ABORTED MICROSPORES Acts as a Master Regulator of Pollen Wall Formation in Arabidopsis

Protein phosphatase 2A B'α and B'β promote pollen wall construction partially through BRASSINAZOLE-RESISTANT 1-activated cysteine protease gene CEP1 in Arabidopsis

A well-constructed pollen wall is essential for pollen fertility, which relies on the contribution of the tapetum. Our results demonstrated an essential role of the tapetum-expressed protein phosphatase 2A (PP2A) B'α and B'β in pollen wall formation. The b'aβ double mutant pollen grain harboured sticky remnants and tectum breakages, resulting in failed release. B'α and B'β functioned partially through dephosphorylating and activating BRASSINAZOLE-RESISTANT 1 (BZR1). The bzr1 bes1 double and higher-order mutants of this BZR1/BES1 family displayed similar defects in the pollen wall, while bzr1-1D, having an active form of the BRZ1 protein, exhibited fertile pollen grains in a B'α and B'β dependent manner. Correspondingly, the level of phospho-BZR1 was increased and dephospho-BZR1 was decreased in b'aβ and bzr1-1D/b'aβ at anther stages 8-9 as compared with Col-0 and bzr1-1D, respectively. A cysteine protease gene CEP1 was identified as a BZR1 target, whose transcriptional activation necessitates brassinosteroid (BR)-responsive elements in the promoter region and the BZR1 DNA binding domain. The mRNA level of CEP1 at stages 8-9 was extremely low in bzr1 and bzr1 bes1, but higher in Col-0 and bzr1-1D depending on B'α and B'β. Furthermore, cep1 mutants displayed similar defects in the pollen wall. In brief, this study uncovered a PP2A-BZR1-CEP1 regulatory module, providing a new insight into pollen maturation mechanisms.

Functional redundancy of transcription factors SlNOR and SlNOR-like1 is required for pollen development in tomato

In tomato, SlNOR and SlNOR-like1, members of the NAC family of transcription factors (TFs), are known to play critical roles in regulating fruit ripening and are highly expressed in floral organs. However, their role in flower development remains unclear. In this study, we generated and functionally characterized a double knockout mutant, nor/nor-like1. Our findings reveal that the pollen abortion of the nor/nor-like1 impedes ovarian enlargement, resulting in fruit formation failure. Histological analyses demonstrate that the pollen wall collapse occurs during the mature pollen stage and leads to the abnormal pollen wall component deposition at the microspore stage, resulting in the male sterility in the double knockout mutant lines. Kyoto Encyclopedia of Genes and Genomes enrichment pathway analyses further suggest that the loss of SlNOR and SlNOR-like1 function affects several metabolic pathways related to pollen development, including 'ABC transporters', 'lipid metabolism', 'phenylpropanoid biosynthesis', 'hormone signal transduction', 'starch and sucrose metabolism', and 'cutin, suberine, and wax biosynthesis'. Furthermore, our results demonstrate that SlNOR and SlNOR-like1 could directly bind to the promoters of key genes associated with pollen wall formation and activate their expression, including ATP-binding cassette transporters of the G family (SlABCG8/9/23), ECERIFERUM (SlCER1), and glycine-rich protein (SlGRP92). These findings suggest that SlNOR and SlNOR-like1 may play a redundant role in the biosynthesis and transport of sporopollenin precursors, cuticular wax biosynthesis, and exine formation. In summary, our study highlights a previously uncharacterized role of SlNOR and SlNOR-like1 in tomato pollen wall formation and male fertility.

Integrated GWAS, BSA-seq, and RNA-seq analyses to identify candidate genes associated with male fertility trait in peach

Male sterility in peach (Prunus persica L.), characterized by the absence of fertile pollen grains in the anther, is determined by a recessive allele in homozygosis of the major gene located on chromosome 6. Developing tightly linked molecular markers can help identify appropriate peach parents or male-sterile plants for early culling in segregating progenies, thereby increasing breeding efficiency. In this study, we performed comprehensive research integrating genome-wide association study, bulked segregant analysis, and tissue-specific transcriptome sequencing for precisely characterizing the genes associated with male sterility and fertility in peach. We identified the candidate gene Prupe.6G027000, which encodes an ATP-binding cassette transporter G family member 26 (ABCG26), as a reliable candidate for controlling the targeted traits, as indicated by gene expression profiling and validated by quantitative real-time polymerase chain reaction, in situ hybridization, and virus-induced gene silencing. Prupe.6G027000 was transcribed preferentially on the tapetum and microspore surface, and its transient silencing caused severe pollen abortion in peach. The genotypes of nonsynonymous single-nucleotide variation (T > C) harbored in the coding region of Prupe.6G027000 exhibited approximately 96.2% consistency with male fertile or sterile phenotype in 579 peach accessions. These findings lay the foundation for dissecting the genetic basis of male fertility traits, and facilitating the establishment of a marker-assisted selection system in peaches.

Identity Transitions of Tapetum Phases: Insights into Vesicular Dynamics and in Mortem Support During Pollen Maturation

Flower development progresses through twelve distinct stages, meticulously regulated to optimize plant reproductive success. At stage 5, the initiation of anther development occurs, which is further categorized into 14 stages divided into two defined phases: phase 1, known as microsporogenesis, and phase 2, termed microgametogenesis-encompassing pollen maturation and anther dehiscence. The maturation of pollen grains must be temporally synchronized with anther dehiscence, with auxin serving as a pivotal spatio-temporal link between these processes, coordinating various aspects of anther development, including stamen elongation, anther dehiscence, and tapetum development. The tapetum, a secretory tissue adjacent to the meiocytes, is essential for nurturing developing pollen grains by secreting components of the pollen wall and ultimately undergoing programmed cell death (PCD). This review primarily focuses on microgametogenesis, the identity and function of the tapetum during the different progression phases, the role of vesicular signaling in delivering external components crucial for pollen grain maturation, and the distinctive process of PCD associated with these developmental processes.

The AMS/DYT1-MYB module interacts with the MED25-MYC-MYB complexes to inhibit jasmonate-regulated floral defense in Arabidopsis

The phytohormone jasmonates (JAs) regulate plant growth and defense responses. The reproductive organs of flowers are devastated by insect herbivores. However, the molecular mechanisms of floral defense remain largely unknown. Here, we found that the Arabidopsis JA receptor CORONATINE INSENSITIVE1 (COI1) and its substrates JA ZIM-domain (JAZ) repressors, and the mediator subunit MEDIATOR25-based MED25-MYC-MYB (MMM) complexes, including MYC2/3/4/5 and MYB28/29/76, mediated floral defense against the insects Helicoverpa armigera, Spodoptera exigua, and Spodoptera frugiperda. The flower-specific IIIa bHLH factors ABORTED MICROSPORES (AMS) and DYSFUNCTIONAL TAPETUM 1 (DYT1) were JAZ-interaction proteins. They interacted with members of the MMM complexes, inhibited the transcriptional activity of MYC2 and MYB28, and repressed floral defense against insects. AMS and DYT1 recruited the flower-specific MYB21/24, and these MYBs interacted with members of MMM complexes, inhibited the MYC2-MYB28 function, and suppressed floral defense against insects. Our study revealed that the JA-COI1-JAZ-MMM pathway mediated flower defense, and the AMS/DYT1-MYB21/24 module antagonized the MMM complexes to repress floral defense against insects.

Genome-wide analysis and characterization of TPD1 family proteins in pearl millet (Cenchrus americanus): Insights into reproductive regulation and phytohormone responses

The Tapetum Determinant 1 (TPD1) family proteins are known to play a crucial role in the regulation of reproduction in plants, including Cenchrus americanus (pearl millet). However, members of TPD1 family proteins have not been fully identified. The current study aims to identify and characterize the TPD1 family proteins in Cenchrus americanus (L.) Morrone. Seven transmembrane proteins (from 127 to 172 aa) comprising TPD1 domain were identified via genome-wide mining. Analysis of gene expression during developmental stages revealed high expression of four CaTPD1s in reproductive organs. Treatment with phytohormones showed that the expression of CaTPD1s was repressed by hormone treatments except CaTPD1_Ch4.1 and CaTPD1_Ch4.3 which are highly expressed in response to brassinolide and auxin, respectively. Screening of cis-elements in the promoter of CaTPD1s revealed various cis-elements related to phytohormone regulation, wound response, abiotic stress defense, and light response. The phylogenetic tree revealed distinct clustering of CaTPD1_Ch6 and CaTPD1_Ch5 among the other CaTPD1s, which revealed close relationships with the orthologs from Arabidopsis and rice that are known to have a critical role in tapetum development and pollen and ovule production. Hence, this study affirms the role of the CaTPD1s genes in the growth and reproduction during pearl millet developmental stages.

