PlantOmicsGWAS: An end-to-end, reproducible framework for plant genome-wide association and genomic prediction using linear and pan-genome references

Genome-wide association studies (GWAS) play a crucial role in unraveling the genetic foundations of complex traits in plants but are also hampered by the application of heterogeneous tools, incompatible file formats and disparate computational environments. Existing GWAS frameworks are often restricted to a single linear reference genome, limiting the capacity for the analysis of structural variations and presence/absence variations (PAV) within plant populations. These issues pose obstacles to reproducibility, scalability, and comprehensive investigations. Here, we present PlantOmicsGWAS, an open-source Python framework for reproducible plant genome-wide association analysis and genomic prediction. It integrates reference indexing, FASTQ quality control, alignment, variant calling, VCF normalization, PLINK conversion, linkage disequilibrium analysis, population-structure estimation, association testing, marker scoring, genomic prediction, and visualization within a unified Linux and HPC workflow. The framework supports conventional linear-reference analyses and includes an optional pangenome-oriented module for working with multiple assemblies and graph-derived variation. Using a Vitis benchmark dataset containing 120 accessions and 118,247 graph-derived variants, PlantOmicsGWAS reduced manual workflow fragmentation and generated standardized association outputs. This tool provides a modular and extensible platform for plant GWAS and pan-GWAS workflows while retaining compatibility with established command-line tools and common genotype formats. The GWAS workflow described herein is adaptable to a range of sequencing methods and plant genomes, bridging research on crop related issues across various biological levels, from the individual organism to entire populations. PlantOmicsGWAS implements Bayesian sparse linear mixed modeling (BSLMM) through GEMMA for multi-trait association discovery, while also supporting FaST-LMM, regression-based approaches, and machine-learning algorithms (Random Forest, XGBoost) as benchmarking alternatives. The PlantOmicsGWAS, a versatile toolkit is available at GitHub https://github.com/plantomicsgwas1-boop/PlantOmicsGwas_V1 and on Linux and HPC platform (https://pypi.org/project/PlantOmicsGwas/1.0.2/).