The PET1-CMS mitochondrial mutation in sunflower is associated with premature programmed cell death and cytochrome c release

Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane

BACKGROUND

Sugarcane is a crucial crop for both sugar and bioethanol production. The nobilization breeding and utilization of wild germplasm have significantly enhanced its productivity. However, the pollen sterility in Saccharum officinarum restricts its role to being a female parent in crosses with Saccharum spontaneum during nobilization breeding, resulting in a narrow genetic basis for modern sugarcane cultivars. Mitochondria, often referred to as the intracellular "energy factories", provide energy for plant life activities, and are also implicated in cytoplasmic male sterility (CMS).

RESULTS

We performed mitochondrial genome assembly and structural analysis of two Saccharum founding species. We discovered that the proportions of repeat sequences are the primary factor contributing to the variations in mitochondrial genome structure and size between the two Saccharum species. Heterologous expression of the mitochondrial chimeric gene ORF113, which is highly expressed in male-sterile S. officinarum flowers, significantly inhibits growth and ATP synthesis in yeast cells, making it a key candidate CMS-related gene in sugarcane. Furthermore, we developed two co-dominant simple sequence repeat (SSR) markers based on the mitochondrial genome, which can effectively distinguish the cytoplasmic types of the two Saccharum species.

CONCLUSION

In this study, we identified structural variants and developed SSR molecular markers in the mitochondrial genomes of both S. officinarum and S. spontaneum. We also identified a novel mitochondrial chimeric ORF as a key candidate CMS-related gene. These findings offer valuable insights into variety identification, genetic resource development, and cross-breeding strategies in sugarcane.

Transcriptomics and metabolomics analyses reveal pollen abortion mechanism in alfalfa early stage male sterile lines

Alfalfa (Medicago sativa L.), a prominent perennial forage in the legume family, is widely cultivated across Europe and America. Given its substantial economic value for livestock, breeding efforts have focused on developing high-yield and high-quality varieties since the discovery of CMS lines. However, progress is restricted by the limitations of existing CMS lines, necessitating the development of new lines and study of the molecular mechanisms underlying pollen abortion. This study investigates early-stage anther development in cytoplasmic male sterile (CMS) alfalfa lines (MSJN1A) in relation to the isotypic maintainer line (MSJN1B). Histological analyses revealed abnormal degradation of tapetal cells post-meiosis in the CMS line. Notably, during the early mononuclear stage, the central vacuoles in the microspores were absent, leading to evident pollen abortion. These findings suggest that pollen abortion in the CMS line is associated with the delayed disintegration of the tapetum and structural anomalies in microspore vacuoles. Non-targeted metabolome sequencing revealed 401 and 405 metabolites at late tetrad and early mononuclear stages of alfalfa, respectively. Among these, 39 metabolites were consistently upregulated, whereas 85 metabolites were downregulated. Differential analysis revealed 45 and 37 unique metabolites at each respective stage. These metabolites were primarily featured in pathways related to energy, phenylpropane, sucrose and starch, and fatty acid metabolism. Integrated analysis demonstrated that differentially expressed genes and differential metabolites were co-enriched in these pathways. Additionally, quantitative real-time PCR and physiological index analysis confirmed downregulation of key genes involved in anther development, illustrating that changes in upstream gene regulation could significantly impact downstream metabolite levels, ultimately influencing pollen fertility. Pollen abortion is related to abnormal phenylpropane metabolism, fatty acid metabolism and starch and sucrose pathway, which provides reference for further research on the causes of pollen abortion of alfalfa.

TaFAR9 and TaFAR10 synergistically regulate fertility conversion of photo-thermo-sensitive genic male sterility lines in wheat by modulating ROS homeostasis

Photo-thermo-sensitive genic male sterility (PTGMS), which exhibits varying fertility levels under different environmental conditions, is a crucial method for heterosis utilization in wheat. However, the mechanisms underlying fertility conversion remain unclear. In the study, three BS type PTGMS lines were analyzed to study fertility conversion characteristics. The results indicated that the fertility conversion occurred during meiosis and was accompanied by an increase in reactive oxygen species (ROS) under a sterile environment. TaFAR9 encoding a novel fatty acyl CoA reductase was identified using transcriptome sequencing. Expression analysis suggested that TaFAR9 was localized in the endoplasmic reticulum (ER), with high expression levels in anthers. Furthermore, the down-regulation of TaFAR9 expression displayed characteristics of male sterility, accompanied by the accumulation of ROS. Cytological analysis revealed abnormal development in the anther and pollen walls of TaFAR9-silenced lines. Additionally, TaFAR9 and TaFAR10 were confirmed to physically interact using molecular docking simulation, yeast two-hybrid, luciferase complementation, and bimolecular fluorescence complementation assays. The reduced expression of TaFAR10 also exhibited male sterility and ROS burst. Moreover, the co-silencing of TaFAR9 and TaFAR10 produced sterility phenotypes that were similar to those observed when silencing TaFAR9 or TaFAR10 individually. Transcriptome analysis suggested that the ROS burst in BSMV: TaFAR9/10 anthers can result in cellular metabolic disorders. These findings indicate that TaFAR9 and TaFAR10 may form heterodimers that synergistically regulate fertility conversion in PTGMS lines by modulating ROS metabolism. And this study offers a fresh insight into the regulatory processes involved in fertility conversion in PTGMS lines.

