Josep M. Casacuberta, Scott Jackson, Olivier Panaud, Michael Purugganan and Jonathan Wendel
Connecting genotype to phenotype is a grand challenge of biology. Over the past 50 years, there have been numerous and powerful advances to meet this challenge, including next-generation sequencing approaches (Jackson et al. 2011), molecular genetic mapping techniques, computational modeling, and the integration of evolutionary theory and tools. In plants, the long history of domestication and breeding has provided multiple insights into the genotype–phenotype equation (Meyer and Purugganan 2013; Olsen and Wendel 2013). Domestication and breeding provide unique systems with which to study the evolution of traits and adaptation to new environments. At present, agriculture faces unprecedented challenges, with the need to continue to increase food quality and food production for a population that will likely exceed 9 billion by 2050, combined with the urgent need to make agriculture more sustainable in an environment that will be altered by climate change (Diouf 2009). Crop wild relatives, however, have evolved under ecological settings that often are more extreme than those under cultivation and thus represent a reservoir of useful adaptive traits. This genetic diversity has mostly been untapped because of a lack of appropriate tools, both at the genetic level and in describing plant phenotypes and adaptation (Mace et al. 2013). In this context, crop improvement needs to undergo a qualitative leap forward by exploiting the knowledge from the interface of the fields of molecular evolution, bioinformatics, plant physiology, and genetics.