Yousef Rahimi
Uppsala
Summary
Ph.D. in Biology with a focus on plant genomics, bioinformatics, and breeding for climate resilience. My research uses high-throughput genomic data and statistical tools to explore genetic diversity and dissect complex traits in crops, with a particular focus on timothy grass, supported by earlier work on wheat. I bring experience in genomic data analysis, molecular lab techniques, and field and controlled-environment trials to advance sustainable plant breeding.
Overview
12
12
years of professional experience
Work History
Researcher (Post-PhD Extension)
Swedish University of Agricultural Sciences
Uppsala
06.2024 - 05.2025
- Constructed genomic libraries for timothy breeding lines from Lantmännen.
- Processed and analyzed sequencing data from NordGen timothy accessions, including alignment, SNP calling, population genomics analyses, and GWAS.
- Performed population structure, differentiation, and evolutionary analyses (e.g., Tajima’s D) on Intermediate wheatgrass populations using skim-seq data.
PhD Researcher
Swedish University of Agricultural Sciences
Uppsala
03.2020 - 05.2024
- Conducted field and greenhouse evaluations to assess the phenotypic diversity of agronomic traits among NordGen timothy accessions.
- Prepared genomic libraries for Illumina sequencing of timothy accessions.
- Applied GATK Best Practices for SNP calling to support genomic analyses
- Performed population structure, genetic diversity, recombination, and selection scan analyses.
- Co-Supervisor – Master's Student, 2022
PhD Researcher
University of Tehran
Karaj
01.2016 - 10.2019
- Conducted field and greenhouse phenotyping to assess agronomic traits in Iranian bread wheat populations, along with in vitro assessments to study early vigor.
- Performed genetic diversity analysis using GBS data to investigate the population structure of bread wheat.
- Carried out GWAS to identify genomic regions associated with agronomic traits and early vigor for use in breeding programs.
Visiting Researcher
Swedish University of Agricultural Sciences
Uppsala
10.2018 - 09.2019
- Conducted root phenotyping to evaluate the response of wheat genotypes under water deficit conditions.
- Performed transcriptome analysis using RNA-sequencing to identify differentially expressed genes and protein networks involved in drought tolerance in wheat.
R&D Specialist
Technology of Natural Sustainable Ecosystem Research
Karaj
10.2016 - 09.2018
- Designed molecular genetics protocols for population genomics research.
- Collaborated with cross-functional teams to complete projects and publications.
- Prepared technical reports and peer-reviewed research articles.
Master Student
Univeristy of Tehran
Karaj
09.2013 - 09.2015
- Conducted gene expression profiling of key genes involved in the menthol biosynthesis pathway in peppermint (Mentha piperita) using qRT-PCR.
- Evaluated phenolic compound content and antioxidant capacity of peppermint under drought stress conditions.
