Roots function underground for water and nutrient supplies and anchorage of plant in soil. While much effort has been focused on improvement of aboveground traits, little is known about the root development and growth in crops like wheat (Triticum aestivum L.). We identified a very short root (VSR) variation in an F1 hybrid between wheat landrace Chinese Spring and synthetic accession TA4152. Seven days after germination, primary roots of the two parental lines reached ~15 cm, but primary roots of the F1 were just ~5 cm long. F2 and BC1 populations segregated into 1 (normal) to 1 (VSR). Genetic analysis indicated VSR is controlled by interaction of two tightly linked dominant genes Vsr1 and Vsr2, which are located in the long arm of chromosome 5D. Transcriptome profiling by microarray hybridization indicated that a large number of defense response genes and some phytohormones-signaling genes were up-regulated in VSR root tips. DAB-staining detected high level of hydrogen peroxide in the VSR root tips of F1 seedlings while very low level in Chinese Spring and TA4152. The VSR phenotype can be partially rescued by supplement of calcium, suggesting that Vsr genes mediate cross-talks between the abiotic and biotic stress signaling pathways.