A developmentally controlled cellular decompartmentalization process executes programmed cell death in the Arabidopsis root cap

Programmed cell death (PCD) is a fundamental cellular process crucial to development, homeostasis, and immunity in multicellular eukaryotes. In contrast to our knowledge on the regulation of diverse animal cell death subroutines, information on execution of PCD in plants remains fragmentary. Here, we make use of the accessibility of the Arabidopsis (Arabidopsis thaliana) root cap to visualize the execution process of developmentally controlled PCD. We identify a succession of selective decompartmentalization events and ion fluxes as part of the terminal differentiation program that is orchestrated by the NO APICAL MERISTEM, ARABIDOPSIS THALIANA ACTIVATING FACTOR, CUP-SHAPED COTYLEDON (NAC) transcription factor SOMBRERO. Surprisingly, the breakdown of the large central vacuole is a relatively late and variable event, preceded by an increase of intracellular calcium levels and acidification, release of mitochondrial matrix proteins, leakage of nuclear and endoplasmic reticulum lumina, and release of fluorescent membrane reporters into the cytosol. In analogy to animal apoptosis, the plasma membrane remains impermeable for proteins during and after PCD execution. Elevated intracellular calcium levels and acidification are sufficient to trigger cell death execution specifically in terminally differentiated root cap cells, suggesting that these ion fluxes act as PCD-triggering signals. This detailed information on the cellular processes occurring during developmental PCD in plants is a pivotal prerequisite for future research into the molecular mechanisms of cell death execution.

Origin of CMS-PET1 cytotype in cultivated sunflower: A new insight

The vast majority of commercial sunflower hybrids worldwide are produced using cytoplasmic male sterility (CMS) of the PET1 type, resulting from the interspecific hybridization of Helianthus petiolaris with Helianthus annuus. Due to the fact that CMS-PET1 was not previously detected in wild sunflower, it was believed that this cytotype could arise during interspecific hybridization and is specific solely for cultivated sunflower. In this study, the open reading frame, orfH522, associated with the CMS-PET1 phenotype, was revealed for the first time in the 3'-flanking region of the mitochondrial atpA gene in wild H. annuus. An analysis of whole genome data from 1089 accessions showed that the frequency of occurrence of CMS-orfH522 in wild H. annuus populations is 3.58%, while in wild H. petiolaris populations, it is 1.26%. In general, the analysis demonstrated that PET1-CMS is a natural cytotype of H. annuus, and the appearance of the CMS phenotype in cultivated sunflowers is associated with the loss of stabilizing nuclear genes of fertility restorers, which occurred during interspecific hybridization. These data can explain the patterns of differential cytoplasmic and nuclear introgression occurring in wild sunflower and are useful for further evolutionary studies.

The boundary of life and death: changes in mitochondrial and cytosolic proteomes associated with programmed cell death of Arabidopsis thaliana suspension culture cells

Introduction

Despite the critical role of programmed cell death (PCD) in plant development and defense responses, its regulation is not fully understood. It has been proposed that mitochondria may be important in the control of the early stages of plant PCD, but the details of this regulation are currently unknown.

Methods

We used Arabidopsis thaliana cell suspension culture, a model system that enables induction and precise monitoring of PCD rates, as well as chemical manipulation of this process to generate a quantitative profile of the alterations in mitochondrial and cytosolic proteomes associated with early stages of plant PCD induced by heat stress. The cells were subjected to PCD-inducing heat levels (10 min, 54°C), with/without the calcium channel inhibitor and PCD blocker LaCl3. The stress treatment was followed by separation of cytosolic and mitochondrial fractions and mass spectrometry-based proteome analysis.

Results

Heat stress induced rapid and extensive changes in protein abundance in both fractions, with release of mitochondrial proteins into the cytosol upon PCD induction. In our system, LaCl3 appeared to act downstream of cell death initiation signal, as it did not affect the release of mitochondrial proteins, but instead partially inhibited changes occurring in the cytosolic fraction, including upregulation of proteins with hydrolytic activity.

Discussion

We characterized changes in protein abundance and localization associated with the early stages of heat stress-induced PCD. Collectively, the generated data provide new insights into the regulation of cell death and survival decisions in plant cells.

A transcriptomic evaluation of the mechanism of programmed cell death of the replaceable bud in Chinese chestnut

Previous studies suggest that the senescence and death of the replaceable bud of the Chinese chestnut cultivar (cv.) "Tima Zhenzhu" involves programmed cell death (PCD). However, the molecular network regulating replaceable bud PCD is poorly characterized. Here, we performed transcriptomic profiling on the chestnut cv. "Tima Zhenzhu" replaceable bud before (S20), during (S25), and after (S30) PCD to unravel the molecular mechanism underlying the PCD process. A total of 5,779, 9,867, and 2,674 differentially expressed genes (DEGs) were discovered upon comparison of S20 vs S25, S20 vs S30, and S25 vs S30, respectively. Approximately 6,137 DEGs common to at least two comparisons were selected for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to interrogate the main corresponding biological functions and pathways. GO analysis showed that these common DEGs could be divided into three functional categories, including 15 cellular components, 14 molecular functions, and 19 biological processes. KEGG analysis found that "plant hormone signal transduction" included 93 DEGs. Overall, 441 DEGs were identified as related to the process of PCD. Most of these were found to be genes associated with ethylene signaling, as well as the initiation and execution of various PCD processes.