Education
Ph.D. - Biology (Plant Genomics and Breeding)
Swedish University of Agricultural Sciences
Uppsala, Sweden06.2024
Ph.D. - Molecular Genetics and Genetic Engineering
University of Tehran
Karaj, Iran. 10-2019
Master of Science - Plant Breeding
University of Tehran
Karaj, Iran09.2015
Bachelor’s Degree - Agronomy and Plant Breeding
Bu-Ali Sina University
Hamedan, Iran08.2013
Skills
- Genomic Data Analysis: GWAS, QTL mapping, LD, population structure, genetic diversity analysis, selection scan, recombination rate estimation
- Transcriptomics: RNA-seq, transcript assembly, differential gene expression analysis, functional enrichment (GO/KEGG, PPI)
- Statistical Analysis: ANOVA, regression, mixed models, stability analysis (R, SAS, JMP)
- Computational Tools & Scripting: R, UNIX/Linux command line, data visualization, scripting for large-scale data analysis
- Molecular Biology: DNA/RNA extraction, PCR, genomic library construction
- Biochemical Assays: Antioxidant enzyme analysis (SOD, PPO), phenolic content quantification, DPPH assay, spectrophotometry
- Field & Greenhouse Research: Trial design, phenotyping, data analysis
Timeline
Researcher (Post-PhD Extension)
Swedish University of Agricultural Sciences
06.2024 - 05.2025
PhD Researcher
Swedish University of Agricultural Sciences
03.2020 - 05.2024
Visiting Researcher
Swedish University of Agricultural Sciences
10.2018 - 09.2019
R&D Specialist
Technology of Natural Sustainable Ecosystem Research
10.2016 - 09.2018
PhD Researcher
University of Tehran
01.2016 - 10.2019
Master Student
Univeristy of Tehran
09.2013 - 09.2015
Ph.D. - Biology (Plant Genomics and Breeding)
Swedish University of Agricultural Sciences
Ph.D. - Molecular Genetics and Genetic Engineering
University of Tehran
Master of Science - Plant Breeding
University of Tehran
Bachelor’s Degree - Agronomy and Plant Breeding
Bu-Ali Sina University
Accomplishments
- Visiting Research Scholarship, Swedish University of Agricultural Sciences (SLU), awarded by the Ministry of Science, Research and Technology, Iran – 2018
- Young Exceptional Talent, awarded by Iran's National Elites Foundation – 2017
- Exceptional Talent Award, Bu-Ali Sina University – September 2015
- Finalist (Top 10), National Science Olympiad – Agriculture & Plant Breeding, Iran (2013)
- National Entrance Exam – Ph.D., Ranked 2nd out of over 1,000 candidates in Plant Breeding, Iran – 2015
- National Entrance Exam – M.Sc., Ranked 2nd out of over 4,000 candidates in Plant Breeding, Iran – 2013
- Ranked 1st in graduating class for both M.Sc. in Plant Breeding (2015) and B.Sc. in Agronomy and Plant Breeding (2013)
Key publications
- Rahimi, Y., Bedada, G., Moreno, S., Gustavsson, A. M., Ingvarsson, P. K., & Westerbergh, A. (2023). Phenotypic Diversity in Domesticated and Wild Timothy Grass, and Closely Related Species for Forage Breeding. Plants, 12(19), 3494.
- Moreno, S., Bedada, G., Rahimi, Y., Ingvarsson, P. K., Westerbergh, A., & Lundquist, P. O. (2023). Response to waterlogging stress in wild and domesticated accessions of timothy (Phleum pratense) and its relatives P. alpinum and P. nodosum. Plants, 12(23), 4033.
- Rahimi, Y., Khahani, B., Jamali, A., Alipour, H., Bihamta, M. R., & Ingvarsson, P. K. (2022). GWAS to identify genomic loci associated with early vigour in bread wheat under simulated water deficit complemented with QTL meta-analysis. G3 (Genes, Genomes, Genetics), jkac320- jkac320.
- Rahimi, Y., Ingvarsson, P. K., Bihamta, M. R., Alipour, H., Taleei, A., & Abadi, S. K. J. (2021). Characterization of Dynamic Regulatory Gene and Protein Networks in Wheat Roots Upon Perceiving Water Deficit Through Comparative Transcriptomics Survey. Frontiers in Plant Science, 12.
- Alipour, H., Abdi, H., Rahimi, Y., & Bihamta, M. R. (2021). Dissection of the genetic basis of genotype-by-environment interactions for grain yield and main agronomic traits in Iranian bread wheat landraces and cultivars. Scientific reports, 11(1), 1-17.
- Alipour, H., Abdi, H., Rahimi, Y., & Bihamta, M. R. (2021). Genotypeby- year interaction for grain yield of Iranian wheat cultivars and its interpretation using Vrn and Ppd functional markers and environmental covariables. Cereal Research Communications, 49(4), 681-690.
- Rahimi, Y., Bihamta, M. R., Taleei, A., Alipour, H., & Ingvarsson, P. K. (2019). Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs. BMC plant biology, 19 (1),541.