Genome- and Transcriptome-Wide Characterization and Expression Analyses of bHLH Transcription Factor Family Reveal Their Relevance to Salt Stress Response in Tomato

The bHLH (basic helix-loop-helix) transcription factors function as crucial regulators in numerous biological processes including abiotic stress responses and plant development. According to our RNA-seq analysis of tomato seedlings under salt stress, we found that, although the bHLH gene family in tomato has been studied, there are still so many tomato bHLH genes that have not been identified and named, which will hinder the later study of SlbHLHs. In total, 195 SlbHLHs that were unevenly distributed onto 12 chromosomes were identified from the tomato genome and were classified into 27 subfamilies based on their molecular features. The collinearity between SlbHLHs and interrelated orthologs from 10 plants further revealed evolutionary insights into SlbHLHs. Cis-element investigations of SlbHLHs promotors further suggested the potential roles of SlbHLHs in tomato development and stress responses. A total of 30 SlbHLHs were defined as the differentially expressed genes in response to salt stress by RNA-seq. The expression profiles of selected SlbHLHs were varyingly and markedly induced by multiple abiotic stresses and hormone treatments. These results provide valuable information to further understand the significance and intricacy of the bHLH transcription factor family, and lay a foundation for further exploring functions and possible regulatory mechanisms of SlbHLH members in abiotic stress tolerance, which will be significant for the study of tomato stress resistance and agricultural productivity.

Molecular and cellular mechanisms of photoperiod- and thermo-sensitive genic male sterility in plants

Photoperiod- and thermo-sensitive genic male sterile (P/TGMS) lines display male sterility under high-temperature/long-day light conditions and male fertility under low-temperature/short-day light conditions. P/TGMS lines are the fundamental basis for the two-line hybrid breeding, which has notably increased the yield potential and grain quality of rice cultivars. In this review, we focus on the research progress on photoperiod- and thermo-sensitive genic male sterility in plants. The essence of P/TGMS line is their ability to produce viable pollen under varying conditions. We overview the processes involved in anther and pollen development, as well as the molecular, cellular, and genetic mechanisms underlying P/TGMS in Arabidopsis, rice, and other crops. Slow development has been identified as a common mechanism of P/TGMS fertility restoration in both Arabidopsis and rice, while reactive oxygen species homeostasis has been implicated in rice P/TGMS. Furthermore, we discuss the prospective applications of P/TGMS and potential solutions to the challenges in this field. This review deepens the understanding of the mechanisms underlying P/TGMS and its utilization in two-line hybrid breeding across diverse crops.

Identification of Retrocopies in Lepidoptera and Impact on Domestication of Silkworm

BACKGROUND

During the domestication of silkworm, an economic insect, its physiological characteristics have changed greatly. RNA-based gene duplication, known as retrocopy, plays an important role in the formation of new genes and genome evolution, but the retrocopies of lepidopteran insects have not been fully identified and analyzed, which not only severely limits researchers from exploring the effects of retrocopies on lepidopteran insects but also affects the studies on the domestication of silkworm.

METHODS

We compared the genomes and proteomes of eight lepidopteran insects and used a series of screening criteria for auxiliary screening to obtain the retrocopies in lepidopteran insects and explored their characteristics. In addition, based on the silkworm transcriptome data from the SilkDB3.0 website, we explored the functions of the retrocopies on the domestication of the silkworm.

RESULTS

A total of 1993 retrocopies and 1208 parental genes in lepidopteran insects were obtained. We revealed that the retrocopies in Lepidoptera do not conform to the "out of X" hypothesis but fit the "out of testis" hypothesis. These retrocopies were subject to strong functional constraints and performed important functions in growth and development. Transcriptome analysis revealed that the expression pattern of the retrocopies and their parental genes were irrelevant. Through the analysis of the retrocopies in silkworm generated after domestication and located in the candidate domestication regions, the possible universal connection between the retrocopies and the domestication of silkworm were found.

CONCLUSIONS

Our study pioneered the exploration of retrocopies in multiple Lepidoptera species and found the potential association between the retrocopies and the domestication of silkworm.

Single-cell transcriptomic and cell‑type‑specific regulatory networks in Polima temperature-sensitive cytoplasmic male sterility of Brassica napus L

BACKGROUND

Thermosensitive male sterility (TMS) is a heritable agronomic trait influenced by the interaction between genotype and environment. The anthers of plants are composed of various specialized cells, each of which plays different roles in plant reproduction. In rapeseed (Brassica napus L.), Polima (pol) temperature-sensitive cytoplasmic male sterility (TCMS) is widely used in two-line breeding because its fertility can be partially restored at certain temperatures. The pol-TCMS line exhibits abnormal anther development and pollen abortion at high (restrictive) temperatures (HT, 25 °C) compared to at low (permissive) temperatures (LT, 16 °C). However, the response of different anther cell types to HT and the dynamic regulation of genes under such conditions remain largely unknown.

RESULTS

We present the first single-cell transcriptomic atlas of Brassica napus early developing flower bud tissues in response to HT. We identified 8 cell types and 17 transcriptionally distinct cell clusters via known marker genes under LT and HT treatment conditions. Under HT conditions, changes in the gene expression patterns of different cell clusters were observed, with the number of down-regulated genes in various cell types exceeding that of up-regulated genes. Pseudotime trajectory analysis revealed that HT strongly affected the development of early stamen/anther tissue cells. In combination with the snRNA-seq, WGCNA, and bulk RNA-seq results, we found that many transcription factors play crucial roles in the response to HT, especially heat response family genes.

CONCLUSIONS

Our study revealed the transcriptional regulatory network of floral bud tissue in the pol-TCMS line under HT/LT conditions and increased our understanding of high-temperature-induced anther developmental abnormalities, which may help researchers utilize TCMS in the two-line breeding of Brassica plants.

Plant terrestrialization: an environmental pull on the evolution of multi-sourced streptophyte phenolics

Phenolic compounds of land plants are varied: they are chemodiverse, are sourced from different biosynthetic routes and fulfil a broad spectrum of functions that range from signalling phytohormones, to protective shields against stressors, to structural compounds. Their action defines the biology of land plants as we know it. Often, their roles are tied to environmental responses that, however, impacted already the algal progenitors of land plants, streptophyte algae. Indeed, many streptophyte algae successfully dwell in terrestrial habitats and have homologues for enzymatic routes for the production of important phenolic compounds, such as the phenylpropanoid pathway. Here, we synthesize what is known about the production of specialized phenolic compounds across hundreds of millions of years of streptophyte evolution. We propose an evolutionary scenario in which selective pressures borne out of environmental cues shaped the chemodiversity of phenolics in streptophytes. This article is part of the theme issue 'The evolution of plant metabolism'.

Analysis of Rfo-Mediated Network in Regulating Fertility Restoration in Brassica oleracea

Ogura cytoplasmic male sterility (CMS) lines play a crucial role in the utilization of heterosis. However, valuable traits, such as disease resistance genes from Ogura CMS hybrids, are challenging to incorporate for germplasm innovation, particularly in cabbage and broccoli. To date, the Rfo-mediated network regulating fertility restoration remains largely unexplored. In this study, we conducted a transcriptomic analysis of broccoli flower buds from Ogura CMS SFB45 and its Rfo-transgenic fertility restoration line, pRfo, at different stages of pollen development. Gene Ontology (GO) terms such as "pollen exine formation", "flavonoid metabolic and biosynthetic processes", and "pollen wall assembly", along with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including "flavonoid biosynthesis", "MAPK signaling pathway-plant", and "ABC transporters", were significantly enriched. We identified five differentially expressed genes (DEGs) involved in tapetum-mediated callose metabolism, thirty-four DEGs related to tapetum-mediated pollen wall formation, three DEGs regulating tapetum programmed cell death (PCD), five MPKs encoding DEGs, and twelve DEGs associated with oxidative phosphorylation. Additionally, yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays demonstrated that RFO directly interacts with ORF138 at the protein level. These findings provide valuable insights into the fertility recovery mechanisms regulated by Rfo in broccoli and offer important clues for breeders aiming to enhance Ogura CMS hybrids in Brassica oleracea.