Oxic effects of Pb-Ce compound pollution on Chinese cabbage and programmed cell death in root tip cells

Heavy metal pollution is increasing, and rare earth elements (REE) play an important role in the environmental impact of heavy metals. Mixed heavy metal pollution is a major issue with complex effects. Despite substantial research on single heavy metal pollution, relatively few studies have focused on pollution from rare earth heavy metal composites. We studied the effects of different concentrations of Ce-Pb on the antioxidant activity in root tip cells and biomass of Chinese cabbage. We also used the integrated biomarker response (IBR) to evaluate the toxic effects of rare earth-heavy metal pollution on Chinese cabbage. We used programmed cell death (PCD) for the first time to reflect the toxicological effects of heavy metals and rare earths and studied the interaction between Ce and Pb in root tip cells in depth. Our results showed that Ce-Pb compound pollution can induce PCD in the root cells of Chinese cabbage, and the toxicity of compound pollutants is greater than that of single pollutants. Our analyses also provide the first evidence that Ce and Pb exert interaction effects in the cell. Ce induces Pb transfer in plant cells. The Pb content in the cell wall decreases from 58% to 45%. Additionally, Pb induced Ce valence changes. Ce (III) decreased from 50% to 43%, while Ce (IV) increased from 50% to 57%, directly resulting in PCD in the roots of Chinese cabbage. These findings improve our understanding of the harmful effects of compound pollution with rare earth metals and heavy metals on plants.

Molecular genetics of cytoplasmic male sterility and restorer-of-fertility for the fine tuning of pollen production in crops

Cytoplasmic male sterility (CMS) is an increasingly important issue within the context of hybrid seed production. Its genetic framework is simple: S-cytoplasm for male sterility induction and dominant allele of the restorer-of-fertility gene (Rf) for suppression of S. However, breeders sometimes encounter a phenotype of CMS plants too complex to be explained via this simple model. The molecular basis of CMS provides clue to the mechanisms that underlie the expression of CMS. Mitochondria have been associated with S, and several unique ORFs to S-mitochondria are thought to be responsible for the induction of male sterility in various crops. Their functions are still the subject of debate, but they have been hypothesized to emit elements that trigger sterility. Rf suppresses the action of S by various mechanisms. Some Rfs, including those that encode the pentatricopeptide repeat (PPR) protein and other proteins, are now considered members of unique gene families that are specific to certain lineages. Additionally, they are thought to be complex loci in which several genes in a haplotype simultaneously counteract an S-cytoplasm and differences in the suite of genes in a haplotype can lead to multiple allelism including strong and weak Rf at phenotypic level. The stability of CMS is influenced by factors such as the environment, cytoplasm, and genetic background; the interaction of these factors is also important. In contrast, unstable CMS becomes inducible CMS if its expression can be controlled. CMS becomes environmentally sensitive in a genotype-dependent manner, suggesting the feasibility of controlling the expression of CMS.

Review on tapetal ultrastructure in angiosperms

MAIN CONCLUSION

The appearance of new cellular structures and characteristics in the tapetum suggests that there is still much to discover that would help to better understand the tapetum functions. The ultrastructure of the tapetum provides important information for the understanding of the functions performed by this tissue. Since there are no reviews on the subject, we aim to collect all the detailed information about the tapetum ultrastructure present until this moment in order to lay the foundations for future research. Detailed information on the tapetal ultrastructure of 80 species from 45 different families: 2 species with invasive non-syncytial tapetum, 11 with plasmodial and 67 with a secretory tapetum was collected. These studies allowed to establish (a) the most usual cytological characteristics of this tissue, (b) unique characteristics and/or cellular structures in tapetum cells, (c) the ultrastructural changes that occur in different types of tapetum, during the progress of microsporogenesis and microgametogenesis, and (d) the most recognized ultrastructural traits of the tapetum that cause androsterility. The structure of these cells is related to their function in each developmental stage. Since most species present their particular ultrastructure and may sometimes, share some traits within families, there is not a model plant on tapetum ultrastructure. However, knowing the general cytological aspect of the tapetum may help distinguish between patterns of cytoplasmic disorganization due to tapetum degeneration from technical failures of the preparation. Moreover, as the amount of species analyzed increases, unknown tapetal organelles or traits may be identified that might be associated to particular functions of this tissue. On the other hand, different ultrastructural changes may be related to the metabolisms and the regulation of normal/abnormal tapetum development.

ORF355 confers enhanced salinity stress adaptability to S-type cytoplasmic male sterility maize by modulating the mitochondrial metabolic homeostasis

Moderate stimuli in mitochondria improve wide-ranging stress adaptability in animals, but whether mitochondria play similar roles in plants is largely unknown. Here, we report the enhanced stress adaptability of S-type cytoplasmic male sterility (CMS-S) maize and its association with mild expression of sterilizing gene ORF355. A CMS-S maize line exhibited superior growth potential and higher yield than those of the near-isogenic N-type line in saline fields. Moderate expression of ORF355 induced the accumulation of reactive oxygen species and activated the cellular antioxidative defense system. This adaptive response was mediated by elevation of the nicotinamide adenine dinucleotide concentration and associated metabolic homeostasis. Metabolome analysis revealed broad metabolic changes in CMS-S lines, even in the absence of salinity stress. Metabolic products associated with amino acid metabolism and galactose metabolism were substantially changed, which underpinned the alteration of the antioxidative defense system in CMS-S plants. The results reveal the ORF355-mediated superior stress adaptability in CMS-S maize and might provide an important route to developing salt-tolerant maize varieties.

