Sajid Ali

Sajid Ali

AgreenSkills session, year: 2nd session, 2015

Receiving laboratory: BGPI Biology and genetics of plant-pathogen interactions, Montpellier

Country of origin : Pakistan




Mobility project

Molecular epidemiology and comparative genomics of rice blast populations from a traditional rice agrosystem

Understanding how the spatio-temporal distribution of varieties shapes the population biology of pathogens at the scale of regional agricultural landscapes, can help the re-engineering of agrosystems to make them less conducive to pathogen evolution and transmission. Magnaporthe oryzae (Mo) causing rice blast is a classical example of rapidly evolving fungal pathogen. To understand how Mo population structure and dynamics are impacted by the spatio-temporal distribution of rice varieties, we study the traditional rice agrosystem from the YuanYang terraces (YYT) in China, characterized by a low disease burden and a high spatio-temporal variability of rice genotypes. The same ∼20 varieties, with different resistance genes, have been grown for more than 200 years without noticeable erosion of resistance. In the landscape, different resistance spectra are combined on small surfaces. At the plot level, rice probably harbors limited genetic diversity because of selfing. To understand the genetic makeup, origin and population biology of Mo in YYT, our objectives will be to delimit the number of Mo populations represented in YYT, to determine their relationship with the four major pandemic lineages of Mo, and to ascertain the relationships among host genotypes infected by a given population of Mo. We will attempt to understand that to which pandemic lineages does Mo found in YYT belong to? Are there multiple Mo sub-populations within each lineage? Are these sub-populations adapted to different hosts? Does farming-induced migrations cause patterns of maladaptation that relieve the disease burden? Another objective will be to map the genomic regions potentially underlying adaptive divergence between Mo populations in YYT. We will seek genomic differences potentially underlying differences in pathogenicity between populations. We hypothesize that the genomic features underlying differential adaptation of populations from the same pandemic lineage are relatively simple (presence/absence).

Biography & research interests

Dr. Sajid Ali, Assistant Professor at the University of Agriculture, Peshawar, Pakistan, has acquired PhD in Genetics, Evolution and Population Biology from Paris-XI University, Paris, France and Post-Doctorate in Population Genetics from Aarhus University, Denmark. He has expertise in pathogen population dynamics at spatial and temporal scale along with in depth knowledge of genetics, breeding and ecological consequences of resistance genes deployment. His research work has resulted in the identification of centre of diversity of wheat yellow rust in Himalayas, its worldwide invasion history and the role of sexual reproduction. His research in crop improvement has resulted in development of a wheat variety “Ghanimat-e-IBGE” along with other breeding lines are in the pipeline. He has strong collaboration with research groups at international level (e.g. in Australia, Denmark, France, Mexico and UK), regional level (e.g. in Nepal, Bhutan, Iran and Afghanistan) and national level. He has research publication in internationally reputed journals like PLOS pathogens, Molecular Ecology, Molecular Ecology Resources, Plant Pathology, Plant Disease, Fungal Genetics and Biology and Ecology and Evolution. He also served as reviewer to many of the above mentioned journals and others, and has been invited to talk at various international conferences including at Oxford University, UK, NIAB, Cambridge UK and Aarhus University Denmark. He has previously completed one research project with INRA, France and one with TAG, UK as collaborator. Currently he is running two research projects as PI, one funded by Govt. of Pakistan and other by USAID-CIMMYT.

Selected publications

1. Walker A-S, Rieux A, Ravigne V, Ali S, Carpentier F, Fournier E. 2017. Fungal adaptation to contemporary fungicide applications: the case of Botrytis cinerea populations from Champagne vineyards (France). Molecular Ecology. 26: 1919-1935.
2. Ali, S, Soubeyrand S, Gladieux P, Giraud T, Leconte M, Gautier A, Mboup M, de Vallavieille-Pope C, Enjalbert J. 2016. CloNcaSe: Estimation of sex frequency and effective population size by clonemate re-sampling in partially clonal organisms. Molecular Ecology Resources. 16: 845-861.
3. Walter S, Ali S, Kemen E, et al. 2016. Molecular markers for tracking the origin and worldwide distribution of invasive strains of Puccinia striiformis. Ecology and Evolution. 6: 790-2804.
4. Hovmøller MS, Walter S, Bayles R, Hubbard A, Flath K, Sommerfeldt N, Leconte M, Rodriguez-Algaba J, Hansen JG, Lassen P, Justesen AF, Ali S, de Vallavieille-Pope C. 2016. Replacement of the European wheat yellow rust population by new races from the centre of diversity in the near-Himalayan region. Plant Pathology. 65: 402-411.
5. Ali S, Gladieux P, Leconte M, Gautier A, Justesen AF, Hovmoller MS, Enjalbert J, De Vallavieille-Pope C. 2014. Origin, migration routes and genetic structure of worldwide populations of the wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici. PLOS Pathogens. 10: e1003903. DOI: 10.1371/journal.ppat.1003903.
6. Ali S, Gladieux P, Rahman H, Saqib MS, Fiaz M, Ahmed H, Leconte M, Gautier A, Justesen AF, Hovmøller MS, Enjalbert J, de Vallavieille-Pope C. 2014. Inferring the contribution of sexual reproduction, migration and off-season survival to the temporal maintenance of microbial populations: a case study on the wheat fungal pathogen Puccinia striiformis f.sp. tritici. Molecular Ecology. 23: 603–617.
7. Ali, S., M. Leconte, A.-S. Walker, J. Enjalbert, and C. De Vallavieille-Pope. 2010. Reduction in the sex ability of worldwide clonal populations of Puccinia striiformis f.sp. tritici. Fungal Genetics and Biology. 47: 828-838.

Awards & patents

Research Productive Award, 2017 for being Productive Scientists of Pakistan – Ministry of Science & technology, Pakistan.
President of Pakistan Award 2007 for having the highest score at university level
2 Gold Medals in B.Sc. (Hons.) and 1 Gold Medal and 1 Silver Medal in M.Sc. (Hons.) through attaining the best score at Faculty and University level.
1st Position in French Master “M2-Santé des plantes”
HEC scholarship for Master leading to PhD for France
Agreenskills+ Fellowship for post-doctoral research, France



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