & Ahmad, A. (2021). Molecular characterization and expression of cyclic nucleotide gated ion channels 19 and 20 in Arabidopsis thaliana for their potential role in salt stress. Saudi Journal of Biological Sciences, 28(10), 5800-5807. https://doi.org/10.1016/j.sjbs.2021.06.027
15. Alghuthaymi, M. A., Ahmad, A., Khan, Z., Khan, S. H., Ahmed, F. K., Faiz, S., ... & Abd-Elsalam, K. A. (2021). Exosome/Liposome-like Nanoparticles: New Carriers for CRISPR Genome Editing in Plants. International Journal of Molecular Sciences, 22(14), 7456. https://doi.org/10.3390/ijms22147456
16. Munawar, N., Ahsan, K., Muhammad, K., Ahmad, A., Anwar, M. A., Shah, I., ... & Al Mughairbi, F. (2021). Hidden role of gut microbiome dysbiosis in schizophrenia: Antipsychotics or psychobiotics as therapeutics?. International Journal of Molecular Sciences, 22(14), 7671. https://doi.org/10.3390/ijms22147671
17. Mubarik, M. S., Wang, X., Khan, S. H., Ahmad, A., Khan, Z., Amjid, M. W., ... & Azhar, M. T. (2021). Engineering broad-spectrum resistance to cotton leaf curl disease by CRISPR-Cas9 based multiplex editing in plants. GM Crops & Food, 1-12. https://doi.org/10.1080/21645698.2021.1938488
18. Syed Ovais Aftab, Muhammad Zubair Ghouri, Muhammad Umer Masood, Zeshan Haider, Zulqurnain Khan, Aftab Ahmad* and Nayla Munawar (2020). Analysis of SARS-CoV-2 RNA-dependent RNA polymerase as a potential therapeutic drug target using a computational approach. Journal of Translational Medicine. https://doi.org/10.1186/s12967-020-02439-0
19. Muhammad Zulhussnain, Muhammad Kashif Zahoor, Hina Rizvi, Muhammad Asif Zahoor, Azhar Rasul, Aftab Ahmad, Humara Naz Majeed, Amer Rasul, Kanwal Ranian and Farhat Jabeen (2020) Insecticidal and Genotoxic effects of some indigenous plant extracts in Culex quinquefasciatus Say Mosquitoes. Scientific Reports-Nature. https://doi.org/10.1038/s41598-020-63815-w
20. Muhammad Ismail, Aftab Ahmad, Muhammad Nadeem, Muhammad Asif Javed, Sultan Habibullah Khan, Iqra Khawaish, Aftab Alam Sthanadar, Sameer H. Qari,
21. Suliman M. Alghanem, Khalid Ali Khan, Muhammad Fiaz Khan, Samina Qamer. Development of DNA barcodes for selected Acacia species by using rbcL and matK DNA markers. DOI: 10.1016/j.sjbs.2020.08.020
22. Sehrish Khan, Muhammad Mahmood, Sajjad Rahman, Farzana Rizvi, Aftab Ahmad* (2020) Evaluation of the CRISPR/Cas9 system for the development of resistance against Cotton leaf curl virus in model plants. Plant Protection Science. https://doi.org/10.17221/105/2019-PPS
23. Muhammad Salman Mubarik, Sultan Habibullah Khan, Bushra Sadia and Aftab Ahmad (2020). CRISPR-Cas9 based Suppression of Cotton Leaf Curl Virus in Nicotiana benthamina International Journal of Agricultural Biology. DOI: 10.17957/IJAB/15.1094
24. Sabin Aslam, Sultan Habibullah Khan, Aftab Ahmad, Abhaya M. Dandekar (2020) The Tale of Cotton Plant: From Wild Type to Domestication, Leading to Its Improvement by Genetic Transformation. American Journal of Molecular Biology. https://doi.org/10.4236/ajmb.2020.102008
25. Zulqurnain Khan, Sultan Habibullah Khan, Muhammad Salman Mubarik and Aftab Ahmad* (2018). Targeted Genome Editing for Cotton Improvement: Chapter Accepted in Book: Cotton: ISBN: 978-953-51-5817-2. Edited by Dr Mehboob-ur-Rahman and Dr Yusuf Zafar published by INTECH publishers. DOI:10.5772/intechopen.73600.
26. Sehrish Khan, Muhammad Shahid Mahmood, Sajjad ur Rahman, Hassan Zafar, Sultan Habibullah Khan, Zulqurnain Khan and Aftab Ahmad* (2018). CRISPR/Cas9: The Jedi against dark empire of diseases. BMC Journal of Biomedical Sciences. DOI: 10.1186/s12929-018-0425-5.