Two-Step Identification of N-, S-, R- and T-Cytoplasm Types in Onion Breeding Lines Using High-Resolution Melting (HRM)-Based Markers

High-resolution melting (HRM) analysis is a powerful detection method for fast, high-throughput post-PCR analysis. A two-step HRM marker system was developed for identification of the N-, S-, R- and T-cytoplasms of onion. In the first step for the identification of N-, S- and R-cytoplasms, one forward primer was designed to the identical sequences of both cox1 and orf725 genes, and two reverse primers specific to the polymorphic sequences of cox1 and orf725 genes were used. For the second step, breeding lines with N-cytoplasm were evaluated with primers developed from the orfA501 sequence to distinguish between N- and T-cytoplasms. An amplicon with primers to the mitocondrial atp9 gene was used as an internal control. The two-step HRM marker system was tested using 246 onion plants. HRM analysis showed that the most common source of CMS, often used by Russian breeders, was S-cytoplasm; the rarest type of CMS was R-cytoplasm; and the proportion of T-cytoplasm among the analyzed breeding lines was 20.5%. The identification of the cytoplasm of a single plant by phenotype takes from 4 to 8 years. The HRM-based system enables quick and easy distinguishing of the four types of onion cytoplasm.

Developmentally regulated mitochondrial biogenesis and cell death competence in maize pollen

BACKGROUND

Cytoplasmic male sterility (CMS) is a maternally inherited failure to produce functional pollen that most commonly results from expression of novel, chimeric mitochondrial genes. In Zea mays, cytoplasmic male sterility type S (CMS-S) is characterized by the collapse of immature, bi-cellular pollen. Molecular and cellular features of developing CMS-S and normal (N) cytoplasm pollen were compared to determine the role of mitochondria in these differing developmental fates.

RESULTS

Terminal deoxynucleotidyl transferase dUTP nick end labeling revealed both chromatin and nuclear fragmentation in the collapsed CMS-S pollen, demonstrating a programmed cell death (PCD) event sharing morphological features with mitochondria-signaled apoptosis in animals. Maize plants expressing mitochondria-targeted green fluorescent protein (GFP) demonstrated dynamic changes in mitochondrial morphology and association with actin filaments through the course of N-cytoplasm pollen development, whereas mitochondrial targeting of GFP was lost and actin filaments were disorganized in developing CMS-S pollen. Immunoblotting revealed significant developmental regulation of mitochondrial biogenesis in both CMS-S and N mito-types. Nuclear and mitochondrial genome encoded components of the cytochrome respiratory pathway and ATP synthase were of low abundance at the microspore stage, but microspores accumulated abundant nuclear-encoded alternative oxidase (AOX). Cytochrome pathway and ATP synthase components accumulated whereas AOX levels declined during the maturation of N bi-cellular pollen. Increased abundance of cytochrome pathway components and declining AOX also characterized collapsed CMS-S pollen. The accumulation and robust RNA editing of mitochondrial transcripts implicated translational or post-translational control for the developmentally regulated accumulation of mitochondria-encoded proteins in both mito-types.

CONCLUSIONS

CMS-S pollen collapse is a PCD event coincident with developmentally programmed mitochondrial events including the accumulation of mitochondrial respiratory proteins and declining protection against mitochondrial generation of reactive oxygen species.

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.

Mitochondrial genomes do not appear to regulate flowering pattern/reproductive strategy in Cannabis sativa

Currently, the amount of genetic data for Cannabis is lacking due to the illegal nature of the plant. Our study used 73 Cannabis sativa whole-genome shotgun libraries to reveal eight different mtDNA haplotypes. The most common haplotype contained 60 of the 73 samples studied and was composed of only dioecious individuals. However, other haplotypes contained a mix of both mating strategies (i.e. monoecious and dioecious). From these haplotype groupings we further examined the fully annotated mitochondrial genomes of four hemp individuals with different mt haplotypes and recorded gene content, copy number variation and synteny. Our results revealed highly syntenic mitochondrial genomes that contained ~60 identifiable sequences for protein-coding genes, tRNAs and rRNAs and no obvious rearrangements or chimeric genes. We found no clear evidence that modern reproductive patterns are due to simple cytoplasmic male sterility mutations. It is likely the interaction between nuclear genetic components and the X/Y sex chromosomes that determines reproductive strategy. Additionally, we added 50 % more mitochondrial genomes to the publicly available repository.

