Sajid Ali

Sajid Ali

session, year:
2015 2nd

Former fellow

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

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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

I am assistant professor at the University of Agriculture, Peshawar, Pakistan, with a PhD from Paris-XI University, Paris, France and Post-Doctorate from Aarhus University, Denmark. Through AgreenSkills funding, I completed by second PostDoctorate at the BGPI, INRA-CIRAD-Montpellier SupAgro, France on the role of spatio-temporal variability in host on the pathogen population using population genomics. My expertise lies in pathogen population dynamics at spatial and temporal scale along with in depth knowledge of genetics, breeding and ecological consequences of resistance genes deployment. My 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. My research in crop improvement has resulted in development of a wheat variety “Ghanimat-e-IBGE” along with other breeding lines are in the pipeline. I have strong collaborations 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. I conducted research projects in collaboration with INRA, France and TAG, UK as collaborator. Currently I have two research projects as PI, one funded by Govt. of Pakistan and other by USAIDCIMMYT. In a mega European Consortium, I am PI from Pakistan in a project awarded by ERC under H2020.

Selected publications

Brar GS,  Ali S, D Qutob, et al., 2018. Genome resequencing and simple sequence repeat markers reveal the existence of divergent lineages in the Canadian Puccinia striiformis f. sp. tritici population with extensive DNA methylation. Environmental Microbiology. Doi: 10.1111/1462-2920.14067.

Ali S, Rodriguez-Algaba J, Thach T, et al., 2017. Yellow rust epidemics worldwide were caused by pathogen races from divergent genetic lineages. Frontiers in Plant Science. 8: 1058. Doi: 10.3389/fpls.2017.01057.

Ali S, Soubeyrand S, Gladieux P, et al., 2016. CloNcaSe: Estimation of sex frequency and effective population size by clonemate re-sampling in partially clonal organisms. Molecular Ecology Resources. 16: 845-861.

Ali S, Gladieux P, Leconte M, Gautier A, et al., 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.

Ali S, Gladieux P, Rahman H, et al., 2014. Inferring the contribution of sexual reproduction, migration and offseason 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. 

Awards & patents

2018 Research Productivity Award for the year 2017 – by Pakistan Council for Science and Technology, Ministry of Science and Technology, Pakistan

2017 Research Productivity Award for the year 2016 – by Pakistan Council for Science and Technology, Ministry of Science and Technology, Pakistan

2016 Award of Agreenskills+ Fellowship for completion of Post-Doc in France

2015 Development of wheat variety “Ghanimat”.

2009 1st position in M2-Santé des plantes – Agrocampus-Ouest, Rennes, France. 2006 President of Pakistan Award –based on the highest score at the overall University level in B.Sc. (Hons)

2008 Higher Education Commission Scholarship for PhD in France.

2008 1 Gold Medals – based on the highest score at the Faculty level in M.Sc. (Hons) 2006 2 Gold Medals – based on the highest score at the Faculty and University level in B.Sc. (Hons)

Talks in annual meetings

Epidemiology and genomics of rice blast in a traditional agrosystem
2017 / P2 Tissue and Individual,P3 Population and Ecosystems / by Sajid Ali / Fellows Speed Presentation


Magnaporthe oryzae, rice blast, plant-fungus interactions, traditional agrosystems, durable resistance, Population genomics, adaptation