- Rahimi, Y., Bihamta, M., Taleei, A., & Ali Pour, H. (2019). Genetic variability assessment of Iranian wheat landraces in term of some agronomic attributes under normal irrigation and rain-fed conditions. Iranian Journal of Field Crop Science, 50(3), 1-16.
- Rahimi, Y., Bihamta, M. R., Taleei, A., Alipour, H., & Ingvarsson, P. K. (2019). Applying an artificial neural network approach for drought tolerance screening among Iranian wheat landraces and cultivars grown under well-watered and rain-fed conditions. Acta Physiologiae Plantarum, 41(9), 156.
- Rahimi, Y., Taleei, A., & Ranjbar, M. (2018). Long-term water deícit modulates antioxidant capacity of peppermint (Mentha piperita L.). Scientia Horticulturae, 237, 36-43.
- Rahimi, Y., Taleei, A., & Ranjbar, M. (2017). Changes in the expression of key genes involved in the biosynthesis of menthol and menthofuran in Mentha piperita L. under drought stress. Acta Physiologiae Plantarum, 39(9), 203.
Conferences and Workshops
Conferences:
- Plant Biology Europe, Marseille, France. July 3-6, 2023. Oral presentation in Domestication in retrospect and the future of breeding, session.
- NordGen PPP Conference-Use of Genetic Resources in Breeding for Climate Change in the Nordic Region, Malmö, Sweden. February 1–2, 2023. Poster presentation.
- The 5th National Legumes Conference, University of Tehran, Iran, Feb 2014. Organizing committee.
Workshops:
- How to become a postdoc. Uppsala, Sweden. May 2023.
- Workshop series II- Methods in modern plant breeding, Uppsala, Sweden. January 2023.
- Breeding at SLU – internal workshop, Umeå, Sweden. August 23- 24, 2022.
- Workshop series I- Methods in modern plant breeding, Uppsala, Sweden. January 2022.
- SLU Grogrund workshop, Malmö, Sweden. December 15-16, 2021.
- Lecturer, Workshop on Application of SAS Statistical Software in Analyzing Agricultural Designs – September 2016
Peer Review Activities
- Reviewer for Planta.
- Reviewer for Plant and soil.
- Reviewer for Genetic resources and crop evolution.
References
- Pär K. Ingvarsson
Department of Plant Biology, SLU, Sweden, Professor in Plant Genomics and Plant Breeding. E-mail: par.ingvarsson@slu.se.
- Anna Westerbergh
Department of Plant Biology, SLU, Sweden, Associate Professor in Genetics and Plant Breeding. E-mail: anna.westerbergh@slu.se.
Key publications
- Rahimi, Y., Bedada, G., Moreno, S., Gustavsson, A. M., Ingvarsson, P. K., & Westerbergh, A. (2023). Phenotypic Diversity in Domesticated and Wild Timothy Grass, and Closely Related Species for Forage Breeding. Plants, 12(19), 3494.
- Moreno, S., Bedada, G., Rahimi, Y., Ingvarsson, P. K., Westerbergh, A., & Lundquist, P. O. (2023). Response to waterlogging stress in wild and domesticated accessions of timothy (Phleum pratense) and its relatives P. alpinum and P. nodosum. Plants, 12(23), 4033.
- Rahimi, Y., Khahani, B., Jamali, A., Alipour, H., Bihamta, M. R., & Ingvarsson, P. K. (2022). GWAS to identify genomic loci associated with early vigour in bread wheat under simulated water deficit complemented with QTL meta-analysis. G3 (Genes, Genomes, Genetics), jkac320- jkac320.
- Rahimi, Y., Ingvarsson, P. K., Bihamta, M. R., Alipour, H., Taleei, A., & Abadi, S. K. J. (2021). Characterization of Dynamic Regulatory Gene and Protein Networks in Wheat Roots Upon Perceiving Water Deficit Through Comparative Transcriptomics Survey. Frontiers in Plant Science, 12.
