Integrating GWAS with a gene co-expression network better prioritizes candidate genes associated with root metaxylem phenes in maize

Root metaxylems are phenotypically diverse structures whose function is particularly important under drought stress. Significant research has dissected the genetic machinery underlying metaxylem phenotypes in dicots, but that of monocots are relatively underexplored. In maize (Zea mays), a robust pipeline integrated a genome-wide association study (GWAS) of root metaxylem phenes under well-watered and water-stress conditions with a gene co-expression network to prioritize the strongest gene candidates. We identified 244 candidate genes by GWAS, of which 103 reside in gene co-expression modules most relevant to xylem development. Several candidate genes may be involved in biosynthetic processes related to the cell wall, hormone signaling, oxidative stress responses, and drought responses. Of those, six gene candidates were detected in multiple root metaxylem phenes in both well-watered and water-stress conditions. We posit that candidate genes that are more essential to network function based on gene co-expression (i.e., hubs or bottlenecks) should be prioritized and classify 33 essential genes for further investigation. Our study demonstrates a new strategy for identifying promising gene candidates and presents several gene candidates that may enhance our understanding of vascular development and responses to drought in cereals. Root metaxylem phenotypes are an under-explored target for crop improvement for drought resilience. A traditional genome-wide association study (GWAS) paired with a gene co-expression network found candidate genes underlying root metaxylem phenes. The best candidates are likely those with relevant functional roles and genes "essential" to network function. Drought stress is a primary limitation to global crop production and is projected to worsen in the coming decades. A better understanding of how plants regulate water transport and use may open avenues toward more drought-tolerant crops. In this study, we demonstrate a new strategy for identifying genes associated with water transport in corn and present several gene candidates that may enhance our understanding of water transport and drought tolerance in corn and other cereals.