Dyed roots reveal inner complexity: Plant roots do so much more than just hold a plant up. As a site for air storage during flooding, mycorrhizal symbiosis, or carbohydrate storage, the more complex root can tap more complicated functions. Taking advantage of a dye that stains less the deeper it penetrates the tissue, Ortiz-Ramírez et al . applied fluorescence-activated cell sorting to the complex cell layers of the maize root. RNA sequencing applied to the single-cell pools defined a developmental map and showed that the mobile transcription factor SHORT-ROOT travels through multiple cell layers and directs this grass root’s anatomical complexity. —PJH

Many plants associate with arbuscular mycorrhizal fungi for nutrient acquisition, while legumes also associate with nitrogen-fixing rhizobial bacteria. Both associations rely on symbiosis signaling and here we show that cereals can perceive lipochitooligosaccharides (LCOs) for activation of symbiosis signaling, surprisingly including Nod factors produced by nitrogen-fixing bacteria. However, legumes show stringent perception of specifically decorated LCOs, that is absent in cereals. LCO perception in plants is activated by nutrient starvation, through transcriptional regulation of Nodulation Signaling Pathway (NSP)1 and NSP2. These transcription factors induce expression of an LCO receptor and act through the control of strigolactone biosynthesis and the karrikin-like receptor DWARF14-LIKE. We conclude that LCO production and perception is coordinately regulated by nutrient starvation to promote engagement with mycorrhizal fungi. Our work has implications for the use of both mycorrhizal and rhizobial associations for sustainable productivity in cereals.

The current agriculture main challenge is to maintain food production while facing multiple threats such as increasing world population, temperature increase, lack of agrochemicals due to health issues and uprising of weeds resistant to herbicides. Developing novel, alternative, and safe methods is hence of paramount importance. Here, we show that complementary peptides (cPEPs) from any gene can be designed to target specifically plant coding genes. External application of synthetic peptides increases the abundance of the targeted protein, leading to related phenotypes. Moreover, we provide evidence that cPEPs can be powerful tools in agronomy to improve plant traits, such as growth, resistance to pathogen or heat stress, without the needs of genetic approaches. Finally, by combining their activity they can also be used to reduce weed growth.

The widespread regenerative capacity of plants is mediated by the ability of specialized cells to reprogram their fate, but the sequential cellular states of regenerating plant cells remain an open question. Here, we characterize the trajectory of cellular reprogramming using single-cell RNA/ATAC-seq, imaging, and mutant analysis. The earliest events were dependent on repressive chromatin modification, where Multiome and genetic analysis showed that Class I histone deacetylases (HDACs) HDA9 and HDA19 were needed to shut down old identities and to prevent a runaway stress response. Cell division mediates a second step needed for the acquisition of many new identity markers, where division rates were tuned by DOF transcription factor OBP1 accelerating and SMR5 , 7 , and 10 decelerating division rates hours later. The results show how plants actively mediate the loss of remnant identities within hours of injury and then tune cell division rates to rapidly reprogram cells to new identities.

Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits. Key traits that distinguish these species are mediated by specialized cell types within organs. Here, we compare the transcriptomes of all cells within roots in three grasses—Zea mays (maize), Sorghum bicolor (sorghum), and outgroup Setaria viridis (Setaria). We first show that single-cell and single-nucleus RNA-seq provide complementary readouts of cell identity, warranting a combined analysis. Comparative cellular analysis shows that the transcriptomes of some cell types diverged more rapidly than others, in part by recruiting gene modules from other cell types. Furthermore, examining the whole genome duplication in maize, we detect extensive dosage compensation in surviving co-expressed homeologs, reinforcing genomic balance1. Homeolog pairs that underwent subfunctionalization2, partitioning their expression among cell types, represented a minor pattern but showed the highest rate of acquiring a novel (non-ancestral) domain. These results fit a conjecture in which mechanisms that maintain stoichiometric balance at the molecular level aid in homeolog retention for extended periods to allow new functions to arise. An unexpected synergy between spatial sub- and neo-functionalization then contributes to changes in transcriptional cell identity.