A collection of domesticated and wild barley cultivars was characterized against Rhizoctonia solani, causing foliar and root-rot disease. The defense responses of roots were improved in modern cultivars vs wild genotypes underpinning agronomic selection and domestication. The phenotypic adapted changes, especially in plant biomass, are one of the dependent events associated with these differences between the two groups. In one modern cultivar, the relative expression of defense-related genes was upregulated in root tissues, particularly PR1 (1200-fold) and PR5 (190-fold) genes when challenged with R. solani. Our results have implications for understanding the evolutionary ecology of soil-root rhizosphere interactions and identifying responsive genotypes to be targeted in breeding selection against root pathogens. These studies provide insights into the regulatory mechanisms at the biochemical and transcriptome level to breeding disease resistance, and the possible function of the SA-dependent pathway in the evolution of plant-microbe interactions and immune responses in the rhizosphere of cereals.