Lihua Zhao

• Peking university, institute of advanced agricultural sciences, China, Weifang

Quantitative gene regulation at the cell population level can be achieved by two fundamentally different modes of regulation at individual gene copies. A 'digital' mode involves binary ON/OFF expression states, with population-level variation arising from the proportion of gene copies in each state, while an 'analog' mode involves graded expression...

Multicellular organisms result from complex developmental processes largely orchestrated through the quantitative spatiotemporal regulation of gene expression. Yet, obtaining absolute counts of messenger RNAs at a three-dimensional resolution remains challenging, especially in plants, owing to high levels of tissue autofluorescence that prevent the...

Homologous recombination (HR) is a conservative DNA repair pathway in which intact homologous sequences are used as a template for repair. How the homology search happens in the crowded space of the cell nucleus is, however, still poorly understood. Here, we measure chromosome and double-strand break (DSB) site mobility in Arabidopsis thaliana, usi...

Multicellular organisms result from complex developmental processes largely orchestrated through the quantitative spatiotemporal regulation of gene expression. Yet, obtaining absolute counts of mRNAs at a 3-dimensional resolution remains challenging, especially in plants, due to high levels of tissue autofluorescence that prevent the detection of d...

The study of the independent evolution of similar characters can highlight important ecological and genetic factors that drive phenotypic evolution. The transition from reproduction by outcrossing to self-fertilization has occurred frequently throughout plant evolution. A common trend in this transition is the reduction of flower features in the se...

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 specie...

Protein ubiquitination is important for the regulation of meiosis in eukaryotes, including plants. However, little is known about the involvement of E2 ubiquitin-conjugating enzymes in plant meiosis. Arabidopsis UBC22 is a unique E2 enzyme, able to catalyze the formation of ubiquitin dimers through lysine 11 (K11). Previous work has shown that ubc2...

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 ovul...

Quantitative real-time PCR (qRT-PCR) is a convenient tool for gene expression analysis. However, reliability of its result is influenced largely by the selection of reference genes. Pineapple molecular breeding is limited due to lack of understanding of sexual organs’ development. Similarly, only a few reference genes have identified for qRT-PCR an...

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-...

In most sexually reproducing plants, a single somatic, sub-epidermal cell in an ovule is selected to differen- tiate into a megaspore mother cell, which is committed to giving rise to the female germline. However, it re- mains unclear how intercellular signaling among so- matic cells results in only one cell in the sub-epidermal layer differentiati...

Angiosperm reproductive development is a complex event that includes floral organ development, male and female gametophyte formation and interaction between the male and female reproductive organs for successful fertilization. Previous studies have revealed the redundant function of ATP binding cassette subfamily G (ABCG) transporters ABCG1 and ABC...

Background: Soil salinization and alkalization are among the major agricultural threats that affect crop productivity worldwide, which are increasing day by day with an alarming rate. In recent years, several halophytes have been investigated for their utilization in soil remediation and to decipher the mechanism of salt-tolerance in these high sa...

Pineapple (Ananas comosus L.), a popular tropical fruit, is a good model for evolutionary analysis and genetic research on adaptation to drought habitats, multiple fruits, and crassulacean acid metabolism (CAM) photosynthesis. Reliable reference genes for the normalization of the levels of development-related and/or stress-responsive genes is impor...

In the original version of this article [1], the spelling of the tenth author name, Moakai Yan, was incorrect. The corrected name is given in this correction article.

Background: An efficient transformation protocol is a primary requisite to study and utilize the genetic potential of any plant species. A quick transformation system is also crucial for the functional analysis of genes along with the study of proteins and their interactions in vivo. Presently, however, quick and effective transformation systems ar...

The accumulation of anthocyanins in response to specific developmental cues or environmental conditions plays a vital role in plant development and protection against stresses. Extensive research has examined the regulation of anthocyanin biosynthetic genes at the transcriptional and post‐transcriptional levels, but the role of chromatin in this re...

(Molecular Plant 10, 1274–1292; October 2017; https://doi.org/10.1016/j.molp.2017.09.007) In the METHODS of this article (page 1288), the information for two antibodies was wrongly provided. The authors of this article request the publication of the corrected one as “ChIP experiments were performed using an H2A.Z polyclonal antibody (from R. Deal,...

In most plants, the female germline starts with the differentiation of one megaspore mother cell (MMC) in each ovule that produces four megaspores through meiosis, one of which survives to become the functional megaspore (FM). The FM further develops into an embryo sac. Little is known regarding the control of MMC formation to one per ovule and the...

