Comparative Expression Profiling Reveals Genes Involved in Megasporogenesis

OsRH52A, a DEAD-box protein, regulates functional megaspore specification and is required for embryo sac development in rice

The development of the embryo sac is an important factor that affects seed setting in rice. Numerous genes associated with embryo sac (ES) development have been identified in plants; however, the function of the DEAD-box RNA helicase family genes is poorly known in rice. Here, we characterized a rice DEAD-box protein, RH52A, which is localized in the nucleus and cytoplasm and highly expressed in the floral organs. The knockout mutant rh52a displayed partial ES sterility, including degeneration of the ES (21%) and the presence of a double-female-gametophyte (DFG) structure (11.8%). The DFG developed from two functional megaspores near the chalazal end in one ovule, and 3.4% of DFGs were able to fertilize via the sac near the micropylar pole in rh52a. RH52A was found to interact with MFS1 and ZIP4, both of which play a role in homologous recombination in rice meiosis. RNA-sequencing identified 234 down-regulated differentially expressed genes associated with reproductive development, including two, MSP1 and HSA1b, required for female germline cell specification. Taken together, our study demonstrates that RH52A is essential for the development of the rice embryo sac and provides cytological details regarding the formation of DFGs.

Gene co-expression network analysis in areca floral organ and the potential role of the AcMADS17 and AcMADS23 in transgenic Arabidopsis

Areca catechu L., a monocot belonging to the palm family, is monoecious, with female and male flowers separately distributed on the same inflorescence. To discover the molecular mechanism of flower development in Areca, we sequenced different floral samples to generate tissue-specific transcriptomic profiles. We conducted a comparative analysis of the transcriptomic profiles of apical sections of the inflorescence with male flowers and the basal section of the inflorescence with female flowers. Based on the RNA sequencing dataset, we applied weighted gene co-expression network analysis (WGCNA) to identify sepal, petal, stamen, stigma and other specific modules as well as hub genes involved in specific floral organ development. The syntenic and expression patterns of AcMADS-box genes were analyzed in detail. Furthermore, we analyzed the open chromatin regions and transcription factor PI binding sites in male and female flowers by assay for transposase-accessible chromatin sequencing (ATAC-seq) assay. Heterologous expression revealed the important role of AcMADS17 and AcMADS23 in floral organ development. Our results provide a valuable genomic resource for the functional analysis of floral organ development in Areca.

OsmiRNA5488 Regulates the Development of Embryo Sacs and Targets OsARF25 in Rice (Oryza sativa L.)

Small RNAs are a class of non-coding RNAs that typically range from 20 to 24 nucleotides in length. Among them, microRNAs (miRNAs) are particularly important regulators for plant development. The biological function of the conserved miRNAs has been studied extensively in plants, while that of the species-specific miRNAs has been studied in-depth. In this study, the regulatory role of a rice-specific OsmiRNA5488 (OsmiR5488) was characterized with the miR5488-overexpressed line (miR5488-OE) and miR5488-silenced line (STTM-5488). The seed-setting rate was notably reduced in miR5488-OE lines, but not in STTM-5488 lines. Cytological observation demonstrated the different types of abnormal mature embryo sacs, including the degeneration of embryo sacs and other variant types, in miR5488-OE lines. The percentage of the abnormal mature embryo sacs accounted for the reduced value of the seed-setting rate. Furthermore, OsARF25 was identified as a target of OsmiR5488 via RNA ligase-mediated 3'-amplifification of cDNA ends, dual luciferase assays, and transient expression assays. The primary root length was decreased with the increases in auxin concentrations in miR5488-OE lines compared to wild-type rice. Summarily, our results suggested that OsmiR5488 regulates the seed-setting rate and down-regulates the targeted gene OsARF25.

