Research Projects
Nitrogen use efficiency in the Swedish Aspen collection SwAsp
2023 - 2026
- Completed high-throughput phenotyping for 336 individuals covering 112 genotypes from 12 provenances on the Wallenberg phenotyping platform at UPSC.
- Measured biomass traits including plant height, stem diameter, and dry weight of leaf, stem, and root tissues.
- Analyzed nitrogen metabolism traits including tissue nitrogen content.
- Performed GWAS based on approximately 6 million SNPs using mixed linear models with population structure correction and latitude as a covariate.
- Conducted functional validation through 15N uptake experiments and grafting assays.
Epigenetics of defense priming and climatic adaptation in Fragaria vesca
2018 - 2023
- Investigated flowering time and stolon production differences in diploid Fragaria vesca ecotypes produced through asexual and sexual reproduction under different temperature conditions.
- Generated transcriptome and methylome datasets and identified differentially expressed genes and differentially methylated genes.
- Performed functional analysis and network analysis of differentially regulated genes.
- Conducted EWAS, meQTL, and methylation polymorphism analyses across multiple ecotypes from different latitudes.
Mechanistic study of the soybean maturity gene E1
2014 - 2016
- Analyzed transcriptome differences between E1 overexpression plants and wild type, followed by qPCR validation.
- Validated small RNA-seq and long non-coding RNA sequencing results.
- Compared expression patterns of differentially expressed genes across tissues, stages, and soybean varieties.
- Constructed Arabidopsis overexpression lines for the putative photoperiod pathway gene GmSPL3b.
Methods and Analysis
- WGBS and DNA methylation analysis, including DMR calling, methylome profiling, and temperature-associated epigenetic variation.
- GWAS and EWAS workflows from genotype or methylation QC through association testing and interpretation.
- RNA-seq, scRNA-seq and snRNA-seq analysis, including clustering, differential expression, and multi-omics integration.
- Visualization using Manhattan plots, Q-Q plots, Circos, ComplexHeatmap, ggplot2, and CMplot.