ArticleJournal of advanced research2022
A novel Synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes.
Article in Journal of advanced research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed, 13 citations in OpenAlex.
- Genome-wide association study of diverse soybean [Glycine max (L.) Merrill] accessions for agronomic and seed composition traits in Rwanda.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Integrative Approaches to Soybean Resilience, Productivity, and Utility: A Review of Genomics, Computational Modeling, and Economic Viability.Plants (Basel, Switzerland) · 2025Review
- Phenotypic characterization of soybean genetic resources at multiple locations: breeding implications for enhancing environmental resilience, yield and protein content.Frontiers in plant science · 2025Article
- Soybean genomics research community strategic plan: A vision for 2024-2028.The plant genome · 2024Article
- Soybean pod shattering resistance allele pdh1 and marker-assisted selection.Plant-environment interactions (Hoboken, N.J.) · 2024Article
- Genome-wide association study reveals GmFulb as candidate gene for maturity time and reproductive length in soybeans (Glycine max).PloS one · 2024Article
- Natural and artificial selection of multiple alleles revealed through genomic analyses.Frontiers in genetics · 2023Article
- Article
- Cataloging SCN resistance loci in North American public soybean breeding programs.Frontiers in plant science · 2023Article
- Candidate Genes Modulating Reproductive Timing in Elite US Soybean Lines Identified in Soybean Alleles ofFrontiers in plant science · 2022Article
- Utilization of Plant Architecture Genes in Soybean to Positively Impact Adaptation to High Yield Environments.Frontiers in plant science · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
introductionGenome-Wide Association Studies (GWAS) identify tagging variants in the genome that are statistically associated with the phenotype because of their linkage disequilibrium (LD) relationship with the causative mutation (CM). When both low-density genotyped accession panels with phenotypes and resequenced data accession panels are available, tagging variants can assist with post-GWAS challenges in CM discovery.
objectivesOur objective was to identify additional GWAS evaluation criteria to assess correspondence between genomic variants and phenotypes, as well as enable deeper analysis of the localized landscape of association.
methodsWe used genomic variant positions as Synthetic phenotypes in GWAS that we named "Synthetic phenotype association study" (SPAS). The extreme case of SPAS is what we call an "Inverse GWAS" where we used CM positions of cloned soybean genes. We developed and validated the Accuracy concept as a measure of the correspondence between variant positions and phenotypes.
resultsThe SPAS approach demonstrated that the genotype status of an associated variant used as a Synthetic phenotype enabled us to explore the relationships between tagging variants and CMs, and further, that utilizing CMs as Synthetic phenotypes in Inverse GWAS illuminated the landscape of association. We implemented the Accuracy calculation for a curated accession panel to an online Accuracy calculation tool (AccuTool) as a resource for gene identification in soybean. We demonstrated our concepts on three examples of soybean cloned genes. As a result of our findings, we devised an enhanced "GWAS to Genes" analysis (Synthetic phenotype to CM strategy, SP2CM). Using SP2CM, we identified a CM for a novel gene.
conclusionThe SP2CM strategy utilizing Synthetic phenotypes and the Accuracy calculation of correspondence provides crucial information to assist researchers in CM discovery. The impact of this work is a more effective evaluation of landscapes of GWAS associations.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.