γ-aminobutyric acid (GABA) alleviated oxidative damage and programmed cell death in fresh-cut pumpkins

The regulation of γ-aminobutyric acid (GABA) on plant anti-oxygenation and programmed cell death (PCD) in fresh-cut pumpkins was investigated. Exogenous GABA positively promoted GABA accumulation and alleviated oxidant damage in pumpkins tissue. Pumpkins treated with GABA showed lower electrolyte leakage, reactive oxygen species (ROS) and MDA content, while higher activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) as compared to the non-treated tissues. Our results also found that GABA treatment retarded DNA degradation and cytochrome c release and delayed the apoptosis of pumpkin cells. On the other hand, the inhibitor of GABA generation, 3-mercaptopropionic acid (3-MP) treatment not only accelerated oxidant damage, but also induced cell death involving chromatin condensation, DNA ladder and cytochrome c releasing. Taken together, our present research indicated that exogenous GABA could alleviate the wound-induced oxidative stress and PCD occurrence in fresh-cut pumpkins.

Transcriptome profiling of flower buds of male-sterile lines provides new insights into male sterility mechanism in alfalfa

BACKGROUND

The use of heterosis to produce hybrid seeds is a challenge to breeding for improved crop yield. In previous studies, we isolated a male sterile alfalfa hybrid and successfully obtained a genetically stable alfalfa male sterile line through backcrossing, henceforth named MS-4. In this study, we used RNA-seq technology to analyze the transcriptome profiles of the male sterile line (MS-4) and the male fertile line (MF) of alfalfa to elucidate the mechanism of male sterility.

RESULTS

We screened a total of 11,812 differentially expressed genes (DEGs) from both MS-4 and MF lines at three different stages of anther development. Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that these DEGs are mainly involved in processes such as energy metabolism, lipid and amino acid metabolism, carbohydrate metabolism, in addition to cell synthesis and aging. The results from protein-protein interaction (PPI) network analysis showed that the ribosomal protein (MS.Gene25178) was the core gene in the network. We also found that transcriptional regulation was an influential factor in the development of anthers.

CONCLUSIONS

Our findings provide new insights into understanding of the fertility changes in the male sterile (MS-4) of alfalfa.

Did doubly uniparental inheritance (DUI) of mtDNA originate as a cytoplasmic male sterility (CMS) system?

Animal and plant species exhibit an astonishing diversity of sexual systems, including environmental and genetic determinants of sex, with the latter including genetic material in the mitochondrial genome. In several hermaphroditic plants for example, sex is determined by an interaction between mitochondrial cytoplasmic male sterility (CMS) genes and nuclear restorer genes. Specifically, CMS involves aberrant mitochondrial genes that prevent pollen development and specific nuclear genes that restore it, leading to a mixture of female (male-sterile) and hermaphroditic individuals in the population (gynodioecy). Such a mitochondrial-nuclear sex determination system is thought to be rare outside plants. Here, we present one possible case of CMS in animals. We hypothesize that the only exception to the strict maternal mtDNA inheritance in animals, the doubly uniparental inheritance (DUI) system in bivalves, might have originated as a mitochondrial-nuclear sex-determination system. We document and explore similarities that exist between DUI and CMS, and we propose various ways to test our hypothesis.

Rice functional genomics: decades' efforts and roads ahead

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

Rice functional genomics: decades' efforts and roads ahead

Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.

Iron insufficiency in floral buds impairs pollen development by disrupting tapetum function

Reduction of crop yield due to iron (Fe) deficiency has always been a concern in agriculture. How Fe insufficiency in floral buds affects pollen development remains unexplored. Here, plants transferred to Fe-deficient medium at the reproductive stage had reduced floral Fe content and viable pollen and showed a defective pollen outer wall, all restored by supplying floral buds with Fe. A comparison of differentially expressed genes (DEGs) in Fe-deficient leaves, roots, and anthers suggested that changes in several cellular processes were unique to anthers, including increased lipid degradation. Co-expression analysis revealed that ABORTED MICROSPORES (AMS), DEFECTIVE IN TAPETAL DEVELOPMENT AND FUNCTION1, and BASIC HELIX-LOOP-HELIX 089/091/010 encode key upstream transcription factors of Fe deficiency-responsive DEGs involved in tapetum function and development, including tapetal ROS homeostasis, programmed cell death, and pollen outer wall formation-related lipid metabolism. Analysis of RESPIRATORY-BURST OXIDASE HOMOLOG E (RBOHE) gain- and loss-of-function under Fe deficiency indicated that RBOHE- and Fe-dependent regulation cooperatively control anther reactive oxygen species levels and pollen development. Since DEGs in Fe-deficient anthers were not significantly enriched in genes related to mitochondrial function, the changes in mitochondrial status under Fe deficiency, including respiration activity, density, and morphology, were probably because the Fe amount was insufficient to maintain proper mitochondrial protein function in anthers. To sum up, Fe deficiency in anthers may affect Fe-dependent protein function and impact upstream transcription factors and their downstream genes, resulting in extensively impaired tapetum function and pollen development.

Orf165 is associated with cytoplasmic male sterility in pepper

Cytoplasmic male sterility (CMS) is a maternally inherited trait that derives from the inability to produce functional pollen in higher plants. CMS results from recombination of the mitochondrial genome. However, understanding of the molecular mechanism of CMS in pepper is limited. In this study, comparative transcriptomic analyses were performed using a near-isogenic CMS line 14A (CMS-14A) and a maintainer line 14B (ML-14B) as experimental materials. A total of 17,349 differentially expressed genes were detected between CMS-14A and ML-14B at the PMC meiosis stage. Among them, six unigenes associated with CMS and 108 unigenes involved in energy metabolism were identified. The gene orf165 was found in CMS-14A. When orf165 was introduced into ML-14B, almost 30% of transgenic plants were CMS. In addition, orf165 expression in transgenic CMS plants resulted in abnormal function of some genes involved in energy metabolism. When orf165 in transgenic CMS plant was silenced, the resulted orf165-silenced plant was male fertile and the expression patterns of some genes associated with energy metabolism were similar to ML-14B. Thus, we confirmed that orf165 influenced CMS in pepper.

