Although there is evidence that phenotypic plasticity can facilitate the evolution of fixed traits in general, it remains an open question whether it is stability or variability of the different characteristics that have adaptive value and therefore be selected? It remains to explore how much of left-behind variation under crop domestication is adaptive under current climate change scenarios and to what extent plasmotype (chloroplast and mitochondria) condition effects of nuclear quantitative trait loci. To start answering these questions, we have modified the classic NAM design to include plasmotype with nucleotype segregation between cultivated barley (Hordeumvulgare cv Noga) and ten diverse H.vulgare ssp. spontaneum wild barley ecotypes. Preliminary analysis of this first Cytonuclear Multi-Parent population (CMPP) shows apparent effects of the plasmotype on growth for the majority of wild donors. Comparative whole-genome and chloroplast sequencing guide follow-up zooming on candidate loci by genome editing, including directed recombination for finer-mapping. We will discuss the caveats, bottlenecks, and solutions to follow-up experiments. Current and future examination of this CMPP population in the SensyPAM clock platform and across different environments in Israel and the US will allow a better understanding of GxGxE interactions, including questioning the possible role of pleiotropic effects of clock plasticity and robustness on agricultural yield.