The evolution and development of sporangia-The fundamental reproductive organ of land plant sporophytes

A key innovation of land plants is the origin and evolution of the sporangium, the fundamental reproductive structure of the diploid sporophyte. In vascular plants, whether the structure is a cone, fertile leaf, or flower-all are clusters of sporangia. The evolution of morphologically distinct sporangia (heterospory) and retention of the gametophyte evolved three times independently as a prerequisite for the evolution of seeds. This review summarizes the development of vascular plant sporangia, molecular genetics of angiosperm sporangia, and provides a framework to investigate evolution and development in vascular plant sporangia.

Adaptive divergence, historical population dynamics, and simulation of suitable distributions for Picea Meyeri and P. Mongolica at the whole-genome level

The taxonomic classification of Picea meyeri and P. mongolica has long been controversial. To investigate the genetic relatedness, evolutionary history, and population history dynamics of these species, genotyping-by-sequencing (GBS) technology was utilized to acquire whole-genome single nucleotide polymorphism (SNP) markers, which were subsequently used to assess population structure, population dynamics, and adaptive differentiation. Phylogenetic and population structural analyses at the genomic level indicated that although the ancestor of P. mongolica was a hybrid of P. meyeri and P. koraiensis, P. mongolica is an independent Picea species. Additionally, P. mongolica is more closely related to P. meyeri than to P. koraiensis, which is consistent with its geographic distribution. There were up to eight instances of interspecific and intraspecific gene flow between P. meyeri and P. mongolica. The P. meyeri and P. mongolica effective population sizes generally decreased, and Maxent modeling revealed that from the Last Glacial Maximum (LGM) to the present, their habitat areas decreased initially and then increased. However, under future climate scenarios, the habitat areas of both species were projected to decrease, especially under high-emission scenarios, which would place P. mongolica at risk of extinction and in urgent need of protection. Local adaptation has promoted differentiation between P. meyeri and P. mongolica. Genotype‒environment association analysis revealed 96,543 SNPs associated with environmental factors, mainly related to plant adaptations to moisture and temperature. Selective sweeps revealed that the selected genes among P. meyeri, P. mongolica and P. koraiensis are primarily associated in vascular plants with flowering, fruit development, and stress resistance. This research enhances our understanding of Picea species classification and provides a basis for future genetic improvement and species conservation efforts.

MAPK20-mediated ATG6 phosphorylation is critical for pollen development in Solanum lycopersicum L

In flowering plants, male gametogenesis is tightly regulated by numerous genes. Mitogen-activated protein kinase (MAPK) plays a critical role in plant development and stress response, while its role in plant reproductive development is largely unclear. The present study demonstrated MAPK20 phosphorylation of ATG6 to mediate pollen development and germination in tomato (Solanum lycopersicum L.). MAPK20 was preferentially expressed in the stamen of tomato, and mutation of MAPK20 resulted in abnormal pollen grains and inhibited pollen viability and germination. MAPK20 interaction with ATG6 mediated the formation of autophagosomes. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that ATG6 was phosphorylated by MAPK20 at Ser-265. Mutation of ATG6 in wild-type (WT) or in MAPK20 overexpression plants resulted in malformed and inviable pollens. Meanwhile, the number of autophagosomes in mapk20 and atg6 mutants was significantly lower than that of WT plants. Our results suggest that MAPK20-mediated ATG6 phosphorylation and autophagosome formation are critical for pollen development and germination.

GhTKPR1_8 functions to inhibit anther dehiscence and reduce pollen viability in cotton

Sporopollenin, as the main component of the pollen exine, is a highly resistant polymer that provides structural integrity under unfavourable environmental conditions. Tetraketone α-pyrone reductase 1 (TKPR1) is essential for sporopollenin formation, catalyzing the reduction of tetraketone carbonyl to hydroxylated α-pyrone. The functional role of TKPR1 in male sterility has been reported in flowering plants such as maize, rice, and Arabidopsis. However, the molecular cloning and functional characterization of TKPR1 in cotton remain unaddressed. In this study, we identified 68 TKPR1s from four cotton species, categorized into three clades. Transcriptomics and RT-qPCR demonstrated that GhTKPR1_8 exhibited typical expression patterns in the tetrad stage of the anther. GhTKPR1_8 was localized to the endoplasmic reticulum. Moreover, ABORTED MICROSPORES (GhAMS) transcriptionally activated GhTKPR1_8 as indicated by luciferase complementation tests. GhTKPR1_8-knockdown inhibited anther dehiscence and reduced pollen viability in cotton. Additionally, overexpression of GhTKPR1_8 in the attkpr1 mutant restored its male sterile phenotype. This study offers novel insights into the investigation of TKPR1 in cotton while providing genetic resources for studying male sterility.

Environmental regulation of male fertility is mediated through Arabidopsis transcription factors bHLH89, 91, and 10

Formation of functional pollen and successful fertilization rely on the spatial and temporal regulation of anther and pollen development. This process responds to environmental cues to maintain optimal fertility despite climatic changes. Arabidopsis transcription factors basic helix-loop-helix (bHLH) 10, 89, and 91 were previously thought to be functionally redundant in their control of male reproductive development, however here we show that they play distinct roles in the integration of light signals to maintain pollen development under different environmental conditions. Combinations of the double and triple bHLH10,89,91 mutants were analysed under normal (200 μmol m-2 s-1) and low (50 μmol m-2 s-1) light conditions to determine the impact on fertility. Transcriptomic analysis of a new conditionally sterile bhlh89,91 double mutant shows differential regulation of genes related to sexual reproduction, hormone signal transduction, and lipid storage and metabolism under low light. Here we have shown that bHLH89 and bHLH91 play a role in regulating fertility in response to light, suggesting that they function in mitigating environmental variation to ensure fertility is maintained under environmental stress.

Revealing the role of CCoAOMT1: fine-tuning bHLH transcription factors for optimal anther development

The tapetum, a crucial innermost layer encompassing male reproductive cells within the anther wall, plays a pivotal role in normal pollen development. The transcription factors (TFs) bHLH010/089/091 redundantly facilitate the rapid nuclear accumulation of DYSFUNCTIONAL TAPETUM 1, a gatekeeper TF in the tapetum. Nevertheless, the regulatory mechanisms governing the activity of bHLH010/089/091 remain unknown. In this study, we reveal that caffeoyl coenzyme A O-methyltransferase 1 (CCoAOMT1) is a negative regulator affecting the nuclear localization and function of bHLH010 and bHLH089, probably through their K259 site. Our findings underscore that CCoAOMT1 promotes the nuclear export and degradation of bHLH010 and bHLH089. Intriguingly, elevated CCoAOMT1 expression resulted in defective pollen development, mirroring the phenotype observed in bhlh010 bhlh089 mutants. Moreover, our investigation revealed that the K259A mutation in the bHLH089 protein disrupted its translocation from the nucleus to the cytosol and impeded its degradation induced by CCoAOMT1. Importantly, transgenic plants with the probHLH089::bHLH089K259A construct failed to rescue proper pollen development or gene expression in bhlh010 bhlh089 mutants. Collectively, these findings emphasize the need to maintain balanced TF homeostasis for male fertility. They firmly establish CCoAOMT1 as a pivotal regulator that is instrumental in achieving equilibrium between the induction of the tapetum transcriptional network and ensuring appropriate anther development.

PEO: Plant Expression Omnibus - a comparative transcriptomic database for 103 Archaeplastida

The Plant Expression Omnibus (PEO) is a web application that provides biologists with access to gene expression insights across over 100 plant species, ~60 000 manually annotated RNA-seq samples, and more than 4 million genes. The tool allows users to explore the expression patterns of genes across different organs, identify organ-specific genes, and discover top co-expressed genes for any gene of interest. PEO also provides functional annotations for each gene, allowing for the identification of genetic modules and pathways. PEO is designed to facilitate comparative kingdom-wide gene expression analysis and provide a valuable resource for plant biology research. We provide two case studies to demonstrate the utility of PEO in identifying candidate genes in pollen coat biosynthesis in Arabidopsis and investigating the biosynthetic pathway components of capsaicin in Capsicum annuum. The database is freely available at https://expression.plant.tools/.

bHLH-regulated routes in anther development in rice and Arabidopsis

Anther development is a complex process essential for plant reproduction and crop yields. In recent years, significant progress has been made in the identification and characterization of the bHLH transcription factor family involved in anther regulation in rice and Arabidopsis, two extensively studied model plants. Research on bHLH transcription factors has unveiled their crucial function in controlling tapetum development, pollen wall formation, and other anther-specific processes. By exploring deeper into regulatory mechanisms governing anther development and bHLH transcription factors, we can gain important insights into plant reproduction, thereby accelerating crop yield improvement and the development of new plant breeding strategies. This review provides an overview of the current knowledge on anther development in rice and Arabidopsis, emphasizing the critical roles played by bHLH transcription factors in this process. Recent advances in gene expression analysis and functional studies are highlighted, as they have significantly enhanced our understanding of the regulatory networks involved in anther development.