Structure of antipodal cells nuclei of wheat embryo sac during programmed cell death

During antipodal cells PCD, polytene chromosomes rearrangement, segregation of nucleoli components and extrusion of nuclear components occur, cytochrome c is released from the mitochondria and DNA breaks appear. We studied in detail the nuclei of cells of the antipodal complex of wheat embryo sac (Triticum aestivum L.) during programmed cell death (PCD). The antipodal complex has been reported to be formed before double fertilisation of the embryo sac. Polyploidisation leads to the formation of giant polytene chromosomes in the nuclei of antipodal cells. These chromosomes are involved in secretory functions and are important for the development of cellular endosperm. Terminal deoxynucleotidyl transferase dUTP nick end labelling assay and immunodetection revealed DNA breaks in the nuclei and release of cytochrome c from mitochondria into the cytoplasm of antipodal cells during PCD. We used transmission electron microscopy, immunodetection and histochemistry to analyse the characteristic structural changes in the nuclei of antipodal cells during PCD. These included sequential structural changes in the nuclei containing polytene chromosomes, segregation of some components of the nucleolus into the bodies of polytene chromosomes, extrusion of nucleolar components and parts of chromosomes into the cytoplasm of antipodal cells and then into the endosperm coenocyte. The obtained results expand the understanding of the structural changes of plant cells with giant polytene chromosomes during PCD.

Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System

In vitro tissue culture plant regeneration is a complicated process that requires stressful conditions affecting the cell functioning at multiple levels, including signaling pathways, transcriptome functioning, the interaction between cellular organelles (retro-, anterograde), compounds methylation, biochemical cycles, and DNA mutations. Unfortunately, the network linking all these aspects is not well understood, and the available knowledge is not systemized. Moreover, some aspects of the phenomenon are poorly studied. The present review attempts to present a broad range of aspects involved in the tissue culture-induced variation and hopefully would stimulate further investigations allowing a better understanding of the phenomenon and the cell functioning.

High-generation near-isogenic lines combined with multi-omics to study the mechanism of polima cytoplasmic male sterility

BACKGROUND

Cytoplasmic male sterility (CMS), which naturally exists in higher plants, is a useful mechanism for analyzing nuclear and mitochondrial genome functions and identifying the role of mitochondrial genes in the plant growth and development. Polima (pol) CMS is the most universally valued male sterility type in oil-seed rape. Previous studies have described the pol CMS restorer gene Rfp and the sterility-inducing gene orf224 in oil-seed rape, located in mitochondria. However, the mechanism of fertility restoration and infertility remains unknown. Moreover, it is still unknown how the fecundity restorer gene interferes with the sterility gene, provokes the sterility gene to lose its function, and leads to fertility restoration.

RESULT

In this study, we used multi-omics joint analysis to discover candidate genes that interact with the sterility gene orf224 and the restorer gene Rfp of pol CMS to provide theoretical support for the occurrence and restoration mechanisms of sterility. Via multi-omics analysis, we screened 24 differential genes encoding proteins related to RNA editing, respiratory electron transport chain, anther development, energy transport, tapetum development, and oxidative phosphorylation. Using a yeast two-hybrid assay, we obtained a total of seven Rfp interaction proteins, with orf224 protein covering five interaction proteins.

CONCLUSIONS

We propose that Rfp and its interacting protein cleave the transcript of atp6/orf224, causing the infertility gene to lose its function and restore fertility. When Rfp is not cleaved, orf224 poisons the tapetum cells and anther development-related proteins, resulting in pol CMS mitochondrial dysfunction and male infertility. The data from the joint analysis of multiple omics provided information on pol CMS's potential molecular mechanism and will help breed B. napus hybrids.

Cellular oxidative stress in programmed cell death: focusing on chloroplastic 1O2 and mitochondrial cytochrome-c release

The programmed cell death (PCD) occurs when the targeted cells have fulfilled their task or under conditions as oxidative stress generated by ROS species. Thus, plants have to deal with the singlet oxygen ¹O₂ produced in chloroplasts. ¹O₂ is unlikely to act as a primary retrograde signal owing to its high reactivity and short half-life. In addition to its high toxicity, the ¹O₂ generated under an excess or low excitation energy might also act as a highly versatile signal triggering chloroplast-to-nucleus retrograde signaling (ChNRS) and nuclear reprogramming or cell death. Molecular and biochemical studies with the flu mutant, which accumulates protochlorophyllide in the dark, demonstrated that chloroplastic ¹O₂-driven EXECUTER-1 (EX1) and EX2 proteins are involved in the ¹O₂-dependent response. Both EX1 and EX2 are necessary for full suppression of ¹O₂-induced gene expression. That is, EXECUTER proteolysis via the ATP-dependent zinc protease (FtsH) is an integral part of ¹O₂-triggered retrograde signaling. The existence of at least two independent ChNRS involving EX1 and β-cyclocitral, and dihydroactinidiolide and OXI1, respectively, seem clear. Besides, this update also focuses on plant PCD and its relation with mitochondrial cytochrome-c (Cytc) release to cytosol. Changes in the dynamics and morphology of mitochondria were shown during the onset of cell death. The mitochondrial damage and translocation of Cytc may be one of the major causes of PCD triggering. Together, this current overview illustrates the complexity of the cellular response to oxidative stress development. A puzzle with the majority of its pieces still not placed.

