Yousef Rahimi

I am a postdoctoral researcher in plant genomics and breeding at the Swedish University of Agricultural Sciences (SLU), working in the Pär K. Ingvarsson Research Group (PKI Lab). My research focuses on understanding and utilising genetic diversity to improve crop performance and resilience to environmental stresses.

I combine population genomics, quantitative genetics, bioinformatics, and plant phenotyping to investigate the genetic basis of complex traits relevant to crop improvement. My work integrates high-throughput sequencing, genome-wide association studies (GWAS), and genomic selection (GS) with field and controlled-environment experiments.

My current research focuses on timothy (Phleum pratense L.), an important forage grass in northern Europe. I investigate genomic diversity, population structure, and the genetic basis of agronomic and stress-related traits to support the development of more productive and climate-resilient forage varieties.

My previous research includes population genomics of intermediate wheatgrass and investigations of drought adaptation and molecular responses to water deficit in bread wheat. My broader goal is to translate genomic knowledge into practical breeding strategies for sustainable crop improvement.

Population genomics and genomic-assisted breeding of timothy (2020–present)

My primary research focuses on the genetic and phenotypic diversity of timothy and its closely related species, including Phleum nodosum and Phleum alpinum.

During my doctoral research at SLU, I investigated variation in plant development, tiller formation, biomass production, and stress-related traits across wild and domesticated genetic resources. This work combined multi-year field experiments, controlled-environment phenotyping, and genomic analyses to explore diversity and identify potentially valuable genetic resources for forage breeding.

My current postdoctoral research extends this work through population-genomic analyses, SNP discovery, genome-wide association studies, and genomic selection in timothy breeding populations.

My research activities include:

• Characterisation of genetic diversity, population structure, and differentiation in wild and domesticated timothy.
• Investigation of genomic variation, recombination, and signatures of selection.
• Identification of genomic regions associated with agronomic and adaptive traits using GWAS.
• Integration of genomic, transcriptomic, metabolomic, and phenotypic data to investigate plant responses to abiotic stresses, including drought, heat, waterlogging, and cold.
• Application of genomic selection (GS) approaches to support timothy breeding.

The overall objective is to improve our understanding of the genetic resources available for timothy breeding and contribute to the development of productive, resilient forage varieties adapted to changing environmental conditions.

Population genomics of intermediate wheatgrass (2024–2025)

I have also worked on genomic analyses of intermediate wheatgrass (Thinopyrum intermedium), a perennial grain crop with potential applications in sustainable agricultural systems.

This research involved analysing skim-sequencing data to investigate genetic diversity, population structure, differentiation, and evolutionary patterns.

Genomics and drought adaptation in bread wheat (2016–2019)

My earlier research focused on the genetic and molecular mechanisms underlying agronomic traits and drought adaptation in bread wheat (Triticum aestivum L.).

I used genome-wide association studies, genotyping-by-sequencing, QTL meta-analysis, and statistical approaches to investigate the genetic basis of early vigour, yield-related traits, and genotype-by-environment interactions under contrasting water availability.

During a research visit to SLU in 2018–2019, I also investigated the molecular responses of wheat roots to water deficit using RNA sequencing and comparative transcriptomic analyses, with particular emphasis on regulatory gene and protein networks involved in stress responses.

These studies contributed to my broader interest in combining genomic and physiological information to understand plant adaptation and improve breeding strategies.

During my PhD studies at SLU, I contributed to teaching at both Bachelor's and Master's levels as a laboratory and teaching assistant. My teaching experience includes practical laboratory sessions and course-related activities in:

• Biology
• Genetics, Cell Biology and Microbiology
• Plant Growth and Development

I have experience supervising and supporting Master's-level research projects at SLU.

2026: Main supervisor of a Master's student at SLU.
2022: Co-supervisor of a Master's student at SLU.

I contribute to the scientific community through peer review and editorial activities.

I have served as a reviewer for international scientific journals, including Plant and Soil, Planta, BMC Plant Biology, Scientific Reports, International Journal of Molecular Sciences, Journal of Applied Genetics, and Genetic Resources and Crop Evolution.

• 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.
• 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, 541.
• 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.
• Rahimi, Y., Bedada, G., Gustavsson, A. M., Ingvarsson, P. K., Lundquist, P. O., & Westerbergh, A. (2026). Development and Tiller Formation in Wild and Domesticated Accessions of Timothy (Phleum pratense) and Its Relatives P. nodosum and P. alpinum. Agriculture, 16(8), 902.
• 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.
• 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.