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Miscanthus is a genus of C4 perennial grasses capable of high biomass potential even in temperate regions making it an ideal industrial crop for the renewable supply of energy and chemicals. Yield is strongly linked to water availability, and many environments have limited water supply where otherwise irradiation and temperature are favourable. A total of 47 Miscanthus genotypes, diverse regarding collection site and genotype, were screened in a high‐throughput phenomics facility under drought to generate high‐quality time‐course data for biomass accumulation and water use. Plants were subjected to three treatments: a watered control, mild drought (20% of field capacity) and a severe drought (water completely withdrawn). Daily visual spectrum images were calibrated to harvested biomass and used to assess biomass accumulation over the experiment. Image analyses were used to determine growth and senescence as functions of time and treatment, plant survival and to relate responses to geographical data. An accurate prediction of plant biomass (R2 = 0.92***) was made by comparing actual harvested biomass and projected shoot area. Dynamic responses in senescence between the multiple genotypes under the three treatments demonstrated stay‐green and senescence responses were not associated with species. Microclimate/geographical modelling indicated that origin of genotype was associated with drought tolerance and this helped explain the different responses within the same species. Water‐use efficiency (WUE), the amount of dry biomass accumulated per kg of water, correlated with summer rainfall. Phenomic analysis of drought responses was shown to have the potential to improve the selection of breeding candidates in Miscanthus and has identified interesting Miscanthus genotypes combining high biomass and high WUE for further characterization.

High salinity land may provide an alternative resource for the cultivation of dedicated biomass crops for renewable energy and chemicals, thus avoiding competition for land use with food crops. The commercial perennial grass Miscanthus giganteu s is a leading biomass crop; however, its response to salt stress is largely unknown. Miscanthus giganteu s was grown in pots irrigated with nine different NaCl concentrations (0, 2.86, 5.44, 7.96, 10.65, 14.68, 17.5, 19.97 and 22.4 dS m super(-1)). Biomass yield was reduced by 50% at 10.65 dS m super(-1) NaCl. Root dry matter inhibition occurred at the highest salt concentration tested, while rhizome dry weight and the ratios of root/rhizome and below-/above-ground dry matter were not affected by elevated salinity. The accumulative effect of increasing salinity reduced stem height and elongation, while photosynthesis was reduced to a smaller extent. The duration and strength of salinity exacerbated the reduction. Water use efficiency (WUE) was maintained except at the highest salinity and plants maintained stomatal conductance (g sub(s)) and leaf water content at low to moderate salinity. Miscanthus giganteu s showed strong induction of the osmoprotectant, proline and no significant increase in malondialdehyde content under increasing salinity. The ash content in leaves, increased, reducing the biomass quality at high salinity concentrations. The effects of salinity on the yield and the availability of land area in European geographical area for agriculture were investigated. Understanding the potential for growth of the C4 biomass crop Miscanthus on underutilized or abandoned land may offer a new range of targets for improved economics, crop management and breeding.

Glioma intratumoral heterogeneity enables adaptation to challenging microenvironments and contributes to therapeutic resistance. We integrated 914 single-cell DNA methylomes, 55,284 single-cell transcriptomes and bulk multi-omic profiles across 11 adult IDH mutant or IDH wild-type gliomas to delineate sources of intratumoral heterogeneity. We showed that local DNA methylation disorder is associated with cell–cell DNA methylation differences, is elevated in more aggressive tumors, links with transcriptional disruption and is altered during the environmental stress response. Glioma cells under in vitro hypoxic and irradiation stress increased local DNA methylation disorder and shifted cell states. We identified a positive association between genetic and epigenetic instability that was supported in bulk longitudinally collected DNA methylation data. Increased DNA methylation disorder associated with accelerated disease progression and recurrently selected DNA methylation changes were enriched for environmental stress response pathways. Our work identified an epigenetically facilitated adaptive stress response process and highlights the importance of epigenetic heterogeneity in shaping therapeutic outcomes. Single-cell DNA methylation and transcriptomic glioma analyses link local DNA methylation disorder and cellular plasticity. Increases in disorder are associated with stress and disease progression, suggesting a role in shaping the therapeutic response.

Glioma intratumoral heterogeneity enables adaptation to challenging microenvironments and contributes to universal therapeutic resistance. Here, we integrated 914 single-cell DNA methylomes, 55,284 single-cell transcriptomes, and bulk multi-omic profiles across 11 adult IDH-mutant or IDH-wild-type gliomas to delineate sources of intratumoral heterogeneity. We found that local DNA methylation instability, or epimutation burden, was elevated in more aggressive tumors, reflected intratumoral variability, linked with transcriptional disruption, and associated with environmental stress response. We show that the activation of cell-state specific transcription factors is impacted by epimutations and that loosened epigenetic control may facilitate cellular plasticity. Our analyses support that somatic copy number alterations (SCNAs) promote epigenetic instability and that SCNAs largely precede epigenetic and transcriptomic diversification during glioma evolution. We confirmed the link between genetic and epigenetic instability by analyzing larger cohorts of bulk longitudinally collected and spatially separated DNA methylation data. Increased DNA methylation instability was associated with accelerated disease progression, and recurrently selected DNA methylation changes were enriched for environmental stress response pathways. Our work provides an integrative framework to better understand glioma evolution and highlights the importance of epigenetic heterogeneity in shaping therapeutic response. Competing Interest Statement R.G.W.V. is a co-founder of and has received research support from Boundless Bio, Inc.