Much of humanity relies on rice (Oryza sativa) as a food source, but cultivation is water intensive and the crop is vulnerable to drought and high temperatures. Under climate change, periods of reduced water availability and high temperature are expected to become more frequent, leading to detrimental effects on rice yields. We engineered the high-yielding rice cultivar 'IR64' to produce fewer stomata by manipulating the level of a developmental signal. We overexpressed the rice epidermal patterning factor OsEPF1, creating plants with substantially reduced stomatal density and correspondingly low stomatal conductance. Low stomatal density rice lines were more able to conserve water, using c. 60% of the normal amount between weeks 4 and 5 post germination. When grown at elevated atmospheric CO , rice plants with low stomatal density were able to maintain their stomatal conductance and survive drought and high temperature (40°C) for longer than control plants. Low stomatal density rice gave equivalent or even improved yields, despite a reduced rate of photosynthesis in some conditions. Rice plants with fewer stomata are drought tolerant and more conservative in their water use, and they should perform better in the future when climate change is expected to threaten food security.

During gastrulation, embryonic cells become specified into distinct germ layers. In mouse, this continues throughout somitogenesis from a population of bipotent stem cells called neuromesodermal progenitors (NMps). However, the degree of self-renewal associated with NMps in the fast-developing zebrafish embryo is unclear. Using a genetic clone-tracing method, we labelled early embryonic progenitors and found a strong clonal similarity between spinal cord and mesoderm tissues. We followed individual cell lineages using light-sheet imaging, revealing a common neuromesodermal lineage contribution to a subset of spinal cord tissue across the anterior-posterior body axis. An initial population subdivides at mid-gastrula stages and is directly allocated to neural and mesodermal compartments during gastrulation. A second population in the tailbud undergoes delayed allocation to contribute to the neural and mesodermal compartment only at late somitogenesis. Cell tracking and retrospective cell fate assignment at late somitogenesis stages reveal these cells to be a collection of mono-fated progenitors. Our results suggest that NMps are a conserved population of bipotential progenitors, the lineage of which varies in a species-specific manner due to vastly different rates of differentiation and growth.

Summary A fundamental question in developmental biology is how the early embryo establishes the spatial coordinate system that is later important for the organization of the embryonic body plan. Although we know a lot about the signaling and gene-regulatory networks required for this process, much less is understood about how these can operate to pattern tissues in the context of the extensive cell movements that drive gastrulation. In zebrafish, germ layer specification depends on the inheritance of maternal mRNAs [ 1 , 2 , 3 ], cortical rotation to generate a dorsal pole of β-catenin activity [ 4 , 5 , 6 , 7 , 8 ], and the release of Nodal signals from the yolk syncytial layer (YSL) [ 9 , 10 , 11 , 12 ]. To determine whether germ layer specification is robust to altered cell-to-cell positioning, we separated embryonic cells from the yolk and allowed them to develop as spherical aggregates. These aggregates break symmetry autonomously to form elongated structures with an anterior-posterior pattern. Both forced reaggregation and endogenous cell mixing reveals how robust early axis specification is to spatial disruption of maternal pre-patterning. During these movements, a pole of Nodal signaling emerges that is required for explant elongation via the planar cell polarity (PCP) pathway. Blocking of PCP-dependent elongation disrupts the shaping of opposing poles of BMP and Wnt/TCF activity and the anterior-posterior patterning of neural tissue. These results lead us to suggest that embryo elongation plays a causal role in timing the exposure of cells to changes in BMP and Wnt signal activity during zebrafish gastrulation. Video Abstract

Abstract:2 During gastrulation, embryonic cells become specified into distinct germ layers. In mouse, 15All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

Pattern formation in development has been principally studied in tissues that are not undergoing extensive cellular rearrangement. However, in most developmental contexts, gene expression domains emerge as cells re-arrange their spatial positions within the tissue, providing an additional, and seldom explored, level of complexity to the process of pattern formation in vivo. To investigate this issue, we addressed the regulation of TBox expression in the pre-somitic mesoderm (PSM) as this tissue develops in zebrafish embryos. Here, cells must differentiate in a manner that leads to well-defined spatial gene expression domains along the tissue while undergoing rapid movements to generate axial length. We find that in vivo, mesoderm progenitors undergo TBox differentiation over a broad range of time scales while in vitro their differentiation is simultaneous. By reverse-engineering a gene regulatory network (GRN)to recapitulate TBox gene expression, we were able to predict the population-level differentiation dynamics observed in culture, but not in vivo. In order to address this discrepancy in differentiation dynamics we developed a Live Modelling framework that allowed us to simulate the GRN on 3D tracking data generated from large-scale time-lapse imaging datasets of the develop-ing PSM. Once the network was simulated on a realistic representation of the cells morphogenetic context, the model was able to recapitulate the range of differentiation time scales observed in vivo, and revealed that these were necessary for TBox gene expression patterns to emerge correctly at the level of the tissue. This work thus highlights a previously unappreciated role for cell movement as a driver of pattern formation in development.