Insights into the role of phytohormones in plant female germline cell specification

Germline specification is a fundamental process in plant reproduction, and the Megaspore Mother Cell (MMC), is a critical cell that differentiates and develops into the female gametophyte. While numerous studies have investigated the molecular mechanisms underlying female germline specification, previous reviews have mainly focused on gene regulatory networks, epigenetic pathways, and small RNAs, neglecting the potential contribution of phytohormones to this process. This review aims to address this gap by highlighting recent advances in MMC formation and discussing the roles of specific phytohormones in female germline specialization. Here, we provide a comprehensive overview of the functions of phytohormones in the formation of MMC and their effects on female gametophyte development. Specifically, it examines the roles of gibberellins (GAs), brassinosteroids (BRs), auxins, and cytokinin, in MMC development. Understanding the function of phytohormones in MMC development is essential for comprehending the complex mechanisms underlying plant reproduction. This review adds valuable insights to the existing knowledge on MMC development, providing a new perspective for future research in the field of plant reproduction.

3D cellular morphometrics of ovule primordium development in Zea mays reveal differential division and growth dynamics specifying megaspore mother cell singleness

Introduction

Differentiation of spore mother cells marks the somatic-to-reproductive transition in higher plants. Spore mother cells are critical for fitness because they differentiate into gametes, leading to fertilization and seed formation. The female spore mother cell is called the megaspore mother cell (MMC) and is specified in the ovule primordium. The number of MMCs varies by species and genetic background, but in most cases, only a single mature MMC enters meiosis to form the embryo sac. Multiple candidate MMC precursor cells have been identified in both rice and Arabidopsis, so variability in MMC number is likely due to conserved early morphogenetic events. In Arabidopsis, the restriction of a single MMC per ovule, or MMC singleness, is determined by ovule geometry. To look for potential conservation of MMC ontogeny and specification mechanisms, we undertook a morphogenetic description of ovule primordium growth at cellular resolution in the model crop maize.

Methods

We generated a collection of 48 three-dimensional (3D) ovule primordium images for five developmental stages, annotated for 11 cell types. Quantitative analysis of ovule and cell morphological descriptors allowed the reconstruction of a plausible developmental trajectory of the MMC and its neighbors.

Results

The MMC is specified within a niche of enlarged, homogenous L2 cells, forming a pool of candidate archesporial (MMC progenitor) cells. A prevalent periclinal division of the uppermost central archesporial cell formed the apical MMC and the underlying cell, a presumptive stack cell. The MMC stopped dividing and expanded, acquiring an anisotropic, trapezoidal shape. By contrast, periclinal divisions continued in L2 neighbor cells, resulting in a single central MMC.

Discussion

We propose a model where anisotropic ovule growth in maize drives L2 divisions and MMC elongation, coupling ovule geometry with MMC fate.

Single-nucleus sequencing deciphers developmental trajectories in rice pistils

Angiosperms possess a life cycle with an alternation of sporophyte and gametophyte generations, which happens in plant organs like pistils. Rice pistils contain ovules and receive pollen for successful fertilization to produce grains. The cellular expression profile in rice pistils is largely unknown. Here, we show a cell census of rice pistils before fertilization through the use of droplet-based single-nucleus RNA sequencing. The ab initio marker identification validated by in situ hybridization assists with cell-type annotation, revealing cell heterogeneity between ovule- and carpel-originated cells. A comparison of 1N (gametophyte) and 2N (sporophyte) nuclei identifies the developmental path of germ cells in ovules with typical resetting of pluripotency before the sporophyte-gametophyte transition, while trajectory analysis of carpel-originated cells suggests previously neglected features of epidermis specification and style function. These findings gain a systems-level view of cellular differentiation and development of rice pistils before flowering and lay a foundation for understanding female reproductive development in plants.

