Welcome to Soy Hub

A hub for soybean-applied genomics predictions based on a curated panel of diverse soybean resequenced accessions (Soy1066).

Explore variation:

Allele Catalog

- Find accessions with certain allele

- Find new alleles in known genes


- Explore variation in promoters

- Search TFs

- Explore CNV


- Mutative allele discovery

- Mutative allele position combinative calculations

Predict new causal mutations:


- Use GWAS results for prediction

- Calculate Accuracy for your markers or candidate causative mutations (CM) based on Soy775 35.7M variant positions


- Check genomic context of your variant positions in empowered haplotype viewer on various resequenced data sets

Reference Interassembly Gene Browser

- Search between reference genotypes, genome assemblies, or annotation versions


Allele Catalog

[1] Chan YO, Dietz N, Zeng S, Wang J, Flint-Garcia S, Salazar-Vidal MN, Škrabišová M, Bilyeu K, Joshi T: The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis. BMC Genomics 2023, 24(1):107.


[1] Chan YO, Biova J, Mahmood A, Dietz N, Bilyeu K, Škrabišová M, Joshi T: Genomic Variations Explorer (GenVarX): A Toolset for Annotating Promoter and CNV Regions Using Genotypic and Phenotypic Differences. Frontiers in Genetics 2023, In Press.


[1] Biová J, Dietz N, Chan YO, Joshi T, Bilyeu K, Škrabišová M: AccuCalc: A Python Package for Accuracy Calculation in GWAS. Genes 2023, 14(1):123.

[2] Škrabišová M, Dietz N, Zeng S, Chan YO, Wang J, Liu Y, Biová J, Joshi T, Bilyeu KD: A novel Synthetic phenotype association study approach reveals the landscape of association for genomic variants and phenotypes. Journal of Advanced Research 2022, 42:117-133.


[1] Biová J, Kaňovská I, Chan YO, Immadi MS, Joshi T, Bilyeu K, Škrabišová M. Natural and artificial selection of multiple alleles revealed through genomic analyses. Front Genet. 2024 Jan 8;14:1320652. doi: 10.3389/fgene.2023.1320652. PMID: 38259621; PMCID: PMC10801239.


[1] Zeng S, Škrabišová M, Lyu Z, Chan YO, Dietz N, Bilyeu K, Joshi T: Application of SNPViz v2.0 using next-generation sequencing data sets in the discovery of potential causative mutations in candidate genes associated with phenotypes. International Journal of Data Mining and Bioinformatics 2021, 25(1-2):65-85.

[2] Zeng S, Škrabišová M, Lyu Z, Chan YO, Bilyeu K, Joshi T: SNPViz v2.0: A web-based tool for enhanced haplotype analysis using large scale resequencing datasets and discovery of phenotypes causative gene using allelic variations. In: 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM): 16-19 Dec. 2020; 2020: 1408-1415.

[3] Langewisch T, Zhang H, Vincent R, Joshi T, Xu D, Bilyeu K: Major soybean maturity gene haplotypes revealed by SNPViz analysis of 72 sequenced soybean genomes. PLoS One 2014, 9(4):e94150.