Despite considerable advances in biotechnology true drought adaptive genes remain elusive in crop species hindering the development of accurate systems for MAS. This presents a major bottleneck to the transition in plant breeding from a process driven by selection to one driven by design. While it is recognized that high quality phenotypic data from an appropriate range of environments are a pre-requisite to the reliable identification of stress adaptive genes, most data are currently confounded by is genetic variation in flowering date. This is not generally considered to be problematic if the population's overall maturity class fits the target environment. However, this is often a false assumption and the most likely reason why QTL studies frequently identify Ppd and Eps loci as those most strongly associated with drought adaptation. While early flowering is a well established drought avoidance strategy many other physiological mechanisms have been documented in crops. In order to determine the genetic basis of these mechanisms, which are likely to be complex, the confounding effect of phenology must be addressed. It is well established in wheat that key developmental processes such as kernel set are determined within relatively narrow developmental windows and can be especially sensitive to environmental conditions including moisture stress. Therefore, genotypes growing side by side but which pass through key developmental stages on different dates are likely to trigger different signal transduction pathways and different stress-adaptive responses at the whole plant level due to variation in weather. To eliminate this confounding factor differences in flowering time in experimental populations must be minimized. This can be achieved by characterizing potential parents for their phenotypic expression and G×E for flowering time in the appropriate range of target environments as well as genotype lines as far as possible for Ppd, Vrn and Eps alleles.