- Alipour, H., Abdi, H., Rahimi, Y., & Bihamta, M. R. (2021). Dissection of the genetic basis of genotype-by-environment interactions for grain yield and main agronomic traits in Iranian bread wheat landraces and cultivars. Scientific reports, 11(1), 1-17.
- Alipour, H., Abdi, H., Rahimi, Y., & Bihamta, M. R. (2021). Genotypeby- year interaction for grain yield of Iranian wheat cultivars and its interpretation using Vrn and Ppd functional markers and environmental covariables. Cereal Research Communications, 49(4), 681-690.
- Rahimi, Y., Bihamta, M. R., Taleei, A., Alipour, H., & Ingvarsson, P. K. (2019). Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs. BMC plant biology, 19 (1),541.
- Rahimi, Y., Bihamta, M., Taleei, A., & Ali Pour, H. (2019). Genetic variability assessment of Iranian wheat landraces in term of some agronomic attributes under normal irrigation and rain-fed conditions. Iranian Journal of Field Crop Science, 50(3), 1-16.
- Rahimi, Y., Bihamta, M. R., Taleei, A., Alipour, H., & Ingvarsson, P. K. (2019). Applying an artificial neural network approach for drought tolerance screening among Iranian wheat landraces and cultivars grown under well-watered and rain-fed conditions. Acta Physiologiae Plantarum, 41(9), 156.
- Rahimi, Y., Taleei, A., & Ranjbar, M. (2018). Long-term water deícit modulates antioxidant capacity of peppermint (Mentha piperita L.). Scientia Horticulturae, 237, 36-43.
- Rahimi, Y., Taleei, A., & Ranjbar, M. (2017). Changes in the expression of key genes involved in the biosynthesis of menthol and menthofuran in Mentha piperita L. under drought stress. Acta Physiologiae Plantarum, 39(9), 203.
Conferences and Workshops
Conferences:
- Plant Biology Europe, Marseille, France. July 3-6, 2023. Oral presentation in Domestication in retrospect and the future of breeding, session.
- NordGen PPP Conference-Use of Genetic Resources in Breeding for Climate Change in the Nordic Region, Malmö, Sweden. February 1–2, 2023. Poster presentation.
- The 5th National Legumes Conference, University of Tehran, Iran, Feb 2014. Organizing committee.
Workshops:
- How to become a postdoc. Uppsala, Sweden. May 2023.
- Workshop series II- Methods in modern plant breeding, Uppsala, Sweden. January 2023.
- Breeding at SLU – internal workshop, Umeå, Sweden. August 23- 24, 2022.
- Workshop series I- Methods in modern plant breeding, Uppsala, Sweden. January 2022.
- SLU Grogrund workshop, Malmö, Sweden. December 15-16, 2021.
- Lecturer, Workshop on Application of SAS Statistical Software in Analyzing Agricultural Designs – September 2016
Peer Review Activities
- Reviewer for Planta.
- Reviewer for Plant and soil.
- Reviewer for Genetic resources and crop evolution.
References
- Pär K. Ingvarsson
Department of Plant Biology, SLU, Sweden, Professor in Plant Genomics and Plant Breeding. E-mail: par.ingvarsson@slu.se.
- Anna Westerbergh
Department of Plant Biology, SLU, Sweden, Associate Professor in Genetics and Plant Breeding. E-mail: anna.westerbergh@slu.se.
Key publications
- Rahimi, Y., Bedada, G., Moreno, S., Gustavsson, A. M., Ingvarsson, P. K., & Westerbergh, A. (2023). Phenotypic Diversity in Domesticated and Wild Timothy Grass, and Closely Related Species for Forage Breeding. Plants, 12(19), 3494.
- Moreno, S., Bedada, G., Rahimi, Y., Ingvarsson, P. K., Westerbergh, A., & Lundquist, P. O. (2023). Response to waterlogging stress in wild and domesticated accessions of timothy (Phleum pratense) and its relatives P. alpinum and P. nodosum. Plants, 12(23), 4033.
