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Background   Miscanthus  is a commercial lignocellulosic biomass crop owing to its high biomass productivity, resilience and photosynthetic capacity at low temperature. These qualities make  Miscanthus  a particularly good candidate for temperate marginal land, where yields can be limited by insufficient or excessive water supply. Differences in response to water stress have been observed among  Miscanthus  species, which correlated to origin. In this study, we compared the physiological and molecular responses among  Miscanthus  species under excessive (flooded) and insufficient (drought) water supply in glasshouse conditions.    Results  A significant biomass loss was observed under drought conditions in all genotypes.  M. x giganteus  showed a lower reduction in biomass yield under drought conditions compared to the control than the other species. Under flooded conditions, biomass yield was as good as or better than control conditions in all species. 4389 of the 67,789 genes (6.4%) in the reference genome were differentially expressed during drought among four  Miscanthus  genotypes from different species. We observed the same biological processes were regulated across  Miscanthus  species during drought stress despite the DEGs being not similar. Upregulated differentially expressed genes were significantly involved in sucrose and starch metabolism, redox, and water and glycerol homeostasis and channel activity. Multiple copies of the starch metabolic enzymes BAM and waxy GBSS-I were strongly up-regulated in drought stress in all  Miscanthus  genotypes, and 12 aquaporins (PIP1, PIP2 and NIP2) were also up-regulated in drought stress across genotypes.    Conclusions  Different phenotypic responses were observed during drought stress among  Miscanthus  genotypes from different species, supporting differences in genetic adaption. The low number of DEGs and higher biomass yield in flooded conditions supported  Miscanthus  use in flooded land. The molecular processes regulated during drought were shared among  Miscanthus  species and consistent with functional categories known to be critical during drought stress in model organisms. However, differences in the regulated genes, likely associated with ploidy and heterosis, highlighted the value of exploring its diversity for breeding.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13068-021-01915-z.

Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species