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

Authors: SKRABISOVA, MARIA - Palacky University; DIETZ, NICHOLAS - University Of Missouri; ZENG, SHUAI - University Of Missouri; CHAN, YEN ON - University Of Missouri; WANG, JUEXIN - University Of Missouri; LIU, YANG - University Of Missouri; BIOVA, JANA - Palacky University; TRUPTI, JOSHI - University Of Missouri; Bilyeu, Kristin

Submitted to: Journal of Advanced Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/8/2022
Publication Date: 12/12/2022
Citation: Skrabisova, M., Dietz, N., Zeng, S., Chan, Y., Wang, J., Liu, Y., Biova, J., Trupti, J., Bilyeu, K.D. 2022. A novel synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes. Journal of Advanced Research. 42:117-133. https://doi.org/10.1016/j.jare.2022.04.004.
DOI: https://doi.org/10.1016/j.jare.2022.04.004

Interpretive Summary: Statistical methods have been developed over the past ten years to empower researchers to identify regions of the genome responsible for important traits. Also in this time-frame has been the massive expansion of genomic marker sets as well as availability of up to thousands of samples of whole genome sequence information for certain species. In this work, we developed new strategies and deployed a novel online tool to improve the analyses of the statistical approaches aimed at finding the genes responsible for important traits in soybean. We demonstrated the effectiveness of our strategies utilizing three examples of genes that had already been cloned. The impact of this work is a more effective approach including an online tool to aid in the discovery of genes controlling important traits.

Technical Abstract: 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 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. Conclusion The 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.