Rice SNF2 family helicase ENL1 is essential for syncytial endosperm development

The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling

Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.

Quantitative Proteomic Analysis Deciphers the Molecular Mechanism for Endosperm Nuclear Division in Early Rice Seed Development

Understanding the molecular mechanisms underlying early seed development is important in improving the grain yield and quality of crop plants. We performed a comparative label-free quantitative proteomic analysis of developing rice seeds for the WT and osctps1-2 mutant, encoding a cytidine triphosphate synthase previously reported as the endospermless 2 (enl2) mutant in rice, harvested at 0 and 1 d after pollination (DAP) to understand the molecular mechanism of early seed development. In total, 5231 proteins were identified, of which 902 changed in abundance between 0 and 1 DAP seeds. Proteins that preferentially accumulated at 1 DAP were involved in DNA replication and pyrimidine biosynthetic pathways. Notably, an increased abundance of OsCTPS1 was observed at 1 DAP; however, no such changes were observed at the transcriptional level. We further observed that the inhibition of phosphorylation increased the stability of this protein. Furthermore, in osctps1-2, minichromosome maintenance (MCM) proteins were significantly reduced compared with those in the WT at 1 DAP, and mutations in OsMCM5 caused defects in seed development. These results highlight the molecular mechanisms underlying early seed development in rice at the post-transcriptional level.

Endosperm Development Traits in a Comparative Analysis of Endospermogenesis and Embryogenesis in Angiosperms

The article discusses the fertilization process, the nucleus position in the primary cell, specifics of early endosperm development, and the principles of its classification. A new, refined classification was proposed for endosperm development modes to include three hierarchic levels: types, subtypes, and variations. Two types were distinguished by the morphogenetic potentials of the micropylar and chalazal primary cells: cellular (karyokinesis is completed with cytokinesis in both cells) and helobial (only karyokinesis takes place in both cells, and the chalazal cell sometimes remains mononucleate). The nuclear endosperm was considered as a subtype of the helobial type. Subtypes were isolated by the extent to which the micropylar and chalazal cells are involved in forming the endosperm. Variations were recognized within the subtypes by the position of walls during the tetrad or triad formation in the cellular endosperm or the number of nuclei in the chalazal cell in the helobial endosperm. The types of embryogenesis are possible to compare with subtypes or even variations of the cellular endosperm type in a comparative analysis of flowering plants, and both of the traits (the contribution of micropylar and chalazal cell derivatives to the endosperm formation and the pattern of primary cell division with the form of the tetrad) should be considered together. Two subtypes and two variations are possible to consider for the helobial endosperm.

Comparative Expression Profiling of Snf2 Family Genes During Reproductive Development and Stress Responses in Rice

Sucrose non-fermenting 2 (Snf2) protein family, as chromatin remodeling factors, is an enormous and the most diverse protein family, which contributes to biological processes of replication, transcription, and DNA repair using the energy of adenosine triphosphate (ATP) hydrolysis. The members of Snf2 family proteins have been well characterized in Arabidopsis, rice, and tomato. Although this family received significant attention, few genes were identified uniquely for their roles in mediating reproductive development and stress tolerance in rice. In the present study, we comprehensively analyzed the expression profiling of Snf2 genes during reproductive development and biotic/abiotic stresses. Our results showed that five proteins (OsCHR712/715/720/726/739) were mainly localized in the nucleus, while OsCHR715/739 were also slightly expressed in the cell membrane. There were abundant cis-acting elements in the putative promoter of Snf2 genes, including dehydration, MeJA, MYB binding site for drought, ABA-responsive, and stress-responsive element. Most of the genes were induced immediately after Magnaporthe oryzae infection at 12 h post-infection (hpi). About 55% of the total genes were upregulated under salt and drought stresses during the entire time, and 22-35% of the total genes were upregulated at 3 h. It was noteworthy that the seven genes (OsCHR705, OsCHR706, OsCHR710, OsCHR714, OsCHR721, OsCHR726, and OsCHR737) were upregulated, and one gene (OsCHR712) was downregulated under salt and drought stresses, respectively. The deficiency of OsCHR726 mutations displayed a hypersensitive phenotype under salt stress. These results will be significantly useful features for the validation of the rice Snf2 genes and facilitate understanding of the genetic engineering of crops with improved biotic and abiotic stresses.