The transcription factors and pathways underpinning male reproductive development in Arabidopsis

As Arabidopsis flowers mature, specialized cells within the anthers undergo meiosis, leading to the production of haploid microspores that differentiate into mature pollen grains, each containing two sperm cells for double fertilization. During pollination, the pollen grains are dispersed from the anthers to the stigma for subsequent fertilization. Transcriptomic studies have identified a large number of genes expressed over the course of male reproductive development and subsequent functional characterization of some have revealed their involvement in floral meristem establishment, floral organ growth, sporogenesis, meiosis, microsporogenesis, and pollen maturation. These genes encode a plethora of proteins, ranging from transcriptional regulators to enzymes. This review will focus on the regulatory networks that control male reproductive development, starting from flower development and ending with anther dehiscence, with a focus on transcription factors and some of their notable target genes.

Transcription Factors and Their Regulatory Roles in the Male Gametophyte Development of Flowering Plants

Male gametophyte development in plants relies on the functions of numerous genes, whose expression is regulated by transcription factors (TFs), non-coding RNAs, hormones, and diverse environmental stresses. Several excellent reviews are available that address the genes and enzymes associated with male gametophyte development, especially pollen wall formation. Growing evidence from genetic studies, transcriptome analysis, and gene-by-gene studies suggests that TFs coordinate with epigenetic machinery to regulate the expression of these genes and enzymes for the sequential male gametophyte development. However, very little summarization has been performed to comprehensively review their intricate regulatory roles and discuss their downstream targets and upstream regulators in this unique process. In the present review, we highlight the research progress on the regulatory roles of TF families in the male gametophyte development of flowering plants. The transcriptional regulation, epigenetic control, and other regulators of TFs involved in male gametophyte development are also addressed.

Single-Cell Transcriptome Atlas and Regulatory Dynamics in Developing Cotton Anthers

Plant anthers are composed of different specialized cell types with distinct roles in plant reproduction. High temperature (HT) stress causes male sterility, resulting in crop yield reduction. However, the spatial expression atlas and regulatory dynamics during anther development and in response to HT remain largely unknown. Here, the first single-cell transcriptome atlas and chromatin accessibility survey in cotton anther are established, depicting the specific expression and epigenetic landscape of each type of cell in anthers. The reconstruction of meiotic cells, tapetal cells, and middle layer cell developmental trajectories not only identifies novel expressed genes, but also elucidates the precise degradation period of middle layer and reveals a rapid function transition of tapetal cells during the tetrad stage. By applying HT, heterogeneity in HT response is shown among cells of anthers, with tapetal cells responsible for pollen wall synthesis are most sensitive to HT. Specifically, HT shuts down the chromatin accessibility of genes specifically expressed in the tapetal cells responsible for pollen wall synthesis, such as QUARTET 3 (QRT3) and CYTOCHROME P450 703A2 (CYP703A2), resulting in a silent expression of these genes, ultimately leading to abnormal pollen wall and male sterility. Collectively, this study provides substantial information on anthers and provides clues for heat-tolerant crop creation.

An affordable and convenient diagnostic marker to identify male and female hop plants

Hop production utilizes exclusively female plants, whereas male plants only serve to generate novel variation within breeding programs through crossing. Currently, hop lacks a rapid and accurate diagnostic marker to determine whether plants are male or female. Without a diagnostic marker, breeding programs may take 1-2 years to determine the sex of new seedlings. Previous research on sex-linked markers was restricted to specific populations or breeding programs and therefore had limited transferability or suffered from low scalability. A large collection of 765 hop genotypes with known sex phenotypes, genotyping-by-sequencing, and genome-wide association mapping revealed a highly significant marker on the sex chromosome (LOD score = 208.7) that predicted sex within our population with 96.2% accuracy. In this study, we developed a PCR allele competitive extension (PACE) assay for the diagnostic SNP and tested three quick DNA extraction methodologies for rapid, high-throughput genotyping. Additionally, the marker was validated in a separate population of 94 individuals from 15 families from the USDA-ARS hop breeding program in Prosser, WA with 96% accuracy. This diagnostic marker is located in a gene predicted to encode the basic helix-loop-helix transcription factor protein, a family of proteins that have been previously implicated in male sterility in a variety of plant species, which may indicate a role in determining hop sex. The marker is diagnostic, accurate, affordable, and highly scalable and has the potential to improve efficiency in hop breeding.

Identification, evolution, and expression of GDSL-type Esterase/Lipase (GELP) gene family in three cotton species: a bioinformatic analysis

BACKGROUND

GDSL esterase/lipases (GELPs) play important roles in plant growth, development, and response to biotic and abiotic stresses. Presently, an extensive and in-depth analysis of GELP family genes in cotton is still not clear enough, which greatly limits the further understanding of cotton GELP function and regulatory mechanism.

RESULTS

A total of 389 GELP family genes were identified in three cotton species of Gossypium hirsutum (193), G. arboreum (97), and G. raimondii (99). These GELPs could be classified into three groups and eight subgroups, with the GELPs in same group to have similar gene structures and conserved motifs. Evolutionary event analysis showed that the GELP family genes tend to be diversified at the spatial dimension and certain conservative at the time dimension, with a trend of potential continuous expansion in the future. The orthologous or paralogous GELPs among different genomes/subgenomes indicated the inheritance from genome-wide duplication during polyploidization, and the paralogous GELPs were derived from chromosomal segment duplication or tandem replication. GELP genes in the A/D subgenome underwent at least three large-scale replication events in the evolutionary process during the period of 0.6-3.2 MYA, with two large-scale evolutionary events between 0.6-1.8 MYA that were associated with tetraploidization, and the large-scale duplication between 2.6-9.1 MYA that occurred during diploidization. The cotton GELPs indicated diverse expression patterns in tissue development, ovule and fiber growth, and in response to biotic and abiotic stresses, combining the existing cis-elements in the promoter regions, suggesting the GELPs involvements of functions to be diversification and of the mechanisms to be a hormone-mediated manner.

CONCLUSIONS

Our results provide a systematic and comprehensive understanding the function and regulatory mechanism of cotton GELP family, and offer an effective reference for in-depth genetic improvement utilization of cotton GELPs.

Molecular Marker-Assisted Mapping, Candidate Gene Identification, and Breeding in Melon (Cucumis melo L.): A Review

Melon (Cucumis melo L.) is an important crop that is cultivated worldwide for its fleshy fruit. Understanding the genetic basis of a plant's qualitative and quantitative traits is essential for developing consumer-favored varieties. This review presents genetic and molecular advances related to qualitative and quantitative phenotypic traits and biochemical compounds in melons. This information guides trait incorporation and the production of novel varieties with desirable horticultural and economic characteristics and yield performance. This review summarizes the quantitative trait loci, candidate genes, and development of molecular markers related to plant architecture, branching patterns, floral attributes (sex expression and male sterility), fruit attributes (shape, rind and flesh color, yield, biochemical compounds, sugar content, and netting), and seed attributes (seed coat color and size). The findings discussed in this review will enhance demand-driven breeding to produce cultivars that benefit consumers and melon breeders.

Carbohydrate metabolism and cytology of S-type cytoplasmic male sterility in wheat

Introduction

Cytoplasmic male sterility (CMS) is an important tool for hybrid heterosis utilization. However, the underlying mechanisms still need to be discovered. An adequate supply of nutrients is necessary for anther development; pollen abortion would occur if the metabolism of carbohydrates were hampered.

Methods

In order to better understand the relationship between carbohydrate metabolism disorder and pollen abortion in S-CMS wheat, the submicroscopic structure of wheat anthers was observed using light microscopy and transmission electron microscopy; chloroplast proteome changes were explored by comparative proteomic analysis; sugar measuring and enzyme assays were performed; and the expression patterns of carbohydrate metabolism-related genes were studied using quantitative real-time PCR (qRT-PCR) method.

Results

These results indicated that the anther and microspore in S-CMS wheat underwent serious structural damage, including premature tapetum degeneration, nutritional shortage, pollen wall defects, and pollen grain malformations. Furthermore, the number of chloroplasts in the anthers of S-CMS lines decreased significantly, causing abnormal carbohydrate metabolism, and disintegration of osmiophilic granules and thylakoids. Meanwhile, some proteins participating in the Calvin cycle and carbohydrate metabolism were abnormally expressed in the chloroplasts of the S-CMS lines, which might lead to chloroplast dysfunction. Additionally, several key enzymes and genes related to carbohydrate metabolism were significantly inhibited in S-CMS.

