Looking Beyond GWAS: Identifying Functional Roles of SNPs Using Metabolic Networks in Arabidopsis and Populus
- Conference: International Conference on Plant Synthetic Biology and Bioengineering
- Year: 2019
- Proceeding: 3rd International Conference on Plant Synthetic Biology, Bioengineering, and Biotechnology
- Group: General Submissions
- Time: Saturday, October 5, 2019 - 12:15pm-12:30pm
SNPeffect was used to explain differential growth and metabolite accumulation in A.thaliana and P. trichocarpa accessions as the outcome of activating and inactivating SNPs in enzyme-coding regions of the genotypes. To this end, we also constructed a P.trichocarpa genome-scale metabolic model, first for a perennial woody tree. As expected, our results indicate that plant growth is a complex polygenic trait governed by carbon and energy partitioning. Growth-affecting SNPs were found to be primarily in glycolysis, amino-acid, and energy metabolism. Faster-growing Arabidopsis genotypes were predicted to have higher fluxes through protein metabolism pathways and employ the energy efficient purine salvage pathway as opposed to de novo purine biosynthesis for generating nucleotides. In poplar, growth-determining SNPs with an upregulating role were in genes from cellulose and lignin biosynthesis, amino acid, and energy metabolism, in line with breeding strategies targeting pathways governing carbon and energy partition. SNPeffect also identified (putatively) functional SNPs in both species, distributed among pathways such as glycolysis, folate, and pyrimidine metabolism.