Does integument arise de novo or from pre-existing structures? ── Insights from the key regulatory genes controlling integument development

The origin of seeds is one of the key innovations in land plant evolution. Ovules are the developmental precursors of seeds. The integument is the envelope structure surrounding the nucellus within the ovule and developing into the seed coat when ovules mature upon fertilization. The question of whether the integument arise de novo or evolve from elaboration of pre-existing structures has caused much debate. By exploring the origin and evolution of the key regulatory genes controlling integument development and their functions during both individual and historical developmental processes, we showed the widespread presence of the homologs of ANT, CUC, BEL1, SPL, C3HDZ, INO, ATS, and ETT in seedless plant genomes. All of these genes have undergone duplication-divergence events in their evolutionary history, with most of the descendant paralogous suffering motif gain and/or loss in the coding regions. Expression and functional characterization have shown that these genes are key components of the genetic program that patterns leaf-like lateral organs. Serial homology can thus be postulated between integuments and other lateral organs in terms of the shared master regulatory genes. Given that the genetic program patterning leaf-like lateral organs formed in seedless plants, and was reused during seed origin, the integument is unlikely to arise de novo but evolved from the stem segment-specific modification of pre-existing serially homologous structures. The master 'switches' trigging the modification to specify the integument identity remain unclear. We propose a successive transformation model of integument origin.

OsDDM1b Controls Grain Size by Influencing Cell Cycling and Regulating Homeostasis and Signaling of Brassinosteroid in Rice

Snf2 family proteins are the crucial subunits of chromatin-remodeling complexes (CRCs), which contributes to the biological processes of transcription, replication, and DNA repair using ATP as energy. Some CRC subunits have been confirmed to be the critical regulators in various aspects of plant growth and development and in epigenetic mechanisms such as histone modification, DNA methylation, and histone variants. However, the functions of Snf2 family genes in rice were poorly investigated. In this study, the relative expression profile of 40 members of Snf2 family in rice was studied at certain developmental stages of seed. Our results revealed that OsCHR741/OsDDM1b (Decrease in DNA methylation 1) was accumulated highly in the early developmental stage of seeds. We further analyzed the OsDDM1b T-DNA insertion loss-of-function of mutant, which exhibited dwarfism, smaller organ size, and shorter and wider grain size than the wild type (Hwayoung, HY), yet no difference in 1,000-grain weight. Consistent with the grain size, the outer parenchyma cell layers of lemma in osddm1b developed more cells with decreased size. OsDDM1b encoded a nucleus, membrane-localized protein and was distributed predominately in young spikelets and seeds, asserting its role in grain size. Meanwhile, the osddm1b was less sensitive to brassinosteroids (BRs) while the endogenous BR levels increased. We detected changes in the expression levels of the BR signaling pathway and feedback-inhibited genes with and without exogenous BR application, and the alterations of expression were also observed in grain size-related genes in the osddm1b. Altogether, our results suggest that OsDDM1b plays a crucial role in grain size via influencing cell proliferation and regulating BR signaling and homeostasis.

Epigenetic Regulation of Megaspore Mother Cell Formation

In flowering plants, the female gametophyte (FG) initiates from the formation of the megaspore mother cell (MMC). Among a pool of the somatic cells in the ovule primordium, only one hypodermal cell undergoes a transition of cell fate to become the MMC. Subsequently, the MMC undergoes a series of meiosis and mitosis to form the mature FG harboring seven cells with eight nuclei. Although SPL/NZZ, the core transcription factor for MMC formation, was identified several decades ago, which and why only one somatic cell is chosen as the MMC have long remained mysterious. A growing body of evidence reveal that MMC formation is associated with epigenetic regulation at multiple layers, including dynamic distribution of histone variants and histone modifications, small RNAs, and DNA methylation. In this review, we summarize the progress of epigenetic regulation in the MMC formation, emphasizing the roles of chromosome condensation, histone variants, histone methylation, small RNAs, and DNA methylation.