Immunopurification of Mitochondria from Arabidopsis

Isolation of mitochondria from plant tissues, especially green leaves, is particularly difficult because of chloroplast contamination. Compared to other techniques for purifying plant mitochondria, the immunopurification method has a number of advantages: it rapidly purifies the mitochondria within several minutes, avoids loss of mitochondrial metabolites, eliminates most other organelles (especially the chloroplasts), keeps the isolated mitochondria intact, requires little starting material, and has the potential to purify tissue-specific mitochondria. Here, we describe a rapid immunopurification protocol for mitochondrial isolation that employs a protein specifically targeted to the outer mitochondrial membrane that acts as an immunopurification handle. © 2021 Wiley Periodicals LLC.

Determinants, and implications, of the shape and size of thylakoids and cristae

Thylakoids are flattened sacs isolated from other membranes; cristae are attached to the rest of the inner mitochondrial membrane by the crista junction, but the crista lumen is separated from the intermembrane space. The shape of thylakoids and cristae involves membranes with small (5-30 nm) radii of curvature. While the mechanism of curvature is not entirely clear, it seems to be largely a function of Curt proteins in thylakoids and Mitochondrial Organising Site and Crista Organising Centre proteins and oligomeric F_OF₁ ATP synthase in cristae. A subordinate, or minimal, role is attributable to lipids with areas of their head group area greater (convex leaflet) or smaller (concave leaflet) than the area of the lipid tail; examples of the latter group are monogalactosyldiglyceride in thylakoids and cardiolipin in cristae. The volume per unit area on the lumen side of the membrane is less than that of the chloroplast stroma or cyanobacterial cytosol for thylakoids, and mitochondrial matrix for cristae. A low volume per unit area of thylakoids and cristae means a small lumen width that is the average of wider spaces between lipid parts of the membranes and the narrower gaps dominated by extra-membrane components of transmembrane proteins. These structural constraints have important implications for the movement of the electron carriers plastocyanin and cytochrome c₆ (thylakoids) and cytochrome c (cristae) and hence the separation of the membrane-associated electron donors to, and electron acceptors from, these water-soluble electron carriers. The donor/acceptor pairs, are the cytochrome fb₆Fe_nh complex and P₇₀₀⁺ in thylakoids, and Complex III and Complex IV of cristae. The other energy flux parallel to the membranes is that of the proton motive force generated by redox-powered H⁺ pumps into the lumen to the proton motive force use in ATP synthesis by H⁺ flux from the lumen through the ATP synthase. For both the electron transport and proton motive force movement, concentration differences of reduced and oxidised electron carriers and protonated and deprotonated pH buffers are involved. The need for diffusion along a congested route of these energy transfer agents may limit the separation of sources and sinks parallel to the membranes of thylakoids and cristae.

Mitochondrial relationships between various chamomile accessions

Matricaria chamomilla L. (GRIN; The Plant List 2013) is an important medicinal plant and one of the most frequently consumed tea plants. In order to assess mitochondrial genome variation of different cultivated chamomile accessions, 36 mitochondrial SNP markers were used in a HRM (high resolution melting) approach. In thirteen accessions of chamomile (n = 155), twenty mitochondrial haplotypes (genetic distances 0.028–0.693) were identified. Three of the accessions (‘Camoflora’, ‘Mat19’ and ‘Manzana’) were monomorphic. The highest genotypic variability was found for the Croatian accession ‘PG029’ with nine mitochondrial haplotypes (mitotypes) and the Argentinian ‘Argenmilla’ with seven mitotypes. However, most of the mitotypes detected in these accessions were infrequent in our sample set, thus disclosing an unusual high amount of substitutions within the mitochondrial genome of these accessions. The mitotypes with the highest frequency in the examined dataset were MT1 (n = 27), MT9 (n = 23) and MT17 (n = 20). All of the frequent mitochondrial lines are distributed not only over several accessions but also over several geographical origins. The origins often build a triplet with on average two to three concurrent lines. The most distantly related accessions were ‘Mat19’ and ‘Camoflora’ (0.539), while ‘PNOS’ and ‘Margaritar’ (0.007) showed the lowest genetic distance.

