Plant responses to environmental stimuli require complex gene expression reprogramming regulated at multiple levels. Cis-regulatory elements (CREs) can activate or repress gene expression through transcription factor (TF) binding. Moreover, the temporal nature of stress responses adds another layer of complexity wherein sets of genes are regulated differently based on their timing of expression during stress response. Understanding the complex cis-regulatory syntax is essential to predict when and where genes are expressed and how sequence variations lead to downstream changes in gene expression. Recent advances in deep-learning approaches have enabled predictions of gene expression from genomic DNA features (Wang et al., 2020; Meng et al., 2021). Previous studies have established the ability of computational models to predict plant spatial transcriptional response using known and novel CREs (Uygun et al., 2017). However, a global model to uncover regulatory elements affecting temporal responses to environmental stimuli is still lacking…

Gene duplications are common in plants and create a potential repertoire for functional novelty. Gene duplicates can arise from a variety of mechanisms and place the newly copied gene in a new chromatin environment with different regulatory contexts. After gene duplication, several fates are possible, but in the overwhelming majority of cases, one of the gene copies accumulates degenerative mutations leading to pseudogenization (Lynch and Conery, 2000). Sometimes, both copies survive, and the duplicated copy accumulates beneficial mutations to gain a novel function. These cases of neofunctionalization of duplicate copies are commonly reported in plants as a source for molecular innovations (Panchy et al., 2016). Partial gene duplications or changes in gene structure following duplication can contribute to such innovations. These partially duplicated and chimeric genes may be important for the formation of novel genes with new functions, but studies characterizing such duplication events are still scarce, especially in plants…

Whole-genome duplication or polyploidy is widespread throughout eukaryotes but is most prevalent in flowering plant lineages. The evolutionary processes following polyploidization, such as genome downsizing, biased fractionation, modulation of gene expression, and epigenomic reprogramming, can profoundly affect genome complexity and generate evolutionarily beneficial genetic diversity. Compared to its diploid and tetraploid progenitors, the allohexaploid common wheat (Triticum aestivum, AABBDD) displays remarkable genome plasticity and broader adaptability, attributed in part to the creation of new genetic diversity following allopolyploidy. How gene copies in the three different subgenomes of wheat are regulated and coordinate molecular responses through combinatorial and dosage-dependent manner is a matter of ongoing research…

The cis-regulatory elements facilitate the binding of sequence-specific transcription factors for activating or repressing the expression of target genes. The expression level of each gene may vary in different cell types due to differential regulatory elements within the accessible chromatin regions (ACRs), which can dictate cell-fate decisions and developmental trajectories. Therefore, it has become essential to identify genome-wide ACRs across cell types and developmental stages to understand the impact of chromatin accessibility on gene expression regulation and, consequently, trait variation.

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.