27. Bushra Riaz, Muhammad Kashif Zahoor, Muhammad Asif Zahoor, Humera Naz Majeed, Aftab Ahmad, Farhat Jabeen, Muhammad Zulhussnain and Kishwar Sultana. (2018). Toxicity, phytochemical composition and enzyme inhibitory activities of some indigenous weed plant extracts in fruit fly, Drosophila melanogaster. Accepted in Evidence Based Complementary and Alternate Medicine. https://doi.org/10.1155/2018/2325659.
28. Hirokazu Kobayashi., Yasuo Niwa and Aftab Ahmad. (2016). Gene for ABC transporter to confer salt tolerance on plants. Patent Registered, Japan Patent Office. 5871222, January. 2016 (According to HEC notification# DG/QA/HEC/Policy-Dec/2008/1140, Dated; 04-November-2008, One Patent is equivalent to 5 publications in impact factor journals).
29. Zulqurnain Khan, Sultan Habibullah Khan, Muhammad Salman Mubarik, Bushra Sadia and Aftab Ahmad* (2016) Use of TALEs and TALEN Technology for Genetic Improvement of Plants: Plant Molecular Biology Reporter. DOI: 10.1007/s11105-016-0997-8
30. Muhammad Salman Mubarik, Sultan Habibullah Khan, Aftab Ahmad, Zulqurnain Khan, Muhammad Sajjad and Iqrar Ahmed Khan (2016) Disruption of Phytoene Desaturase Gene Using Transient Expression of Cas9:gRNA Complex: International Journal of Agriculture and Biology. DOI: 10.17957/IJAB/15.0199.
31. Aftab Ahmad, Yasuo Niwa, Shingo Goto, Takeshi Ogawa, Masanori Shimizu, Kyoko Kobayashi and Hirokazu Kobayashi (2015) bHLH106 Integrates Functions of Multiple Genes through their G-Box to Confer Salt Tolerance on Arabidopsis. PLOS ONE .DOI: 10.1371/journa.pone.0126872.
32. Aftab Ahmad, Yasuo Niwa, Shingo Goto, Kyoko Kobayashi, Masanori Shimizu, Sohei Ito, Yumiko Usui, Tsutomo Nakayama and Hirokazu Kobayashi (2015) Genome-Wide Screening of Salt Tolerant Genes by Activation-Tagging Using Dedifferentiated Calli of Arabidopsis and Its Application to Finding Gene for Myo-Inositol-1-P-Synthase. PLOS ONE. DOI: 10.1371/journal.pone.0115502.
33. Aftab Ahmad, Izumi Kaji, Yukiko Murakami, Nana Funato, Takeshi Ogawa, Masanori Shimizu, Yasuo Niwa, and Hirokazu Kobayashi. (2009) Transformation of Arabidopsis with plant-derived DNA sequences necessary for selecting transformants and driving an objective gene. Biosci. Biotechnol. Biochem., 73, 936-938. (IF-1.2)

Book Chapters:

1. Abd-Elsalam, K. A., & Ahmad, A. (2024). Regulations of genome edited plants: notes from editors. In Global Regulatory Outlook for CRISPRized Plants (pp. 1-20). Academic Press.
2. Khan, S., Zafar, H., & Ahmad, A. (2024). Reagents and their delivery systems in CRISPR/Cas. In Global Regulatory Outlook for CRISPRized Plants (pp. 71-90). Academic Press.
3. Ahmad, A., Abd-Elsalam, K. A., Ali, M., Majeed, H. N., Arif, A., Munir, A., ... & Munawar, N. (2024). Regulatory triggers of CRISPR-edited crops. In Global Regulatory Outlook for CRISPRized Plants (pp. 91-112). Academic Press.
4. Ahmad, A., Munir, A., Zafar, H., Zahoor, M. K., Hassan, S., & Khan, S. H. (2024). Tracking footprints of CRISPR-based genome editing. In Global Regulatory Outlook for CRISPRized Plants (pp. 113-145). Academic Press.
5. Munawar, N., Ahsan, K., & Ahmad, A. (2024). CRISPR-edited plants’ social, ethical, policy, and governance issues. In Global Regulatory Outlook for CRISPRized Plants (pp. 367-396). Academic Press.
6. Ahmad, A., Munir, A., Munawar, N., Khan, S. H., Khan, Z., & Akhtar, B. (2024). Regulations of multiplex genome-edited crops and CRISPR/Cas gene drives. In Global Regulatory Outlook for CRISPRized Plants (pp. 397-445). Academic Press.
7. Ahmad, A., Arif, A., & Munir, A. (2024). CRISPR technology commercialization and biosafety. In Global Regulatory Outlook for CRISPRized Plants (pp. 461-514). Academic Press.
8. Ghouri, M. Z., Munawar, N., Aftab, S. O., & Ahmad, A. (2023). Regulation of CRISPR edited food and feed: legislation and future. In GMOs and Political Stance (pp. 261-287). Academic Press. DOI: https://doi.org/10.1016/B978-0-12-823903-2.00004-4.