Cereal Endosperms: Development and Storage Product Accumulation

The persistent triploid endosperms of cereal crops are the most important source of human food and animal feed. The development of cereal endosperms progresses through coenocytic nuclear division, cellularization, aleurone and starchy endosperm differentiation, and storage product accumulation. In the past few decades, the cell biological processes involved in endosperm formation in most cereals have been described. Molecular genetic studies performed in recent years led to the identification of the genes underlying endosperm differentiation, regulatory network governing storage product accumulation, and epigenetic mechanism underlying imprinted gene expression. In this article, we outline recent progress in this area and propose hypothetical models to illustrate machineries that control aleurone and starchy endosperm differentiation, sugar loading, and storage product accumulations. A future challenge in this area is to decipher the molecular mechanisms underlying coenocytic nuclear division, endosperm cellularization, and programmed cell death.

Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution

Adaptation to cool climates has occurred several times in different angiosperm groups. Among them, Pooideae, the largest grass subfamily with ∼3,900 species including wheat and barley, have successfully occupied many temperate regions and play a prominent role in temperate ecosystems. To investigate possible factors contributing to Pooideae adaptive evolution to cooling climates, we performed phylogenetic reconstruction using five gene sets (with 1,234 nuclear genes and their subsets) from 157 transcriptomes/genomes representing all 15 tribes and 24 of 26 subtribes. Our phylogeny supports the monophyly of all tribes (except Diarrheneae) and all subtribes with at least two species, with strongly supported resolution of their relationships. Molecular dating suggests that Pooideae originated in the late Cretaceous, with subsequent divergences under cooling conditions first among many tribes from the early middle to late Eocene and again among genera in the middle Miocene and later periods. We identified a cluster of gene duplications (CGD5) shared by the core Pooideae (with 80% Pooideae species) near the Eocene–Oligocene transition, coinciding with the transition from closed to open habitat and an upshift of diversification rate. Molecular evolutionary analyses homologs of CBF for cold resistance uncovered tandem duplications during the core Pooideae history, dramatically increasing their copy number and possibly promoting adaptation to cold habitats. Moreover, duplication of AP1/FUL-like genes before the Pooideae origin might have facilitated the regulation of the vernalization pathway under cold environments. These and other results provide new insights into factors that likely have contributed to the successful adaptation of Pooideae members to temperate regions.

The parent-of-origin lncRNA MISSEN regulates rice endosperm development

The cereal endosperm is a major factor determining seed size and shape. However, the molecular mechanisms of endosperm development are not fully understood. Long noncoding RNAs (lncRNAs) function in various biological processes. Here we show a lncRNA, MISSEN, that plays an essential role in early endosperm development in rice (Oryza sativa). MISSEN is a parent-of-origin lncRNA expressed in endosperm, and negatively regulates endosperm development, leading to a prominent dent and bulge in the seed. Mechanistically, MISSEN functions through hijacking a helicase family protein (HeFP) to regulate tubulin function during endosperm nucleus division and endosperm cellularization, resulting in abnormal cytoskeletal polymerization. Finally, we revealed that the expression of MISSEN is inhibited by histone H3 lysine 27 trimethylation (H3K27me3) modification after pollination. Therefore, MISSEN is the first lncRNA identified as a regulator in endosperm development, highlighting the potential applications in rice breeding.

CTP synthase is essential for early endosperm development by regulating nuclei spacing

Cereal grain endosperms are an important source of human nutrition. Nuclear division in early endosperm development plays a major role in determining seed size; however, this development is not well understood. We identified the rice mutant endospermless 2 (enl2), which shows defects in the early stages of endosperm development. These phenotypes arise from mutations in OsCTPS1 that encodes a cytidine triphosphate synthase (CTPS). Both wild-type and mutant endosperms were normal at 8 h after pollination (HAP). In contrast, at 24 HAP, enl2 endosperm had approximately 10-16 clumped nuclei while wild-type nuclei had increased in number and migrated to the endosperm periphery. Staining of microtubules in endosperm at 24 HAP revealed that wild-type nuclei were evenly distributed by microtubules while the enl2-2 nuclei were tightly packed due to their reduction in microtubule association. In addition, OsCTPS1 interacts with tubulins; thus, these observations suggest that OsCTPS1 may be involved in microtubule formation. OsCTPS1 transiently formed macromolecular structures in the endosperm during early developmental stages, further supporting the idea that OsCTPS1 may function as a structural component during endosperm development. Finally, overexpression of OsCTPS1 increased seed weight by promoting endosperm nuclear division, suggesting that this trait could be used to increase grain yield.

High-resolution spatiotemporal transcriptome analyses during cellularization of rice endosperm unveil the earliest gene regulation critical for aleurone and starchy endosperm cell fate specification

The major tissues of the cereal endosperm are the starchy endosperm (SE) in the inner and the aleurone layer (AL) at the outer periphery. The fates of the cells that comprise these tissues are determined according to positional information; however, our understanding of the underlying molecular mechanisms remains limited. Here, we conducted a high-resolution spatiotemporal analysis of the rice endosperm transcriptome during early cellularization. In rice, endosperm cellularization proceeds in a concentric pattern from a primary alveolus cell layer, such that developmental progression can be defined by the number of cell layers. Using laser-capture microdissection to obtain precise tissue sections, transcriptomic changes were followed through five histologically defined stages of cellularization from the syncytial to 3-cell layer (3 L) stage. In addition, transcriptomes were compared between the inner and the outermost peripheral cell layers. Large differences in the transcriptomes between stages and between the inner and the peripheral cells were found. SE attributes were expressed at the alveolus-cell-layer stage but were preferentially activated in the inner cell layers that resulted from periclinal division of the alveolus cell layer. Similarly, AL attributes started to be expressed only after the 2 L stage and were localized to the outermost peripheral cell layer. These results indicate that the first periclinal division of the alveolus cell layer is asymmetric at the transcriptome level, and that the cell-fate-specifying positional cues and their perception system are already operating before the first periclinal division. Several genes related to epidermal identity (i.e., type IV homeodomain-leucine zipper genes and wax biosynthetic genes) were also found to be expressed at the syncytial stage, but their expression was localized to the outermost peripheral cell layer from the 2 L stage onward. We believe that our findings significantly enhance our knowledge of the mechanisms underlying cell fate specification in rice endosperm.

The maternally expressed polycomb group gene OsEMF2a is essential for endosperm cellularization and imprinting in rice

Cellularization is a key event in endosperm development. Polycomb group (PcG) genes, such as Fertilization-Independent Seed 2 (FIS2), are vital for the syncytium-to-cellularization transition in Arabidopsis plants. In this study, we found that OsEMF2a, a rice homolog of the Arabidopsis PcG gene Embryonic Flower2 (EMF2), plays a role similar to that of FIS2 in regard to seed development, although there is limited sequence similarity between the genes. Delayed cellularization was observed in osemf2a, associated with an unusual activation of type I MADS-box genes. The cell cycle was persistently activated in osemf2a caryopses, which was likely caused by cytokinin overproduction. However, the overaccumulation of auxin was not found to be associated with the delayed cellularization. As OsEMF2a is a maternally expressed gene in the endosperm, a paternally inherited functional allele was unable to recover the maternal defects of OsEMF2a. Many imprinted rice genes were deregulated in the defective hybrid seeds of osemf2a (♀)/9311 (♂) (m9). The paternal expression bias of some paternally expressed genes was disrupted in m9 due to either the activation of maternal alleles or the repression of paternal alleles. These findings suggest that OsEMF2a-PRC2-mediated H3K27me3 is necessary for endosperm cellularization and genomic imprinting in rice.

OsLFR is essential for early endosperm and embryo development by interacting with SWI/SNF complex members in Oryza sativa

Rice (Oryza sativa L.) endosperm provides the developing embryo with nutrients and provides human beings with a staple food. The embryo eventually develops into a new sporophyte generation. Despite their important roles, the molecular mechanisms underlying early-stage endosperm and embryo development remain elusive. Here, we established the fundamental functions of rice OsLFR, an ortholog of the Arabidopsis SWI/SNF chromatin-remodeling complex (CRC) component LFR. OsLFR was expressed primarily in the rice spikelets and seeds, and the OsLFR protein was localized to the nucleus. We conducted genetic, cellular and molecular analyses of loss-of-function mutants and transgenic rescue lines. OsLFR depletion resulted in homozygous lethality in the early seed stage through endosperm and embryo defects, which could be successfully recovered by the OsLFR genomic sequence. Cytological observations revealed that the oslfr endosperm had relatively fewer free nuclei, had abnormal and arrested cellularization, and demonstrated premature programed cell death: the embryo was reduced in size and failed to differentiate. Transcriptome profiling showed that many genes, involved in DNA replication, cell cycle, cell wall assembly and cell death, were differentially expressed in a knockout mutant of OsLFR (oslfr-1), which was consistent with the observed seed defects. Protein-protein interaction analysis showed that OsLFR physically interacts with several putative rice SWI/SNF CRC components. Our findings demonstrate that OsLFR, possibly as one component of the SWI/SNF CRC, is an essential regulator of rice seed development, and provide further insights into the regulatory mechanism of early-stage rice endosperm and embryo development.

Segregation Distortion Observed in the Progeny of Crosses Between Oryza sativa and O. meridionalis Caused by Abortion During Seed Development

Wild rice relatives having the same AA genome as domesticated rice (Oryza sativa) comprise the primary gene pool for rice genetic improvement. Among them, O. meridionalis and O. rufipogon are found in the northern part of Australia. Three Australian wild rice strains, Jpn1 (O. rufipogon), Jpn2, and W1297 (O. meridionalis), and one cultivated rice cultivar Taichung 65 (T65) were used in this study. A recurrent backcrossing strategy was adopted to produce chromosomal segment substitution lines (CSSLs) carrying chromosomal segments from wild relatives and used for trait evaluation and genetic analysis. The segregation of the DNA marker RM136 locus on chromosome 6 was found to be highly distorted, and a recessive lethal gene causing abortion at the seed developmental stage was shown to be located between two DNA markers, KGC6_10.09 and KGC6_22.19 on chromosome 6 of W1297. We name this gene as SEED DEVELOPMENT 1 (gene symbol: SDV1). O. sativa is thought to share the functional dominant allele Sdv1-s (s for sativa), and O. meridionalis is thought to share the recessive abortive allele sdv1-m (m for meridionalis). Though carrying the sdv1-m allele, the O. meridionalis accessions can self-fertilize and bear seeds. We speculate that the SDV1 gene may have been duplicated before the divergence between O. meridionalis and the other AA genome Oryza species, and that O. meridionalis has lost the function of the SDV1 gene and has kept the function of another putative gene named SDV2.

Kernel size-related genes revealed by an integrated eQTL analysis during early maize kernel development

In maize, kernel traits strongly impact overall grain yields, and it is known that sophisticated spatiotemporal programs of gene expression coordinate kernel development, so advancing our knowledge of kernel development can help efforts to improve grain yields. Here, using phenotype, genotype and transcriptomics data of maize kernels at 5 and 15 days after pollination (DAP) for a large association mapping panel, we employed multiple quantitative genetics approaches-genome-wide association studies (GWAS) as well as expression quantitative trait loci (eQTL) and quantitative trait transcript (QTT) analyses-to gain insights about molecular genetic basis of kernel development in maize. This resulted in the identification of 137 putative kernel length-related genes at 5 DAP, of which 43 are located in previously reported QTL regions. Strikingly, we identified an eQTL that overlaps the locus encoding a maize homolog of the recently described m⁶ A methylation reader protein ECT2 from Arabidopsis; this putative ^epi eQTL is associated with 53 genes and may represent a master epi-transcriptomic regulator of kernel development. Notably, among the genes associated with this ^epi eQTL, 10 are for the main storage proteins in the maize endosperm (zeins) and two are known regulators of zein expression or endosperm development (Opaque2 and ZmICE1). Collectively, beyond cataloging and characterizing genomic attributes of a large number of eQTL associated with kernel development in maize, our study highlights how an eQTL approach can bolster the impact of both GWAS and QTT studies and can drive insights about the basic biology of plants.

Wild tomato endosperm transcriptomes reveal common roles of genomic imprinting in both nuclear and cellular endosperm

Genomic imprinting is a conspicuous feature of the endosperm, a triploid tissue nurturing the embryo and synchronizing angiosperm seed development. An unknown subset of imprinted genes (IGs) is critical for successful seed development and should have highly conserved functions. Recent genome-wide studies have found limited conservation of IGs among distantly related species, but there is a paucity of data from closely related lineages. Moreover, most studies focused on model plants with nuclear endosperm development, and comparisons with properties of IGs in cellular-type endosperm development are lacking. Using laser-assisted microdissection, we characterized parent-specific expression in the cellular endosperm of three wild tomato lineages (Solanum section Lycopersicon). We identified 1025 candidate IGs and 167 with putative homologs previously identified as imprinted in distantly related taxa with nuclear-type endosperm. Forty-two maternally expressed genes (MEGs) and 17 paternally expressed genes (PEGs) exhibited conserved imprinting status across all three lineages, but differences in power to assess imprinted expression imply that the actual degree of conservation might be higher than that directly estimated (20.7% for PEGs and 10.4% for MEGs). Regardless, the level of shared imprinting status was higher for PEGs than for MEGs, indicating dissimilar evolutionary trajectories. Expression-level data suggest distinct epigenetic modulation of MEGs and PEGs, and gene ontology analyses revealed MEGs and PEGs to be enriched for different functions. Importantly, our data provide evidence that MEGs and PEGs interact in modulating both gene expression and the endosperm cell cycle, and uncovered conserved cellular functions of IGs uniting taxa with cellular- and nuclear-type endosperm.

ANAPHASE PROMOTING COMPLEX/CYCLOSOME-mediated cyclin B1 degradation is critical for cell cycle synchronization in syncytial endosperms

Although it is known that in most angiosperms mitosis in early endosperm development is syncytial and synchronized, it is unclear how the synchronization is regulated. We showed previously that APC11, also named ZYG1, in Arabidopsis activates zygote division by interaction and degradation of cyclin B1. Here, we report that the mutation in APC11/ZYG1 led to unsynchronized mitosis and over-accumulation of cyclin B1-GUS in the endosperm. Mutations in two other APC subunits showed similar defects. Transgenic expression of stable cyclin B1 in the endosperm also caused unsynchronized mitosis. Further, downregulation of APC11 generated multi-nucleate somatic cells with unsynchronized mitotic division. Together, our results suggest that APC/C-mediated cyclin B1 degradation is critical for cell cycle synchronization.

OsGCD1 is essential for rice fertility and required for embryo dorsal-ventral pattern formation and endosperm development

Rice fertility is critical for rice reproduction and is thus a focus of interest. Most studies have addressed male sterility and its relation to rice production. The mechanisms of regulation of embryogenesis and endosperm development are essential for rice reproduction, but remain largely unknown. Here, we report a functional analysis of the rice gene OsGCD1, which encodes a highly conserved homolog of Arabidopsis GCD1 (GAMETE CELLS DEFECTIVE1). OsGCD1 mutants were generated using the CRISPR/Cas9 system and subjected to functional analysis. The homozygote mutants cannot be obtained, whereas heterozygotes showed altered phenotypes. In the majority of aborted seeds, the endosperm nucleus divided a limited number of times. The free nuclei were distributed only at the micropylar end of embryo sacs, and their oriented positioning was blocked. In addition, aleurone differentiation was interrupted. The embryo developed slowly, and pattern formation, particularly the dorsal-ventral pattern and symmetry establishment, of embryos was disturbed. Thus, the embryos showed various morphological and structural dysplasias. Our findings reveal that OsGCD1 is essential for rice fertility and is required for dorsal-ventral pattern formation and endosperm free nucleus positioning, suggesting a critical role in sexual reproduction of both monocotyledon and dicotyledon plants.

