Post-GWAS Prioritization of Genome-Phenome Associations in Sorghum

This study presents an innovative approach for understanding the genetic underpinnings of two key phenotypes in Sorghum bicolor: maximum canopy height and maximum growth rate. Genome-Wide Association Studies (GWAS) are widely used to decipher the genetic basis of traits in organisms, but the challenge lies in selecting an appropriate statistically significant threshold for analysis. Our goal was to employ GWAS to pinpoint the genetic markers associated with the phenotypes of interest using specific permissive-filtered threshold values that allows the inclusion of broader collections of explanatory candidate genes. Then, we utilized a pattern recognition technique to prioritize a set of informative genes, which hold potential for further investigation and could find applications in Artificial Intelligence systems. Utilizing a subset of the Sorghum Bioenergy Association Panel cultivated at the Maricopa Agricultural Center in Arizona, we sought to unveil patterns between phenotypic similarity and genetic proximity among accessions in order to organize Single Nucleotide Polymorphisms (SNPs) which are likely to be associated with the phenotypic trait. Additionally, we explored the impact of this method by considering all SNPs versus focusing on SNPs classified through the GWAS pre-filter. Experimental results indicated that our approach effectively prioritizes SNPs and genes influencing the phenotype of interest. Moreover, this methodology holds promise in the feature selection from genomic data for predicting complex phenotypic traits influenced by numerous genes and environmental conditions and could pave the way for further research in this field. ### Competing Interest Statement Author Curtis Lisle is employed by KnowledgeVis LLC. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.