Characterization of germline development and identification of genes associated with germline specification in pineapple

Understanding germline specification in plants could be advantageous for agricultural applications. In recent decades, substantial efforts have been made to understand germline specification in several plant species, including Arabidopsis, rice, and maize. However, our knowledge of germline specification in many agronomically important plant species remains obscure. Here, we characterized the female germline specification and subsequent female gametophyte development in pineapple using callose staining, cytological, and whole-mount immunolocalization analyses. We also determined the male germline specification and gametophyte developmental timeline and observed male meiotic behavior using chromosome spreading assays. Furthermore, we identified 229 genes that are preferentially expressed at the megaspore mother cell (MMC) stage during ovule development and 478 genes that are preferentially expressed at the pollen mother cell (PMC) stage of anther development using comparative transcriptomic analysis. The biological functions, associated regulatory pathways and expression patterns of these genes were also analyzed. Our study provides a convenient cytological reference for exploring pineapple germline development and a molecular basis for the future functional analysis of germline specification in related plant species.

High-throughput single-cell transcriptomics reveals the female germline differentiation trajectory in Arabidopsis thaliana

Female germline cells in flowering plants differentiate from somatic cells to produce specialized reproductive organs, called ovules, embedded deep inside the flowers. We investigated the molecular basis of this distinctive developmental program by performing single-cell RNA sequencing (scRNA-seq) of 16,872 single cells of Arabidopsis thaliana ovule primordia at three developmental time points during female germline differentiation. This allowed us to identify the characteristic expression patterns of the main cell types, including the female germline and its surrounding nucellus. We then reconstructed the continuous trajectory of female germline differentiation and observed dynamic waves of gene expression along the developmental trajectory. A focused analysis revealed transcriptional cascades and identified key transcriptional factors that showed distinct expression patterns along the germline differentiation trajectory. Our study provides a valuable reference dataset of the transcriptional process during female germline differentiation at single-cell resolution, shedding light on the mechanisms underlying germline cell fate determination.

Zhimin Hou, Yanhui Liu et al. used single cell RNA-seq to analyze the model organism, Arabidopsis thaliana, at three stages during female germline differentiation. They reconstructed the continuous trajectory of female germline differentiation, providing a valuable reference for future investigation of germline cell fate determination in A. thaliana.

The leucine-rich repeat receptor-like kinase OsERL plays a critical role in anther lobe formation in rice

In Arabidopsis, ERECTA (ER) subfamily of leucine-rich repeat (LRR) receptor kinases (LRR-RKs) play important roles in cell division and cell elongation. However, the functions of OsER genes in rice are still very much unknown. In this study, sixty-seven TILLING and four gene-edited mutants were identified for one of the three OsERs, OsERL, and used for functional analyses. Results showed that mutations in OsERL led to striking defects in anther development. Compete male sterility and reduced numbers of anther lobes, more severe than knockout mutants, were observed in mutants with amino acid substitutions in the kinase domain. Among alleles with amino acid changes in LRRs, only one mutation in the 16^th LRR showed evident phenotype, suggesting a role of the LRR in ligand sensing. OsERL is expressed in shoot apcies, internodes and anthers, and within the anther OsERL is expressed in sporophytic and tapetal cells. Cell biological analyses revealed that mutations in OsERL led to defected periclinal division in archesporial cells in anthers, suggesting a critical role of OsERL in rice anther development.

Floral transcriptomes reveal gene networks in pineapple floral growth and fruit development

Proper flower development is essential for sexual reproductive success and the setting of fruits and seeds. The availability of a high quality genome sequence for pineapple makes it an excellent model for studying fruit and floral organ development. In this study, we sequenced 27 different pineapple floral samples and integrated nine published RNA-seq datasets to generate tissue- and stage-specific transcriptomic profiles. Pairwise comparisons and weighted gene co-expression network analysis successfully identified ovule-, stamen-, petal- and fruit-specific modules as well as hub genes involved in ovule, fruit and petal development. In situ hybridization confirmed the enriched expression of six genes in developing ovules and stamens. Mutant characterization and complementation analysis revealed the important role of the subtilase gene AcSBT1.8 in petal development. This work provides an important genomic resource for functional analysis of pineapple floral organ growth and fruit development and sheds light on molecular networks underlying pineapple reproductive organ growth.