Discussion

Based on these results, we proposed a carbohydrate metabolism pathway for anther abortion in S-type cytoplasmic male sterility, which would encourage further exploration of the pollen abortion mechanisms for CMS wheat.

Ethylene produced in carpel primordia controls CmHB40 expression to inhibit stamen development

Sex determination evolved to control the development of unisexual flowers. In agriculture, it conditions how plants are cultivated and bred. We investigated how female flowers develop in monoecious cucurbits. We discovered in melon, Cucumis melo, a mechanism in which ethylene produced in the carpel is perceived in the stamen primordia through spatially differentially expressed ethylene receptors. Subsequently, the CmEIN3/CmEIL1 ethylene signalling module, in stamen primordia, activates the expression of CmHB40, a transcription factor that downregulates genes required for stamen development and upregulates genes associated with organ senescence. Investigation of melon genetic biodiversity revealed a haplotype, originating in Africa, altered in EIN3/EIL1 binding to CmHB40 promoter and associated with bisexual flower development. In contrast to other bisexual mutants in cucurbits, CmHB40 mutations do not alter fruit shape. By disentangling fruit shape and sex-determination pathways, our work opens up new avenues in plant breeding.

Genome-Wide Identification and Expression Analysis of the bHLH Transcription Factor Family in Wintersweet (Chimonanthus praecox)

Wintersweet (Chimonanthus praecox (L.) Link, Calycanthaceae) is an esteemed ornamental flowering shrub known for its distinct blooming period in winter, vibrant color petals, and captivating floral fragrance. Basic helix-loop-helix (bHLH) transcription factors (TFs) play pivotal roles as key regulators in secondary metabolites biosynthesis, growth, and development in plants. However, the systematic analysis of the bHLH family members and their role in the regulation of floral traits in Wintersweet remains insufficiently understood. To bridge this knowledge gap, we conducted a comprehensive genome-wide analysis of the C. praecox bHLH (CpbHLH) gene family, identifying a total of 131 CpbHLH genes across 11 chromosomes. Phylogenetic analysis classified these CpbHLH genes into 23 subfamilies, wherein most members within the same subfamily exhibited analogous intron/exon patterns and motif composition. Moreover, the expansion of the CpbHLH gene family was primarily driven by segmental duplication, with duplicated gene pairs experiencing purifying selection during evolution. Transcriptomic analysis revealed diverse expression patterns of CpbHLH genes in various tissues and distinct stages of Wintersweet flower development, thereby suggesting their involvement in a diverse array of physiological processes. Furthermore, yeast 2-hybrid assay demonstrated interaction between CpbHLH25 and CpbHLH59 (regulators of floral scent and color) as well as with CpbHLH112 and CpMYB2, suggesting potential coordinately regulation of secondary metabolites biosynthesis in Wintersweet flowers. Collectively, our comprehensive analysis provides valuable insights into the structural attributes, evolutionary dynamics, and expression profiles of the CpbHLH gene family, laying a solid foundation for further explorations of the multifaceted physiological and molecular roles of bHLH TFs in Wintersweet.

A single-nucleotide substitution of CjTKPR1 determines pollen production in the gymnosperm plant Cryptomeria japonica

Pollinosis, also known as pollen allergy or hay fever, is a global problem caused by pollen produced by various plant species. The wind-pollinated Japanese cedar (Cryptomeria japonica) is the largest contributor to severe pollinosis in Japan, where increasing proportions of people have been affected in recent decades. The MALE STERILITY 4 (MS4) locus of Japanese cedar controls pollen production, and its homozygous mutants (ms4/ms4) show abnormal pollen development after the tetrad stage and produce no mature pollen. In this study, we narrowed down the MS4 locus by fine mapping in Japanese cedar and found TETRAKETIDE α-PYRONE REDUCTASE 1 (TKPR1) gene in this region. Transformation experiments using Arabidopsis thaliana showed that single-nucleotide substitution ("T" to "C" at 244-nt position) of CjTKPR1 determines pollen production. Broad conservation of TKPR1 beyond plant division could lead to the creation of pollen-free plants not only for Japanese cedar but also for broader plant species.

Genome-Wide Identification and Expression Profiling of Cytochrome P450 Monooxygenase Superfamily in Foxtail Millet

The cytochrome P450 monooxygenases (CYP450) are the largest enzyme family in plant metabolism and widely involved in the biosynthesis of primary and secondary metabolites. Foxtail millet (Setaria italica (L.) P. Beauv) can respond to abiotic stress through a highly complex polygene regulatory network, in which the SiCYP450 family is also involved. Although the CYP450 superfamily has been systematically studied in a few species, the research on the CYP450 superfamily in foxtail millet has not been completed. In this study, three hundred and thirty-one SiCYP450 genes were identified in the foxtail millet genome by bioinformatics methods, which were divided into four groups, including forty-six subgroups. One hundred and sixteen genes were distributed in thirty-three tandem duplicated gene clusters. Chromosome mapping showed that SiCYP450 was distributed on seven chromosomes. In the SiCYP450 family of foxtail millet, 20 conserved motifs were identified. Cis-acting elements in the promoter region of SiCYP450 genes showed that hormone response elements were found in all SiCYP450 genes. Of the three hundred and thirty-one SiCYP450 genes, nine genes were colinear with the Arabidopsis thaliana genes. Two hundred SiCYP450 genes were colinear with the Setaria viridis genes, including two hundred and forty-five gene duplication events. The expression profiles of SiCYP450 genes in different organs and developmental stages showed that SiCYP450 was preferentially expressed in specific tissues, and many tissue-specific genes were identified, such as SiCYP75B6, SiCYP96A7, SiCYP71A55, SiCYP71A61, and SiCYP71A62 in the root, SiCYP78A1 and SiCYP94D9 in leaves, and SiCYP78A6 in the ear. The RT-PCR data showed that SiCYP450 could respond to abiotic stresses, ABA, and herbicides in foxtail millet. Among them, the expression levels of SiCYP709B4, SiCYP71A11, SiCYP71A14, SiCYP78A1, SiCYP94C3, and SiCYP94C4 were significantly increased under the treatment of mesotrione, florasulam, nicosulfuron, fluroxypyr, and sethoxydim, indicating that the same gene might respond to multiple herbicides. The results of this study will help reveal the biological functions of the SiCYP450 family in development regulation and stress response and provide a basis for molecular breeding of foxtail millet.

Biosynthesis and transport of pollen coat precursors in angiosperms

The pollen coat is a hydrophobic mixture on the pollen grain surface, which plays an important role in protecting male gametes from various environmental stresses and microorganism attacks, and in pollen-stigma interactions during pollination in angiosperms. An abnormal pollen coat can result in humidity-sensitive genic male sterility (HGMS), which can be used in two-line hybrid crop breeding. Despite the crucial functions of the pollen coat and the application prospect of its mutants, few studies have focused on pollen coat formation. In this Review, the morphology, composition and function of different types of pollen coat are assessed. On the basis of the ultrastructure and development process of the anther wall and exine found in rice and Arabidopsis, the genes and proteins involved in the biosynthesis of pollen coat precursors and the possible transport and regulation process are sorted. Additionally, current challenges and future perspectives, including potential strategies utilizing HGMS genes in heterosis and plant molecular breeding, are highlighted.

Comparative Transcriptome Analysis Reveals a Potential Regulatory Network for Ogura Cytoplasmic Male Sterility in Cabbage (Brassica oleracea L.)

Ogura cytoplasmic male sterility (CMS) lines are widely used breeding materials in cruciferous crops and play important roles in heterosis utilization; however, the sterility mechanism remains unclear. To investigate the microspore development process and gene expression changes after the introduction of orf138 and Rfo, cytological observation and transcriptome analysis were performed using a maintainer line, an Ogura CMS line, and a restorer line. Semithin sections of microspores at different developmental stages showed that the degradation of tapetal cells began at the tetrad stage in the Ogura CMS line, while it occurred at the bicellular microspore stage to the tricellular microspore stage in the maintainer and restorer lines. Therefore, early degradation of tapetal cells may be the cause of pollen abortion. Transcriptome analysis results showed that a total of 1287 DEGs had consistent expression trends in the maintainer line and restorer line, but were significantly up- or down-regulated in the Ogura CMS line, indicating that they may be closely related to pollen abortion. Functional annotation showed that the 1287 core DEGs included a large number of genes related to pollen development, oxidative phosphorylation, carbohydrate, lipid, and protein metabolism. In addition, further verification elucidated that down-regulated expression of genes related to energy metabolism led to decreased ATP content and excessive ROS accumulation in the anthers of Ogura CMS. Based on these results, we propose a transcriptome-mediated induction and regulatory network for cabbage Ogura CMS. Our research provides new insights into the mechanism of pollen abortion and fertility restoration in Ogura CMS.