- Rahimi, Y., Khahani, B., Jamali, A., Alipour, H., Bihamta, M. R., & Ingvarsson, P. K. (2022). GWAS to identify genomic loci associated with early vigour in bread wheat under simulated water deficit complemented with QTL meta-analysis. G3 (Genes, Genomes, Genetics), jkac320- jkac320.
- Rahimi, Y., Ingvarsson, P. K., Bihamta, M. R., Alipour, H., Taleei, A., & Abadi, S. K. J. (2021). Characterization of Dynamic Regulatory Gene and Protein Networks in Wheat Roots Upon Perceiving Water Deficit Through Comparative Transcriptomics Survey. Frontiers in Plant Science, 12.
- Alipour, H., Abdi, H., Rahimi, Y., & Bihamta, M. R. (2021). Dissection of the genetic basis of genotype-by-environment interactions for grain yield and main agronomic traits in Iranian bread wheat landraces and cultivars. Scientific reports, 11(1), 1-17.
- Alipour, H., Abdi, H., Rahimi, Y., & Bihamta, M. R. (2021). Genotypeby- year interaction for grain yield of Iranian wheat cultivars and its interpretation using Vrn and Ppd functional markers and environmental covariables. Cereal Research Communications, 49(4), 681-690.
- Rahimi, Y., Bihamta, M. R., Taleei, A., Alipour, H., & Ingvarsson, P. K. (2019). Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs. BMC plant biology, 19 (1),541.
- Rahimi, Y., Bihamta, M., Taleei, A., & Ali Pour, H. (2019). Genetic variability assessment of Iranian wheat landraces in term of some agronomic attributes under normal irrigation and rain-fed conditions. Iranian Journal of Field Crop Science, 50(3), 1-16.
- Rahimi, Y., Bihamta, M. R., Taleei, A., Alipour, H., & Ingvarsson, P. K. (2019). Applying an artificial neural network approach for drought tolerance screening among Iranian wheat landraces and cultivars grown under well-watered and rain-fed conditions. Acta Physiologiae Plantarum, 41(9), 156.
- Rahimi, Y., Taleei, A., & Ranjbar, M. (2018). Long-term water deficit modulates antioxidant capacity of peppermint (Mentha piperita L.). Scientia Horticulturae, 237, 36-43.
- Rahimi, Y., Taleei, A., & Ranjbar, M. (2017). Changes in the expression of key genes involved in the biosynthesis of menthol and menthofuran in Mentha piperita L. under drought stress. Acta Physiologiae Plantarum, 39(9), 203.
Conferences and Workshops
Conferences:
- Plant Biology Europe, Marseille, France. July 3-6, 2023. Oral presentation in Domestication in retrospect and the future of breeding, session.
- NordGen PPP Conference-Use of Genetic Resources in Breeding for Climate Change in the Nordic Region, Malmö, Sweden. February 1–2, 2023. Poster presentation.
- The 5th National Legumes Conference, University of Tehran, Iran, Feb 2014. Organizing committee.
Workshops:
- How to become a postdoc. Uppsala, Sweden. May 2023.
- Workshop series II- Methods in modern plant breeding, Uppsala, Sweden. January 2023.
- Breeding at SLU – internal workshop, Umeå, Sweden. August 23- 24, 2022.
- Workshop series I- Methods in modern plant breeding, Uppsala, Sweden. January 2022.
- SLU Grogrund workshop, Malmö, Sweden. December 15-16, 2021.
- Lecturer, Workshop on Application of SAS Statistical Software in Analyzing Agricultural Designs – September 2016
Peer Review Activities
- Reviewer for Planta.
- Reviewer for Plant and soil.
- Reviewer for Genetic resources and crop evolution.
References
- Pär K. Ingvarsson
Department of Plant Biology, SLU, Sweden, Professor in Plant Genomics and Plant Breeding. E-mail: par.ingvarsson@slu.se.
- Anna Westerbergh
Department of Plant Biology, SLU, Sweden, Associate Professor in Genetics and Plant Breeding. E-mail: anna.westerbergh@slu.se.
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