ArticleThe Plant journal : for cell and molecular biology2020
SNPeffect: identifying functional roles of SNPs using metabolic networks.
Article in The Plant journal : for cell and molecular biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 30 citations in OpenAlex.
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- Fermi calculations enable quick downselection of target genes and process optimization in photosynthetic systems.Plant physiology · 2025Review
- Genome-scale metabolic modelling identifies reactions mediated by SNP-SNP interactions associated with yeast sporulation.NPJ systems biology and applications · 2025Article
- A Guide to Metabolic Network Modeling for Plant Biology.Plants (Basel, Switzerland) · 2025Review
- A brief clinical genetics review: stepwise diagnostic processes of a monogenic disorder-hypertriglyceridemia.Translational pediatrics · 2024Review
- Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective.Metabolites · 2024Review
- Deep learning the cis-regulatory code for gene expression in selected model plants.Nature communications · 2024Article
- Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat.The plant genome · 2024Review
- The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.PLoS computational biology · 2023Article
- Exome-based new allele-specific PCR markers and transferability for sodicity tolerance in bread wheat (Plant direct · 2023Article
- Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley.Journal of advanced research · 2023Article
- Toward mechanistic modeling and rational engineering of plant respiration.Plant physiology · 2023Article
- Characterization of effects of genetic variants via genome-scale metabolic modelling.Cellular and molecular life sciences : CMLS · 2021Review
- The chromosome-level reference genome assembly forPlant communications · 2021Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genetic sources of phenotypic variation have been a focus of plant studies aimed at improving agricultural yield and understanding adaptive processes. Genome-wide association studies identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. Here, we propose a complementary analysis (SNPeffect) that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect is used to explain differential growth rate and metabolite accumulation in A. thaliana and P. trichocarpa accessions as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicate that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.