Whole-transcriptome analyses identify key differentially expressed mRNAs, lncRNAs, and miRNAs associated with male sterility in watermelon

Male sterility is a valuable trait for watermelon breeding, as watermelon hybrids exhibit obvious heterosis. However, the underlying regulatory mechanism is still largely unknown, especially regarding the related non-coding genes. In the present study, approximately 1035 differentially expressed genes (DEGs), as well as 80 DE-lncRNAs and 10 DE-miRNAs, were identified, with the overwhelming majority down-regulated in male-sterile floral buds. Enrichment analyses revealed that the general phenylpropanoid pathway as well as its related metabolisms was predicted to be altered in a mutant compared to its fertile progenitor. Meanwhile, the conserved genetic pathway DYT1-TDF1-AMS-MS188-MS1, as well as the causal gene ClAMT1 for the male-sterile mutant Se18, was substantially disrupted during male reproductive development. In addition, some targets of the key regulators AMS and MS188 in tapetum development were also down-regulated at a transcriptional level, such as ABCG26 (Cla004479), ACOS5 (Cla022956), CYP703A2 (Cla021151), PKSA (Cla021099), and TKPR1 (Cla002563). Considering lncRNAs may act as functional endogenous target mimics of miRNAs, competitive endogenous RNA networks were subsequently constructed, with the most complex one containing three DE-miRNAs, two DE-lncRNAs, and 21 DEGs. Collectively, these findings not only contribute to a better understanding of genetic regulatory networks underlying male sterility in watermelon, but also provide valuable candidates for future research.

Rice anther tapetum: a vital reproductive cell layer for sporopollenin biosynthesis and pollen exine patterning

The tapetum is the innermost layer of the four layers of the rice anther that provides protection and essential nutrients to pollen grain development and delivers precursors for pollen exine formation. The tapetum has a key role in the normal development of pollen grains and tapetal programmed cell death (PCD) that is linked with sporopollenin biosynthesis and transport. Recently, many genes have been identified that are involved in tapetum formation in rice and Arabidopsis. Genetic mutation in PCD-associated genes could affect normal tapetal PCD, which finally leads to aborted pollen grains and male sterility in rice. In this review, we discuss the most recent research on rice tapetum development, including genomic, transcriptomic and proteomic studies. Furthermore, tapetal PCD, sporopollenin biosynthesis, ROS activity for tapetum function and its role in male reproductive development are discussed in detail. This will improve our understanding of the role of the tapetum in male fertility using rice as a model system, and provide information that can be applied in rice hybridization and that of other major crops.

The full-length Auxin Response Factor 8 isoform ARF8.1 controls pollen cell wall formation and directly regulates TDF1, AMS and MS188 expression

Auxin Response Factor 8 plays a key role in late stamen development: its splice variants ARF8.4 and ARF8.2 control stamen elongation and anther dehiscence. Here, we characterized the role of ARF8 isoforms in pollen fertility. By phenotypic and ultrastructural analysis of arf8-7 mutant stamens, we found defects in pollen germination and viability caused by alterations in exine structure and pollen coat deposition. Furthermore, tapetum degeneration, a prerequisite for proper pollen wall formation, is delayed in arf8-7 anthers. In agreement, the genes encoding the transcription factors TDF1, AMS, MS188 and MS1, required for exine and pollen coat formation, and tapetum development, are downregulated in arf8-7 stamens. Consistently, the sporopollenin content is decreased, and the expression of sporopollenin synthesis/transport and pollen coat protein biosynthetic genes, regulated by AMS and MS188, is reduced. Inducible expression of the full-length isoform ARF8.1 in arf8-7 inflorescences complements the pollen (and tapetum) phenotype and restores the expression of the above transcription factors. Chromatin immunoprecipitation-quantitative polymerase chain reaction assay revealed that ARF8.1 directly targets the promoters of TDF1, AMS and MS188. In conclusion, the ARF8.1 isoform controls pollen and tapetum development acting directly on the expression of TDF1, AMS and MS188, which belong to the pollen/tapetum genetic pathway.

Genome-wide identification and expression analysis of the bHLH gene family in passion fruit (Passiflora edulis) and its response to abiotic stress

Passion fruit is a tropical fruit crop with significant agricultural, economic and ornamental values. The growth and development of passion fruit are greatly affected by climatic conditions. In plants, the basic helix-loop-helix (bHLH) gene family plays essential roles in the floral organ and fruit development, as well as stress response. However, the characteristics and functions of the bHLH genes of passion fruit remain unclear. Here, 138 passion fruit bHLH members were identified and classified into 20 subfamilies. The structural analysis illustrated that PebHLH proteins of the specific subfamily are relatively conserved. Collinearity analysis indicated that the expansion of the PebHLH gene family mainly took place by segmental duplication, and the structural diversity of duplicated genes might contribute to their functional diversity. PebHLHs, which potentially regulate different floral organ and fruit development, were further screened out, and many of these genes were differentially expressed under various stress treatments. The co-presence of different cis-regulatory elements involved in developmental regulation, hormone and stress responses in the promoter regions of PebHLHs might be closely related to their diverse regulatory roles. Overall, this study will be helpful for further functional investigation of PebHLHs and provides clues for improvement of the passion fruit breeding.

A Systematic Investigation of Lipid Transfer Proteins Involved in Male Fertility and Other Biological Processes in Maize

Plant lipid transfer proteins (LTPs) play essential roles in various biological processes, including anther and pollen development, vegetative organ development, seed development and germination, and stress response, but the research progress varies greatly among Arabidopsis, rice and maize. Here, we presented a preliminary introduction and characterization of the whole 65 LTP genes in maize, and performed a phylogenetic tree and gene ontology analysis of the LTP family members in maize. We compared the research progresses of the reported LTP genes involved in male fertility and other biological processes in Arabidopsis and rice, and thus provided some implications for their maize orthologs, which will provide useful clues for the investigation of LTP transporters in maize. We predicted the functions of LTP genes based on bioinformatic analyses of their spatiotemporal expression patterns by using RNA-seq and qRT-PCR assays. Finally, we discussed the advances and challenges in substrate identification of plant LTPs, and presented the future research directions of LTPs in plants. This study provides a basic framework for functional research and the potential application of LTPs in multiple plants, especially for male sterility research and application in maize.

Comprehensive Insight into Tapetum-Mediated Pollen Development in Arabidopsis thaliana

In flowering plants, pollen development is a key process that is essential for sexual reproduction and seed set. Molecular and genetic studies indicate that pollen development is coordinatedly regulated by both gametophytic and sporophytic factors. Tapetum, the somatic cell layer adjacent to the developing male meiocytes, plays an essential role during pollen development. In the early anther development stage, the tapetal cells secrete nutrients, proteins, lipids, and enzymes for microsporocytes and microspore development, while initiating programmed cell death to provide critical materials for pollen wall formation in the late stage. Therefore, disrupting tapetum specification, development, or function usually leads to serious defects in pollen development. In this review, we aim to summarize the current understanding of tapetum-mediated pollen development and illuminate the underlying molecular mechanism in Arabidopsis thaliana.

Transcriptome and metabolome reveal the effects of three canopy types on the flavonoids and phenolic acids in 'Merlot' (Vitis vinifera L.) berry pericarp

The flavonoids and phenolic acids in grape berries greatly influence the quality of wine. Various methods are used to shape and prune grapevines, but their effects on the flavonoids and phenolic acids remain unclear. The flavonoids and phenolic acids in the berry pericarps from grapevines pruned using three types of leaf canopy, namely, V-shaped, T-shaped, and vertical shoot-positioned (VSP) canopies, were compared in this study. Results showed that the V-shaped canopy was more favorable for the accumulation of flavonoids and phenolic acids. Transcriptome and metabolome analyses revealed that the differentially expressed genes (DEGs) and differentially regulated metabolites (DRMs) were significantly enriched in the flavonoid and phenylpropanoid biosynthesis pathways. A total of 96 flavonoids and 32 phenolic acids were detected among the DRMs. Their contents were higher in the V-shaped canopy than in the T-shaped and VSP canopies. Conjoint analysis of transcriptome and metabolome showed that nine DEGs (e.g., cytochrome P450 98A9 and 98A2) were significantly correlated to nine phenolic acids (e.g., gentisic acid and neochlorogenic acid) and three genes (i.e., chalcone isomerase, UDP-glycosyltransferase 88A1, and caffeoyl-CoA O-methyltransferase) significantly correlated to 15 flavonoids (e.g., baimaside and tricin-7-O-rutinoside). These genes may be involved in the regulation of various flavonoids and phenolic acids in grape berries, but their functions need validation. This study provides novel insights into the effects of leaf canopy on flavonoids and phenolic acids in the skin of grape berries and reveals the potential regulatory networks involved in this phenomenon.