Haploid embryo production in rice and maize induced by PsASGR-BBML transgenes

The PsASGR - BBML transgene, derived from a wild apomictic grass species, can induce parthenogenesis, embryo formation without fertilization, in rice and maize, leading to the formation of haploid plants. The ability to engineer apomictic crop plants using genes identified from naturally occurring apomicts will depend on the ability of those genes to function in crop plants. The PsASGR-BBML transgene, derived from the apomictic species Pennisetum squamulatum, promotes parthenogenesis in sexual pearl millet, a member of the same genus, leading to the formation of haploid embryos. This study determined that the PsASGR-BBML transgene can induce haploid embryo development in two major monocot crops, maize and rice. Transgene variations tested included two different promoters and the use of both genomic and cDNA PsASGR-BBML-derived sequences. Haploid plants were recovered from mature caryopses (seed) of rice and maize lines at variable rates. The PsASGR-BBML transgenes failed to induce measurable haploid seed development in the model genetic plant system Arabidopsis thaliana. Complexity of embryo development, as documented in transgenic rice lines, identifies the need for further characterization of the PsASGR-BBML gene.

Chromatin Remodeling and Plant Immunity

Chromatin remodeling, an important facet of the regulation of gene expression in eukaryotes, is performed by two major types of multisubunit complexes, covalent histone- or DNA-modifying complexes, and ATP-dependent chromosome remodeling complexes. Snf2 family DNA-dependent ATPases constitute the catalytic subunits of ATP-dependent chromosome remodeling complexes, which accounts for energy supply during chromatin remodeling. Increasing evidence indicates a critical role of chromatin remodeling in the establishment of long-lasting, even transgenerational immune memory in plants, which is supported by the findings that DNA methylation, histone deacetylation, and histone methylation can prime the promoters of immune-related genes required for disease defense. So what are the links between Snf2-mediated ATP-dependent chromosome remodeling and plant immunity, and what mechanisms might support its involvement in disease resistance?

Mechanisms of endosperm initiation

KEY MESSAGE

Overview of developmental events and signalling during central cell maturation and early endosperm development with a focus on mechanisms of sexual and autonomous endosperm initiation. Endosperm is important for seed viability and global food supply. The mechanisms regulating the developmental transition between Female Gametophyte (FG) maturation and early endosperm development in angiosperms are difficult to study as they occur buried deep within the ovule. Knowledge of the molecular events underlying this developmental window of events has significantly increased with the combined use of mutants, cell specific markers, and plant hormone sensing reporters. Here, we review recent discoveries concerning the developmental events and signalling of FG maturation, fertilization, and endosperm development. We focus on the regulation of the initiation of endosperm development with and without fertilization in Arabidopsis and the apomict Hieracium, comparing this to what is known in monocots where distinct differences in developmental patterning may underlie alternative mechanisms of suppression and initiation. The Polycomb Repressive Complex 2 (PRC2), plant hormones, and transcription factors are iteratively involved in early fertilization-induced endosperm formation in Arabidopsis. Auxin increases and PRC2 complex inactivation can also induce fertilization-independent endosperm proliferation in Arabidopsis. Function of the PRC2 complex member FERTILIZATION-INDEPENDENT ENDOSPERM and two loci AutE and LOP are required for autonomous endosperm development in apomictic Hieracium. A comparative understanding of cues required for early endosperm development will facilitate genetic engineering approaches for the development of resilient seed crops, especially if an option for fertilization-independent endosperm formation was possible to combat stress-induced crop failure.

Fluorescent Protein Aided Insights on Plastids and their Extensions: A Critical Appraisal

Multi-colored fluorescent proteins targeted to plastids have provided new insights on the dynamic behavior of these organelles and their interactions with other cytoplasmic components and compartments. Sub-plastidic components such as thylakoids, stroma, the inner and outer membranes of the plastid envelope, nucleoids, plastoglobuli, and starch grains have been efficiently highlighted in living plant cells. In addition, stroma filled membrane extensions called stromules have drawn attention to the dynamic nature of the plastid and its interactions with the rest of the cell. Use of dual and triple fluorescent protein combinations has begun to reveal plastid interactions with mitochondria, the nucleus, the endoplasmic reticulum and F-actin and suggests integral roles of plastids in retrograde signaling, cell to cell communication as well as plant-pathogen interactions. While the rapid advances and insights achieved through fluorescent protein based research on plastids are commendable it is necessary to endorse meaningful observations but subject others to closer scrutiny. Here, in order to develop a better and more comprehensive understanding of plastids and their extensions we provide a critical appraisal of recent information that has been acquired using targeted fluorescent protein probes.