The study of pattern formation has benefited from reverse-engineering gene regulatory network (GRN) structure from spatio-temporal quantitative gene expression data. Traditional approaches omit tissue morphogenesis, hence focusing on systems where the timescales of pattern formation and morphogenesis can be separated. In such systems, pattern forms as an emergent property of the underlying GRN. This is not the case in many animal patterning systems, where patterning and morphogenesis are simultaneous. To address pattern formation in these systems we need to adapt our methodologies to explicitly accommodate cell movements and tissue shape changes. In this work we present a novel framework to reverse-engineer GRNs underlying pattern formation in tissues experiencing morphogenetic changes and cell rearrangements. By combination of quantitative data from live and fixed embryos we approximate gene expression trajectories (AGETs) in single cells and use a subset to reverse-engineer candidate GRNs using a Markov Chain Monte Carlo approach. GRN fit is assessed by simulating on cell tracks (live-modelling) and comparing the output to quantitative data-sets. This framework outputs candidate GRNs that recapitulate pattern formation at the level of the tissue and the single cell. To our knowledge, this inference methodology is the first to integrate cell movements and gene expression data, making it possible to reverse-engineer GRNs patterning tissues undergoing morphogenetic changes.

A fundamental question in developmental biology is how the early embryo breaks initial symmetry to establish the spatial coordinate system later important for the organisation of the embryonic body plan. In zebrafish, this is thought to depend on the inheritance of maternal mRNAs [1][2][3], cortical rotation to generate a dorsal pole of beta-catenin activity [4][5][6][7][8] and the release of Nodal signals from the yolk syncytial layer (YSL) [9][10][11][12]. Recent work aggregating mouse embryonic stem cells has shown that symmetry breaking can occur in the absence of extra-embryonic tissue [19,20]. To test whether this is also true in zebrafish, we separated embryonic cells from the yolk and allowed them to develop as aggregates. These aggregates break symmetry autonomously to form elongated structures with an anterior-posterior pattern. Extensive cell mixing shows that any pre-existing asymmetry is lost prior to the breaking morphological symmetry, revealing that the maternal pre-pattern is not strictly required for early embryo patterning. Following early signalling events after isolation of embryonic cells reveals that a pole of Nodal activity precedes and is required for elongation. The blocking of PCP-dependent convergence and extension movements disrupts the establishment of opposing poles of BMP and Wnt/TCF activity and the patterning of anterior-posterior neural tissue. These results lead us to suggest that convergence and extension plays a causal role in the establishment of morphogen gradients and pattern formation during zebrafish gastrulation.Our current understanding of pattern formation during early development relies heavily on the notion of opposing signalling gradients that set-up rudimentary body plans [17]. These gradients establish cell fates in space that in turn lead to the population specific cell behaviours that dictate the complex cell and tissue rearrangement of gastrulation and axial elongation. In zebrafish, opposing Nodal and BMP signalling gradients are thought to be necessary and su cient for the establishment of the body plan as shown by experiments in which deployment of such gradients in animal caps leads to the formation of a complete AP axis [13]. In addition to controlling cell fate assignments, a recent study has demonstrated that Nodal signalling is a key driver of convergence and extension movements and is su cient to generate these behaviours when expressed within zebrafish animal caps [14]. Furthermore, BMP levels have been shown to be important for controlling cell movements during both gastrulation [21] and posterior body elongation [22]. These observations raise the possibility that opposing BMP and nodal signalling gradients are upstream of both morphogenesis and patterning. However, the causal relationships of these processes are di cult to dissociate in situations where continuous external signalling sources are present, either from overexpression experiments or from the extra-embryonic signals present during early development. To follow how cells can develop and p...

Establishment of the vertebrate body plan requires a combination of extra-embryonic signalling to establish morphogen gradients, and an underlying self-assembly mechanism that contributes to pattern regulation and robustness. Gastruloids are aggregates of mouse embryonic stem cells that break morphological symmetry and polariseBrachyuryexpression in the absence of extra-embryonic signals. However, the mechanism by which symmetry breaking occurs is not yet known. During gastrulation and body axis elongation, retinoic acid (RA) andCyp26a1are polarised along the anteroposterior axis, and this is critical for balancing the decision of cells to self-renew or differentiate. We found that symmetry-breaking in gastruloids is coincident with the separation ofAldh1a2andCyp26a1expression, and that feedback fromBrais critical for maintaining polarisedCyp26a1gene expression in the gastruloid posterior region. Furthermore, we reveal a short temporal window where RA signalling can negatively influence bothBraandCyp26a1expression. These observations lead us to suggest a mechanism of how initial gastruloid patterning, subsequent elongation, and evolving network topologies can create defined boundaries of RA signalling that permits proper axial patterning and gastruloid growth.