Comparative transcriptome analysis provides insight into the important pathways and key genes related to the pollen abortion in the thermo-sensitive genic male sterile line 373S in Brassica napus L

The thermo-sensitive genic male sterility (TGMS) system plays a key role in the production of two-line hybrids in rapeseed (Brassica napus). To uncover key cellular events and genetic regulation associated with TGMS, a combined study using cytological methods and RNA-sequencing analysis was conducted for the rapeseed TGMS line 373S. Cytological studies showed that microspore cytoplasm of 373S plants was condensed, the microspore nucleus was degraded at an early stage, the exine was irregular, and the tapetum developed abnormally, eventually leading to male sterility. RNA-sequencing analysis identified 430 differentially expressed genes (298 upregulated and 132 downregulated) between the fertile and sterile samples. Gene ontology analysis demonstrated that the most highly represented biological processes included sporopollenin biosynthetic process, pollen exine formation, and extracellular matrix assembly. Kyoto encyclopedia of genes and genomes analysis indicated that the enriched pathways included amino acid metabolism, carbohydrate metabolism, and lipid metabolism. Moreover, 26 transcript factors were identified, which may be associated with abnormal tapetum degeneration and exine formation. Subsequently, 19 key genes were selected, which are considered to regulate pollen development and even participate in pollen exine formation. Our results will provide important insight into the molecular mechanisms underlying TGMS in rapeseed.

Global transcriptome analysis reveals potential genes associated with genic male sterility of rapeseed (Brassica napus L.)

Rapeseed is the third leading source of edible oil in the world. Genic male sterility (GMS) lines provide crucial material for harnessing heterosis for rapeseed. GMS lines have been widely used successfully for rapeseed hybrid production. The physiological and molecular mechanism of pollen development in GMS lines of rapeseed (Brassica napus L.) need to be determined for the creation of hybrids and cultivation of new varieties. However, limited studies have focused on systematically mining genes that regulate the pollen development of GMS lines in B. napus. In the present study, to determine the stage at which pollen development begins to show abnormality in the GMS lines, we performed semi-thin section analysis of the anthers with five pollen development stages. The results indicated that the abnormal pollen development in DGMS lines might start at the meiotic stage, and abnormal pollen development in RGMS lines probably occurred before the tetrad stage. To investigate the critical genes and pathways involved in pollen development in GMS lines, we constructed and sequenced 24 transcriptome libraries for the flower buds from the fertile and sterile lines of two recessive GMS (RGMS) lines (6251AB and 6284AB) and two dominant GMS (DGMS) lines (4001AB and 4006AB). A total of 23,554 redundant DEGs with over two-fold change between sterile and fertile lines were obtained. A total of 346 DEGs were specifically related to DGMS, while 1,553 DEGs were specifically related to RGMS. A total of 1,545 DEGs were shared between DGMS and RGMS. And 253 transcription factors were found to be differentially expressed between the sterile and fertile lines of GMS. In addition, 6,099 DEGs possibly related to anther, pollen, and microspore development processes were identified. Many of these genes have been reported to be involved in anther and microspore developmental processes. Several DEGs were speculated to be key genes involved in the regulation of fertility. Three differentially expressed genes were randomly selected and their expression levels were verified by quantitative PCR (qRT-PCR). The results of qRT-PCR largely agreed with the transcriptome sequencing results. Our findings provide a global view of genes that are potentially involved in GMS occurrence. The expression profiles and function analysis of these DEGs were provided to expand our understanding of the complex molecular mechanism in pollen and sterility development in B. napus.

TaEXPB5 functions as a gene related to pollen development in thermo-sensitive male-sterility wheat with Aegilops kotschyi cytoplasm

The thermo-sensitive cytoplasmic male-sterility line with Aegilops kotschyi cytoplasm (K-TCMS) is completely male sterile under low temperature (< 18 ℃) during Zadoks growth stages 45-52, whereas its fertility can be restored under hot temperature (≥ 20 ℃). The K-TCMS line may facilitate hybrid breeding and hybrid wheat production. Therefore, to elucidate the molecular mechanisms of its male sterility/fertility conversion, we conducted the association analysis of proteins and transcript expression to screen fertility related genes using RNA-seq, iTRAQ, and PRM-based assay. A gene encoding expansin protein in wheat, TaEXPB5, was isolated in K-TCMS line KTM3315A, which upregulated expression in the fertility anthers. Subcellular localization analysis suggested that TaEXPB5 protein localized to nucleus and cell wall. The silencing of TaEXPB5 displayed pollen abortion and the declination of fertility. Further, cytological investigation indicated that the silencing of TaEXPB5 induced the early degradation of tapetum and abnormal development of pollen wall. These results implied that TaEXPB5 may be essential for anther or pollen development and male fertility of KTM3315A. These findings provide a novel insight into molecular mechanism of fertility conversion for thermo-sensitive cytoplasmic male-sterility wheat, and contribute to the molecular breeding of hybrid wheat in the future.

Sporophytic control of pollen meiotic progression is mediated by tapetum expression of ABORTED MICROSPORES

Pollen development is dependent on the tapetum, a sporophytic anther cell layer surrounding the microspores that functions in pollen wall formation but is also essential for meiosis-associated development. There is clear evidence of crosstalk and co-regulation between the tapetum and microspores, but how this is achieved is currently not characterized. ABORTED MICROSPORES (AMS), a tapetum transcription factor, is important for pollen wall formation, but also has an undefined role in early pollen development. We conducted a detailed investigation of chromosome behaviour, cytokinesis, radial microtubule array (RMA) organization, and callose formation in the ams mutant. Early meiosis initiates normally in ams, shows delayed progression after the pachytene stage, and then fails during late meiosis, with disorganized RMA, defective cytokinesis, abnormal callose formation, and microspore degeneration, alongside abnormal tapetum development. Here, we show that selected meiosis-associated genes are directly repressed by AMS, and that AMS is essential for late meiosis progression. Our findings indicate that AMS has a dual function in tapetum-meiocyte crosstalk by playing an important regulatory role during late meiosis, in addition to its previously characterized role in pollen wall formation. AMS is critical for RMA organization, callose deposition, and therefore cytokinesis, and is involved in the crosstalk between the gametophyte and sporophytic tissues, which enables synchronous development of tapetum and microspores.

The methyl-CpG-binding domain family member PEM1 is essential for Ubisch body formation and pollen exine development in rice

Pollen exine is composed of finely-organized nexine, bacula and tectum, and is crucial for pollen viability and function. Pollen exine development involves a complicated molecular network that coordinates the interaction between pollen and tapetal cells, as well as the biosynthesis, transport and assembly of sporopollenin precursors; however, our understanding of this network is very limited. Here, we report the roles of PEM1, a member of methyl-CpG-binding domain family, in rice pollen development. PEM1 expressed constitutively and, in anthers, its expression was detectable in tapetal cells and pollen. This predicted PEM1 protein of 240 kDa had multiple epigenetic-related domains. pem1 mutants exhibited abnormal Ubisch bodies, delayed exine occurrence and, finally, defective exine, including invisible bacula, amorphous and thickened nexine and tectum layer structures, and also had the phenotype of increased anther cuticle. The mutation in PEM1 did not affect the timely degradation of tapetum. Lipidomics revealed much higher wax and cutin contents in mutant anthers than in wild-type. Accordingly, this mutation up-regulated the expression of a set of genes implicated in transcriptional repression, signaling and diverse metabolic pathways. These results indicate that PEM1 mediates Ubisch body formation and pollen exine development mainly by negatively modulating the expression of genes. Thus, the PEM1-mediated molecular network represents a route for insights into mechanisms underlying pollen development. PEM1 may be a master regulator of pollen exine development.

