Project description:Development of cereal crops with high nitrogen-use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improve crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse sorghum lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry (GC-MS) were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxa, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low-N stress. This indicates that the shift in the sorghum microbiome due to low-N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low-N stress.

2023-08-29 | MSV000092783 | MassIVE

Rice root response atlas

Project description:Rice has evolved regulatory programs and specialized cell types that allow the plant to withstand different environments. To understand how rice root systems cope with water stresses, we profiled translatomes (ribosome-associated mRNAs) and accessible chromatin of developmentally-defined root cell populations from well-watered and drained control (aerobic control), water deficit, waterlogged, fully submerged plants and recovery conditions. Whereas, the waterlogging responses are limited to specific root domains, water deficit and submergence signatures are extensive, and mostly reversible after 1 day of recovery, relative to control roots. Root systems were also evaluated in rice cultivated in a paddy field. Specific responses include a halt in the cell-cycle and DNA synthesis-related genes translation in meristematic tissue under submergence and exo/endodermis suberin-related pathways bolstering under water deficit. Chromatin accessibility and translatome data integration was used to generate inferred regulatory networks that are dynamically regulated by changing water availability. The data collection is further enriched by translatome and chromatin accessibility data for the root systems of plate-grown seedlings (7 day old) and those cultivated in a paddy field (49 day old). An atlas of eight cell population translatomes for field-grown plants exhibited robust cell type expression. Collectively, these data for specific cell populations at multiple developmental ages and in multiple environments including growth two limiting water stresses will serve as a community resource.

2022-05-02 | GSE180100 | GEO

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