Investigating Maize Yield-Related Genes in Multiple Omics Interaction Network Data

Zea mays (maize) is the highest yielding food crop globally, feeding large numbers of people across the planet. It is thus especially important to explore the key genes that affect maize production with prior knowledge. Merging multiple datasets of different types can improve the accuracy of candidate genes prediction results, so we constructed interaction networks using gene, mRNA, protein, and expression profile datasets. A network propagation schedule was used considering combined scores obtained by integrating both network scores and significance scores for each candidate gene based on the guilt-by-association principle. An SVM model was used to optimize the weighted parameters to achieve more reliable results, according to the accuracy of label classification. We found that integrating multiple omics data with more data types improves the reliability of the results. We investigated the GO terms particularly associated with the top 100 candidate genes and the known genes, and analyzed the roles that these genes play in determining the phenotype of maize. We hope that the candidate genes identified here will provide a biological perspective and contribute to maize breeding research.

I. Introduction

As one of the most widely consumed staple food globally, maize is the main cereal grain as measured by yield, whose production is used for livestock feed and human consumption [1]. Researchers have long investigated how to increase maize production by exploring related traits that are affected directly or indirectly by genes [2], [3]. The identification of trait-related genes with prior knowledge should strengthen our understanding of the associated molecular mechanisms and promote applied biotechnology efforts to deeply explore developmental processes in maize breeding [4].