This study aimed to identify the genetic control of morphological, water status, and root traits in four inbred lines and their pre-selected hybrid combinations of popcorn, and to identify the best parents and hybrids. The plants were grown under greenhouse conditions, and with two water conditions—water-stressed (WS) and well-watered (WW). We evaluated shoot biomass (SB), whole plant leaf area (WPLA), chlorophyll content, carbon isotope discrimination, net CO2 assimilation rate, the stomatal conductance, transpiration, cumulative plant transpiration, and root weight density in three sections. The reductions in SB and WPLA are attributed to stomatal causes, given the maintenance of water condition values in water-stressed plants. In fact, the stomata were closed for long periods during plant growth under the water-stressed condition, as indicated by the more negative carbon isotope discrimination values. The root weight density, regardless of soil depth and water conditions, was higher in hybrids. There was a preponderance of non-additive effects in the control of morphological and root traits, especially in the WS condition, and heterosis was shown to be the fundamental strategy for obtaining superior hybrids. For water status traits, it is essential to choose the female parent in the crossing block, given the maternal effect expressed by net CO2 assimilation rate, stomatal conductance, and transpiration.
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