Identification of long non-coding RNAs and microRNAs involved in anther development in the tropical Camellia oleifera

BACKGROUND

Explored the molecular science of anther development is important for improving productivity and overall yield of crops. Although the role of regulatory RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), in regulating anther development has been established, their identities and functions in Camellia oleifera, an important industrial crop, have yet not been clearly explored. Here, we report the identification and characterization of genes, lncRNAs and miRNAs during three stages of the tropical C. oleifera anther development by single-molecule real-time sequencing, RNA sequencing and small RNA sequencing, respectively.

RESULTS

These stages, viz. the pollen mother cells stage, tetrad stage and uninucleate pollen stage, were identified by analyzing paraffin sections of floral buds during rapid expansion periods. A total of 18,393 transcripts, 414 putative lncRNAs and 372 miRNAs were identified, of which 5,324 genes, 115 lncRNAs, and 44 miRNAs were differentially accumulated across three developmental stages. Of these, 44 and 92 genes were predicted be regulated by 37 and 30 differentially accumulated lncRNAs and miRNAs, respectively. Additionally, 42 differentially accumulated lncRNAs were predicted as targets of 27 miRNAs. Gene ontology enrichment indicated that potential target genes of lncRNAs were enriched in photosystem II, regulation of autophagy and carbohydrate phosphatase activity, which are essential for anther development. Functional annotation of genes targeted by miRNAs indicated that they are relevant to transcription and metabolic processes that play important roles in microspore development. An interaction network was built with 2 lncRNAs, 6 miRNAs and 10 mRNAs. Among these, miR396 and miR156 family were up-regulated, while their targets, genes (GROWTH REGULATING FACTORS and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes) and lncRNAs, were down-regulated. Further, the trans-regulated targets of these lncRNAs, like wall-associated kinase2 and phosphomannose isomerase1, are involved in pollen wall formation during anther development.

CONCLUSIONS

This study unravels lncRNAs, miRNAs and miRNA-lncRNA-mRNA networks involved in development of anthers of the tropical C. oleifera lays a theoretical foundation for further elucidation of regulatory roles of lncRNAs and miRNAs in anther development.

Arabidopsis TWISTED DWARF1 regulates stamen elongation by differential activation of ABCB1,19-mediated auxin transport

Despite clear evidence that a local accumulation of auxin is likewise critical for male fertility, much less is known about the components that regulate auxin-controlled stamen development. In this study, we analyzed physiological and morphological parameters in mutants of key players of ABCB-mediated auxin transport, and spatially and temporally dissected their expression on the protein level as well as auxin fluxes in the Arabidopsis stamens. Our analyses revealed that the FKBP42, TWISTED DWARF1 (TWD1), promotes stamen elongation and, to a lesser extent, anther dehiscence, as well as pollen maturation, and thus is required for seed development. Most of the described developmental defects in twd1 are shared with the abcb1 abcb19 mutant, which can be attributed to the fact that TWD1-as a described ABCB chaperone-is a positive regulator of ABCB1- and ABCB19-mediated auxin transport. However, reduced stamen number was dependent on TWD1 but not on investigated ABCBs, suggesting additional players downstream of TWD1. We predict an overall housekeeping function for ABCB1 during earlier stages, while ABCB19 seems to be responsible for the key event of rapid elongation at later stages of stamen development. Our data indicate that TWD1 controls stamen development by differential activation of ABCB1,19-mediated auxin transport in the stamen.

The Transcription Factors TaTDRL and TaMYB103 Synergistically Activate the Expression of TAA1a in Wheat, Which Positively Regulates the Development of Microspore in Arabidopsis

Pollen fertility plays an important role in the application of heterosis in wheat (Triticum aestivum L.). However, the key genes and mechanisms underlying pollen abortion in K-type male sterility remain unclear. TAA1a is an essential gene for pollen development in wheat. Here, we explored the mechanism involved in its transcriptional regulation during pollen development, focusing on a 1315-bp promoter region. Several cis-acting elements were identified in the TAA1a promoter, including binding motifs for Arabidopsis thaliana AtAMS and AtMYB103 (CANNTG and CCAACC, respectively). Evolutionary analysis indicated that TaTDRL and TaMYB103 were the T. aestivum homologs of AtAMS and AtMYB103, respectively, and encoded nucleus-localized transcription factors containing 557 and 352 amino acids, respectively. TaTDRL and TaMYB103 were specifically expressed in wheat anthers, and their expression levels were highest in the early uninucleate stage; this expression pattern was consistent with that of TAA1a. Meanwhile, we found that TaTDRL and TaMYB03 directly interacted, as evidenced by yeast two-hybrid and bimolecular fluorescence complementation assays, while yeast one-hybrid and dual-luciferase assays revealed that both TaTDRL and TaMYB103 could bind the TAA1a promoter and synergistically increase its transcriptional activity. Furthermore, TaTDRL-EAR and TaMYB103-EAR transgenic Arabidopsis plants displayed abnormal microspore morphology, reduced pollen viability, and lowered seed setting rates. Additionally, the expression of AtMS2, a TAA1a homolog, was significantly lower in the two repressor lines than in the corresponding overexpression lines or WT plants. In summary, we identified a potential transcriptional regulatory mechanism associated with wheat pollen development.

Genome-Wide Characterization and Analysis of the bHLH Transcription Factor Family in Suaeda aralocaspica, an Annual Halophyte With Single-Cell C4 Anatomy

Basic helix-loop-helix (bHLH) transcription factors play important roles in plant growth, development, metabolism, hormone signaling pathways, and responses to abiotic stresses. However, comprehensive genomic and functional analyses of bHLH genes have not yet been reported in desert euhalophytes. Suaeda aralocaspica, an annual C4 halophyte without Kranz anatomy, presents high photosynthetic efficiency in harsh natural habitats and is an ideal plant for identifying transcription factors involved in stress resistance. In this study, 83 bHLH genes in S. aralocaspica were identified and categorized into 21 subfamilies based on conserved motifs, gene structures, and phylogenetic analysis. Functional annotation enrichment revealed that the majority of SabHLHs were enriched in Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways involved in the response to stress conditions, as transcription factors. A number of cis-acting elements related to plant hormones and stress responses were also predicted in the promoter regions of SabHLHs, which were confirmed by expression analysis under various abiotic stress conditions (NaCl, mannitol, low temperature, ABA, GA3, MeJA, and SA); most were involved in tolerance to drought and salinity. SabHLH169 (076) protein localized in the nucleus was involved in transcriptional activity, and gene expression could be affected by different light qualities. This study is the first comprehensive analysis of the bHLH gene family in S. aralocaspica. These data will facilitate further characterization of their molecular functions in the adaptation of desert plants to abiotic stress.

Comparative transcriptome analysis of resistant and susceptible wheat in response to Rhizoctonia cerealis

BACKGROUND

Sheath blight is an important disease caused by Rhizoctonia cerealis that affects wheat yields worldwide. No wheat varieties have been identified with high resistance or immunity to sheath blight. Understanding the sheath blight resistance mechanism is essential for controlling this disease. In this study, we investigated the response of wheat to Rhizoctonia cerealis infection by analyzing the cytological changes and transcriptomes of common wheat 7182 with moderate sensitivity to sheath blight and H83 with moderate resistance.

RESULTS

The cytological observation showed that the growth of Rhizoctonia cerealis on the surface and its expansion inside the leaf sheath tissue were more rapid in the susceptible material. According to the transcriptome sequencing results, a total of 88685 genes were identified in both materials, including 20156 differentially expressed genes (DEGs) of which 12087 was upregulated genes and 8069 was downregulated genes. At 36 h post-inoculation, compared with the uninfected control, 11498 DEGs were identified in resistant materials, with 5064 downregulated genes and 6434 upregulated genes, and 13058 genes were detected in susceptible materials, with 6759 downregulated genes and 6299 upregulated genes. At 72 h post-inoculation, compared with the uninfected control, 6578 DEGs were detected in resistant materials, with 2991 downregulated genes and 3587 upregulated genes, and 7324 genes were detected in susceptible materials, with 4119 downregulated genes and 3205 upregulated genes. Functional annotation and enrichment analysis showed that the main pathways enriched for the DEGs included biosynthesis of secondary metabolites, carbon metabolism, plant hormone signal transduction, and plant-pathogen interaction. In particular, phenylpropane biosynthesis pathway is specifically activated in resistant variety H83 after infection. Many DEGs also belonged to the MYB, AP2, NAC, and WRKY transcription factor families.

CONCLUSIONS

Thus, we suggest that the normal functioning of plant signaling pathways and differences in the expression of key genes and transcription factors in some important metabolic pathways may be important for defending wheat against sheath blight. These findings may facilitate further exploration of the sheath blight resistance mechanism in wheat and the cloning of related genes.