Genotyping of WT, septuple mutant and complementation lines with a genomic ICK7 fragment. An ICK7 genomic fragment was introduced into the septuple mutant. Many transformants (6/40) with normal silique length were observed and the analysis of two independent transformants (1243–4 and 1243–23) is shown here. PCR was used to determine the genotypes o...

Phenotyping of WT, ick12567 and septuple mutant plants. (A) Seedlings of WT, ick12567 and septuple mutants at 26 days after planting in soil. (B) Fresh seedling weight of 21-day-old WT, ick12567 and septuple mutants. For each line, 3 pots each with 5 plants were used in the analysis. The averages and standard deviations are shown. (C—E) Leaf area (...

Genotyping of WT, septuple mutant and complementation lines with a genomic ICK4 fragment. An ICK4 genomic fragment (including 2040 bp before ATG, 1028 bp of the coding region and 717 bp of the region after the STOP codon) was introduced into the septuple mutant. Multiple independent lines were identified that showed complementation of the silique l...

RT-PCR and phenotyping of WT, ick4, ick467, ick123467 and septuple mutants. (A) Analysis of ICK transcripts in the WT (the first lane), ick4 (the second lane), ick467 (the third lane), ick123467 (the fourth lane) and septuple mutant (the fifth lane), with WT genomic DNA as a control (the last lane). Gene-specific primers were used for amplifying th...

Identification of megaspore mother cells (MMCs) in meiosis by ASY1 immunostaining. Developing ovules were prepared and immunostained with an antibody against ASY1, which is specifically expressed during meiosis. (A—C) WT ovules at MMC (A), meiosis (B) and FG1 (C) stages. (D—I) Mutant ovules at MMC (D), meiosis (E—H) and FG1 (I) stages. One to four...

Early megagametogenesis in WT and ick septuple mutant. WT (A) and septuple (B—D) ovules at FG2 stage. The WT ovule had one pair of nuclei. The mutant ovules had two (B), three (C) and four (D) pairs of nuclei, with each pair likely derived from a functional megaspore. The two nuclei in each pair are close to each other and have similar appearance....

Observation of female gametes in mature embryo sacs in the WT and ick septuple mutant. The flower buds just before opening were emasculated and left for 1 day. Ovules (from about 15 gynoecia for each line) were prepared and observed under a microscope with DIC optics. If one central cell (secondary) nucleus and one egg nucleus, usually close to eac...

Genotyping and RT-PCR of ick3 and ick4 T-DNA insertion mutants. (A) Genotyping of ick3 (SALK_053533) and ick4 (Sail_548_B03) single mutants with WT as a control. For both genes, a pair of gene-specific primers was used for amplifying the full-length WT coding sequence of ICK3 or ICK4 while a T-DNA left border primer and a gene specific primer were...

Crosses used to produce various ick mutants from ICK single mutants and ick12567 mutant. (PDF)

Genotyping and RT-PCR of ick septuple mutant. (A) Gene-specific primers for ICK1, ICK2, ICK3, ICK4, ICK5, ICK6 and ICK7 were used to confirm the genotype of ICK septuple mutant with WT genomic DNA as a control. (B) Analysis of ICK transcripts in the WT (first lane) and septuple mutant (second lane), with WT genomic DNA as a control (third lane). Ge...

Reciprocal crosses to determine the transmission of the short silique phenotype through the parents. Reciprocal crosses (indicated as female X male) were made between the WT and septuple mutant. The length of fully-elongated siliques was measured. In each treatment, four plants with 4 siliques for each plant were used. The averages and standard dev...

RT-PCR and phenotyping of WT, septuple mutant and complementation lines with a genomic ICK4 fragment. (A) ICK4 transcript analysis. cDNAs synthesized from total RNAs were used to detect the ICK4 transcripts in WT, septuple mutant and two complementation lines (T2 generation). Actin (ACT8) was amplified as a control. (B) Silique length of WT, septup...

RT-PCR and phenotyping of WT, septuple mutant and transformants with ICK7. (A) ICK7 transcript analysis. cDNAs synthesized from total RNAs were used to detect the ICK7 transcripts in WT, septuple mutant and two transformants with ICK7 genomic fragment. Actin (ACT8) was amplified as a control. (B) Silique length of WT, septuple mutant and the two tr...

Analysis of surviving megaspores in WT and septuple mutant ovules with one MMC. Ovules with a single MMC were identified based on callose staining with aniline blue and DIC microscopy. For each ovule, the callose fluorescence image is shown at the top and the DIC image at the bottom. The numbers in the images indicate the 1st to 4th megaspore posit...

