A novel Synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes

Introduction: Genome-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.Objectives: Our 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. Methods: We 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.Results: The 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 fur-ther, that utilizing CMs as Synthetic phenotypes in Inverse GWAS illuminated the landscape of associa-tion. 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 con-cepts 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.Conclusion: The SP2CM strategy utilizing Synthetic phenotypes and the Accuracy calculation of corre-spondence provides crucial information to assist researchers in CM discovery. The impact of this work is a more effective evaluation of landscapes of GWAS associations. (c) 2022 The Authors. Published by Elsevier B.V. on behalf of Cairo University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Automated summary

This article introduces the use of synthetic phenotypes and the accuracy calculation to evaluate the correspondence between genomic variants and phenotypes, leading to a more effective evaluation of GWAS associations. The findings provide crucial information for researchers in causative mutation discovery.