Engineering topics
Publications and source records attributed to Morgan, Mallory.
Aninteractive mapshowingPopulus trichocarpaGWAS sub-population structure identified by DBSCAN clustering, which were derived from a UMAP projection of the top 8 PCs of LD-pruned pangenome SNP data. Geographic origins are searchable by genotype or river system using the search bar.
Aninteractive UMAP plotderived from the top 8 PCs of LD-prunedPopulus trichocarpapangenome SNP data. Points are colored by ADMIXTURE population structure (k=3) and geographic origins are searchable by genotype or river system using the search bar.
An interactive map showing Populus trichocarpa GWAS population structure estimated by ADMIXTURE (k=3, selected as optimal from k=2-11). Sampling locations are colored by their predominant ancestry proportion among the three inferred populations and geographic origins are searchable by genotype or river system using the search bar.
This narrative presents a demonstration of RWRtools methods to the important bioenergy feedstock Panicum virgatum (Switchgrass) by leveraging networks from the model plant Arabidopsis thaliana. We used a genome-wide association study (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with Switchgrass shoot biomass. We then assigned these SNPs to Switchgrass genes, and using Phytozome (Goodstein et al., 2012), assigned these 38 Switchgrass GWAS genes to 32 Arabidopsis orthologs. These 32 genes are the starting set of genes (i.e. the seed gene set) for this demo narrative.