Analysis of mature pollen grains in WT and ick septuple mutant. Mature pollen grains from ten nascent flowers each line were collected and stained with DAPI. Vegetative and sperm cell nuclei were observed and counted under a fluorescence microscope (Leica DM2500) with a 63× (NA = 1.40) oil lens. (PDF)

Development of functional megaspore (FM) in ovules of the WT and ick septuple mutant. The ovules were checked and those at functional megaspore stage were included in the analysis. They were observed under a microscope with DIC optics. The presence and number of functional megaspores in ovules (from about 15 gynoecia) were counted. (PDF)

Frequency of twin seedlings in the WT and ick septuple mutant. WT and septuple mutant seeds were plated on ½ MS plates. Four days after plating, seedlings were screened under a dissecting microscope for the occurrence of twin seedlings. (PDF)

Genotyping of WT, ick4, ick467, ick123467 and septuple mutants. Gene-specific primers for ICK1, ICK2, ICK3, ICK4, ICK5, ICK6 and ICK7 genes, and a T-DNA left border primer were used to confirm the genotypes of WT, ick4, ick467, ick123467 and septuple mutants. (PDF)

Number of megaspore mother cells determined by DIC, DMC1 immunostaining and callose deposition patterns. (A) WT and septuple ovules at stage 2-II were surveyed under a DIC microscope and determined for the number of enlarged MMC-like cells prior to meiosis. Number of ovules counted: WT = 129 and mutant = 149. (B) Number of MMCs undergoing meiosis a...

Analysis of endosperm development and presence of extra central cells after fertilization in the WT and ick septuple mutant. Three days after flowers opened, ovules were collected and prepared for DIC observation. Only the ovules containing at least one developing embryo were included (about 20 gynoecia from each line used). All the WT ovules had o...

Background: Soybean, a major legume crop native to East Asia, presents a wealth of resources for utilization. The basic leucine zipper (bZIP) transcription factors play important roles in various biological processes including developmental regulation and responses to environmental stress stimuli. Currently, little information is available regardi...

Significance In flowering plants, the female germ line begins as a single cell known as the megaspore mother cell (MMC) in each ovule. The mechanisms that restrict MMC fate to a single cell remain largely unknown. We show that the Arabidopsis cytochrome P450 gene KLU acts through the chromatin remodeling complex SWR1 to promote WRKY28 expression in...

Pineapple (Ananas comosus L.) cultivation commonly relies on asexual reproduction which is easily impeded by many factors in agriculture production. Sexual reproduction might be a novel approach to improve the pineapple planting. However, genes controlling pineapple sexual reproduction are still remain elusive. In different organisms a conserved su...

WUSCHEL-related homeobox (WOX) gene family has important role in plant developmental process and represents a class of plant specific transcription factors that are involved in early phase of embryogenesis by coordinating gene transcription. Recent available pineapple whole genome sequences provide a base for detail comprehensive phylogenetic analy...

Auxin response factors (ARFs) are transcription factors that bind with auxin response elements to regulate the expression of auxin responsive genes. The ARF genes family is characterized by a large multigene family in plants and plays important roles in plant development. However, the ARF gene family has not yet been identified in pineapple, one of...

In most sexually reproducing plants, a single somatic, sub-epidermal cell in an ovule is selected to differentiate into a megaspore mother cell, which is committed to giving rise to the female germline. However, it remains unclear how intercellular signaling among somatic cells results in only one cell in the sub-epidermal layer differentiating int...

Flowering plants display a remarkable diversity in inflorescence architecture, and pedicel length is one of the key contributors to this diversity. In Arabidopsis thaliana , the receptor‐like kinase ERECTA ( ER ) mediated signaling pathway plays important roles in regulating inflorescence architecture by promoting cell proliferation. However, the r...

Megasporogenesis is essential for female fertility and requires the accomplishment of meiosis and the formation of functional megaspores. The inaccessibility and low abundance of female meiocytes make it particularly difficult to elucidate the molecular basis underlying megasporogenesis. We used high-throughput tag-sequencing analysis to identify g...

In flowering plants, meiocytes develop from subepidermal cells in anthers and ovules. The mechanisms that integrate gene-regulatory processes with meiotic programs during reproductive development remain poorly characterized. Here, we show that Arabidopsis thaliana plants deficient in ACTIN-RELATED PROTEIN6 (ARP6), a subunit of the SWR1 ATP-dependen...