A Comprehensive Suite of Tools for Allele Discovery and Phenotype Improvement in SoyKB and KBCommons Frameworks for Crops

The whole-genome re-sequenced (WGRS) data availability has increased drastically as the sequencing technologies have improved over time. Nonetheless, conducting research with WGRS data without the enhancement of other data and tools is highly challenging. Hence, a comprehensive suite of tools, variant calling pipeline (SnakyVC), Allele Catalog pipeline (AlleleCatalog), Allele Catalog Tool, Genomic Variation Explorer (GenVarX), and Multiple Allele Discovery (MADis) Tool, have been developed for allelic variation explorations and phenotype distribution inferences. The Allele Catalog Tool is powered by Allele Catalog datasets generated using the SnakyVC and AlleleCatalog pipeline. The SnakyVC pipeline can parallelly process sequencing data to generate the Variant Call Format (VCF) files, and the AlleleCatalog pipeline takes VCF files to perform imputations, functional effect predictions, and assembles alleles for each gene to generate Allele Catalog datasets. The Allele Catalog Tool introduces a novel method to uniquely group alleles and annotations within coding regions and summarize accession into counts based on improvement status. Its capabilities also include connecting variant positions to phenotypes for phenotype distributions and associating accessions with metadata. Besides that, GenVarX offers exploration capabilities for allelic variations related to transcription factor binding in promoter regions, structural variations in copy number variation regions, and phenotype distribution visualizations of those variations to understand the impact on gene expression and phenotype alterations. Furthermore, the MADis Tool conducts statistical scoring tests on variant positions within a candidate gene and a phenotypic trait to pinpoint the most effective combination of variant positions associated with causative mutations. This analysis provides potential insight into causative mutations that occur simultaneously to impact the phenotype of crops. All the tools are hosted on the SoyKB and KBCommons web portals. Researchers can use this tool to identify novel alleles of genes and select crop accessions to improve selective breeding strategies and agricultural traits of plants.