9. Munawar, N., Ahmad, A. (2022). An Introduction to Genome Editing Techniques. In: Ahmad, A., Khan, S.H., Khan, Z. (eds) The CRISPR/Cas Tool Kit for Genome Editing. Springer, Singapore. https://doi.org/10.1007/978-981-16-6305-5_1.
10. Ahmad, A. et al. (2022). Bioinformatic Tools in CRISPR/Cas Platform. In: Ahmad, A., Khan, S.H., Khan, Z. (eds) The CRISPR/Cas Tool Kit for Genome Editing. Springer, Singapore. https://doi.org/10.1007/978-981-16-6305-5_3.
11. Sidra Ashraf, Muhammad Zubair Ghouri, Muhammad Asif Javed, Hassan Zafar, Hazrat Ali and Aftab Ahmad (2022). Delivery Methods for CRISPR/Cas Reagents. In: Ahmad, A., Khan, S.H., Khan, Z. (eds) The CRISPR/Cas Tool Kit for Genome Editing. Springer, Singapore. https://doi.org/10.1007/978-981-16-6305-5_4.
12. Sidra Ashraf, Muhammad Zubair Ghouri, Muhammad Asif Javed, Sultan Habibullah Khan, Kamel Abd-Elsalam and Aftab Ahmad (2022) Beyond Genome Editing: CRISPR Approaches. Accepted in book “The CRISPR/Cas Toolkit for Genome Editing” by Springer Nature. https://doi.org/10.1007/978-981-16-6305-5_6.
13. Khan, Z., Khan, S.H., Ahmad, A. (2022). Challenges and Future Prospects of CRISPR Technology. In: Ahmad, A., Khan, S.H., Khan, Z. (eds) The CRISPR/Cas Tool Kit for Genome Editing. Springer, Singapore. DOI: https://doi.org/10.1007/978-981-16-6305-5_10.
14. Nayla Munawar and Aftab Ahmad (2020). The CRISPR/Cas systems: An introduction. published in book “CRISPR Crops: The Future of Food Security”. Edited by Aftab Ahmad, Sultan Habibullah Khan and Zulqurnain Khan. 2021 by Springer Nature. ISBN 978-981-15-7141-1: DOI: https://doi.org/10.1007/978-981-15-7142-8_1.
15. Muhammad Aamir Aslam, Masooma Hammad, Aftab Ahmad, Josef Altenbuchner, Hazrat Ali (2020). Delivery methods, Resources and design tools in CRISPR/Cas. Published in book “CRISPR Crops: The Future of Food Security”. Edited by Aftab Ahmad, Sultan Habibullah Khan and Zulqurnain Khan. 2021 by Springer Nature. ISBN 978-981-15-7141-1: DOI: https://doi.org/10.1007/978-981-15-7142-8_3.
16. Muhammad Kashif Zahoor, Aftab Ahmad, Muhammad Asif Zahoor, Humara Naz Majeed, Muhammad Zulhussnain, Kanwal Ranian (2020). CRISPR/Cas based insect resistance in crops. Published in book “CRISPR Crops: The Future of Food Security”. Edited by Aftab Ahmad, Sultan Habibullah Khan and Zulqurnain Khan. 2021 by Springer Nature. ISBN 978-981-15-7141-1: DOI: https://doi.org/10.1007/978-981-15-7142-8_4.
17. Aftab Ahmed, Sidra Ashraf, Nayla Munawar, Amer Jamil, Abdul Ghaffar and Muhammad Shahbaz. (2020) CRISPR/Cas mediated Abiotic Stress Tolerance in Crops. Published in book “CRISPR Crops: The Future of Food Security”. Edited by Aftab Ahmad, Sultan Habibullah Khan and Zulqurnain Khan. 2021 by Springer Nature. ISBN 978-981-15-7141-1:
18. Aftab Ahmad, Muhammad Zubair Ghouri, Nayla Munawar, Muhammad Ismail, Sidra Ashraf, and Syed Ovais Aftab (2020). Regulatory, Ethical and Social Aspects of CRISPR Crops. Published in book “CRISPR Crops: The Future of Food Security”. Edited by Aftab Ahmad, Sultan Habibullah Khan and Zulqurnain Khan. 2021 by Springer Nature. ISBN 978-981-15-7141-1: DOI: https://doi.org/10.1007/978-981-15-7142-8_9.
19. Zulqurnain Khan, Sultan Habibullah Khan and Aftab Ahmad (2020). Challenges and Future Perspective of CRISPR/Cas Technology for Crop Improvement. Published in book “CRISPR Crops: The Future of Food Security”. DOI: https://doi.org/10.1007/978-981-15-7142-8_10.

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Research Gate link

A. Publications: