MultiGWAS: An integrative tool for Genome Wide Association Studies (GWAS) in tetraploid organisms

Abstract

The Genome-Wide Association Studies (GWAS) are essential to determine the genetic bases of either ecological or economic phenotypic variation across individuals within populations of model and non-model organisms. For this research question, current practice is the replication of the GWAS testing different parameters and models to validate the reproducibility of results. However, straightforward methodologies that manage both replication and tetraploid data are still missing. To solve this problem, we designed the MultiGWAS, a tool that does GWAS for diploid and tetraploid organisms by executing in parallel four software, two for polyploid data (GWASpoly and SHEsis) and two for diploids data (PLINK and TASSEL). MultiGWAS has several advantages. It runs either in the command line or in an interface. It manages different genotype formats, including VCF. It executes both the full and naive models using several quality filters. Besides, it calculates a score to choose the best gene action model across GWASPoly and TASSEL. Finally, it generates several reports that facilitate the identification of false associations from both the significant and the best-ranked association SNP among the four software. We tested MultiGWAS with tetraploid potato data. The execution demonstrated that the Venn diagram and the other companion reports (i.e., Manhattan and QQ plots, heatmaps for associated SNP profiles, and chord diagrams to trace associated SNP by chromosomes) were useful to identify associated SNP shared among different models and parameters. Therefore, we confirmed that MultiGWAS is a suitable wrapping tool that successfully handles GWAS replication in both diploid and tetraploid organisms.

Continuous Mapping Identifies Loci Associated With Weevil Resistance [Cosmopolites sordidus (Germar)] in a Triploid Banana Population

“…With the advances in sequencing and genotyping, tools for polyploids have raised interest ( Bourke et al, 2018b ). Still, most of the tools developed for polyploids apply for even ploidy levels, especially 4x which make up the majority of the polyploid species ( Comai, 2005 ; Ferrão et al, 2021 ; Garreta et al, 2021 ); in contrast, resources to construct linkage maps and perform QTL analyses in odd ploidy levels are limited.…”

“…With the advances in sequencing and genotyping, tools for polyploids have raised interest (Bourke et al, 2018b). Still, most of the tools developed for polyploids apply for even ploidy levels, especially 4x which make up the majority of the polyploid species (Comai, 2005;Ferrão et al, 2021;Garreta et al, 2021); in contrast, resources to construct linkage maps and perform QTL analyses in odd ploidy levels are limited. Bourke et al (2018a) developed the polymapR software, which is a powerful tool for the construction of linkage maps in populations of all ploidy levels with allele dosage genotype calls, including populations from 4x × 2x crosses.…”

Two decades of association mapping: Insights on disease resistance in major crops

“…FarmCPU is consider the best multi locus GWAS approach and it controls both false positives and false negatives (Kaler et al, 2020). There are some challenges in the GWAS for polyploidy species (Garreta et al, 2021). To overcome these challenges only few software packages like GWASpoly and SHEsis (Rosyara et al, 2016;Shen et al, 2016) that accept only polyploidy genomic data were developed.…”

“…To overcome these challenges only few software packages like GWASpoly and SHEsis (Rosyara et al, 2016;Shen et al, 2016) that accept only polyploidy genomic data were developed. In addition, to tackle these challenges, a multi GWAS tool is being developed that runs GWAS analysis for both diploid and tetraploid species simultaneously utilizing four software packages (Garreta et al, 2021). Development of improved model to reduce the challenges like population structure and relatedness is continuing to be an important research topic.…”