The considerable drought tolerance of wild cereal crop progenitors has diminished during domestication in the pursuit of higher productivity. Regaining this trait in cereal crops is essential for global food security but requires novel genetic insight.

Here, we assessed the molecular evidence for natural variation of drought tolerance in wild barley (Hordeum spontaneum), wild emmer wheat (Triticum dicoccoides), and model grass allotetraploid Brachypodium hybridum and diploid progenitor species Brachypodium stacei collected from contrasting dry and moist habitats at Evolution Canyon, Israel (ECI). We report that prevailing moist vs. dry conditions have differentially shaped the stomatal and photosynthetic traits of these wild cereals in their respective habitats. Evidence of genomic landscape of mutation profiles accounting for the differences in slope-specific DEGs in Triticum dicoccoides and Hordeum spontaneum, driven by the xeric site conditions on the African Slope at ECI.

We observed that the allopolyploid B. hybridum employs a drought escape strategy via the maintenance of significantly higher photosynthetic capacity and a shorter flowering time than the aridic B. stacei. Co-expression gene module ‘circadian rhythm’ was linked to significant drought-induced delay in flowering time in Brachypodium genotypes.

The biased homeolog expression pattern and transferable dominance of subgenomes of B. hybridum illustrated that the allopolyploid species may utilize the expression patterns of both progenitor species under drought conditions to survive.

Our results provide new genetic information for the breeding of resilient wheat and barley in a changing global climate increasingly frequent drought events.