Microbe associated molecular pattern (MAMP)-triggered immunity (MTI) is an important component of the plant innate immunity response to invading pathogens. Although several MTI responses can be measured in different plant species, their magnitude is likely plant-species specific and even cultivar specific. In this work, we show that the variation in gene expression, either under untreated or treated conditions, is inherited. In addition, genes with potential additive and non-additive effects were identified in two mapping lines, several of these with a potential function in the control of the innate immunity. Likewise, we observed that some genes differentially expressed across the parental and mapping lines showed different DNA methylation patterns. Finally, a gene regulatory module analysis identified key networks that likely control soybean innate immunity. The data presented represent the basis for further functional analysis that can lead to a better understanding of the soybean innate immunity response. Overall design: RNA-Seq data collected from Glycine max leaves treated with MAMPs of two parental lines of a RIL population and two individual RILs.