Identification and characterization of Arabidopsis thaliana mitochondrial F1F0-ATPase inhibitor factor 1

Mitochondrial F1F0-ATP synthase (F1F0-ATPase) inhibitor factor 1 (IF1) has been extensively characterized as an endogenous inhibitor that prevents the hydrolysis of adenosine-5'-triphosphate (ATP) by mitochondrial ATPases in mammals and yeasts; however, IF1's functions in plants remain unclear. Here, a comprehensive bioinformatic analysis was performed to identify plant mitochondrial F1F0-ATPase IF1 orthologs. Plant IF1s contain a conserved F1F0-ATPase inhibitory domain, but lack the antiparallel α-helical coiled-coil structure compared with mammalian IF1s. A subcellular localization analysis in Arabidopsis thaliana revealed that AtIF1-green fluorescent protein was present only in mitochondria. Additionally, AtIF1 was widely expressed in diverse organs and intense β-glucuronidase staining was observed in reproductive tissues and germinating seeds. Compared with the wild-type and p35S:AtIF1-if1 etiolated seedlings, the ATP/ADP ratio was significantly lower in the AtIF1 T-DNA knockout seedlings (if1 mutant) growing under dark conditions, suggesting that AtIF1 can influence the energy state of cells. A significant reduction in seed yield and strong growth retardation under dark conditions were observed in the if1 mutant line. Furthermore, if1 plants exhibited a substantially decreased sensitivity to abscisic acid. Thus, the A. thaliana mitochondrial IF1, which is a conserved F1F0-ATPase inhibitor, is crucial for plant growth and responses to abscisic acid.

Characterization and transcriptome analysis of a dominant genic male sterile cotton mutant

BACKGROUND

Male sterility is an efficient trait for hybrid seed production and germplasm innovation. Until now, most studies on male sterility were on cytoplasmic and recessive genic sterility, with few on dominant genic male sterility, especially in cotton, due to lack of such mutant.

RESULTS

We discovered a natural male sterile (MS) Sea Island cotton (G. barbadense) mutant. Genetic analysis showed the mutation was caused by a dominant mutation in a single nuclear gene. Comparative cytological observation of anther sections from MS and wild-type (WT) uncovered cellular differences in anther at and after the tetrad stage of pollen mother cells (PMC). In the MS anthers, the outer wall of pollen grains was free of spinules, the tapetum was vacuolated and showed delayed degradation, consequently, no functional pollen grains. Comparison of transcriptomes from meiosis, tetrad, mononuclear and binuclear pollen, and pollen maturation stages identified 13,783 non-redundant differentially expressed genes (DEGs) between MS and WT. Based on the number of DEGs, analyses of enriched GO terms and KEGG pathways, it was evident that significant transcriptomic changes occurred at and after the tetrad stage, consistent with cytological observation, and that the major differences were on metabolism of starch, sucrose, ascorbate, aldarate, alanine, aspartate and glutamate, and biosynthesis of cutin, suberine and wax. WGCNA analysis identified five modules containing 920 genes highly related to anther development, especially the greenyellow module with 54 genes that was highly associated with PMC meiosis and tetrad formation. A NAC transcription factor (Gh_D11G2469) was identified as a hub gene for this module, which warrants further functional characterization.

CONCLUSIONS

We demonstrated that the MS trait was controlled by a single dominant nuclear gene and caused by delayed tapetum degradation at the tetrad stage. Comparative transcriptome analysis and gene network construction identified DEGs, enriched GO terms and metabolic pathways, and hub genes potentially associated with anther development and the MS trait. These results contribute to our understanding of dominant genic male sterility (DGMS) and provided source for innovation of cotton germplasm.

Comparative Transcriptome Analysis Reveals the Potential Mechanism of Abortion in Tobacco sua-Cytoplasmic Male Sterility

sua-CMS (cytoplasmic male sterility) is the only male sterile system in tobacco breeding, but the mechanism of abortion is unclear. Cytological characteristics show that abortion in the sua-CMS line msZY occurs before the differentiation of sporogenous cells. In this study, a comparative transcriptomic analysis was conducted on flower buds at the abortion stage of msZY and its male fertile control ZY. A total of 462 differentially expressed genes were identified in msZY and ZY, which were enriched via protein processing in the endoplasmic reticulum (ER), oxidative phosphorylation, photosynthesis, and circadian rhythm-plant by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Most genes were downregulated in the ER stress pathway, heat-shock protein family, F1F0-ATPase encoding by the mitochondrial genome, and differentiation of stamens. Genes in the programmed cell death (PCD) pathway were upregulated in msZY. The transcriptome results were consistent with those of qRT-PCR. Ultrastructural and physiological analyses indicted active vacuole PCD and low ATP content in msZY young flower buds. We speculated that PCD and a deficiency in ATP synthesis are essential for the abortion of sua-CMS. This study reveals the potential mechanism of abortion of tobacco sua-CMS.

The role of auxin in developmentally regulated programmed cell death in lace plant

PREMISE

Lace plant (Aponogeton madagascariensis) leaves are remodeled via developmental programmed cell death (PCD) to produce perforations located equidistantly between longitudinal and transverse veins. Auxin has been implicated in other developmental PCD processes in plants; however, the role of auxin in perforation formation in lace plant is unknown. Here the role of auxin in developmental PCD in lace plant was studied using two auxin inhibitors N-1-naphthylphthalamic acid (NPA), an auxin transport inhibitor, and auxinole, a potent auxin antagonist.

METHODS

Sterile cultures of lace plants were propagated and treated with NPA or auxinole. Leaf length, leaf width, and number of perforations were then analyzed. Vein patterning and perforation area were further examined in NPA-treated plants. Downstream PCD transduction events were investigated via spectrophotometric assays, histochemical staining, and immuno-probing.

RESULTS

Lace plants treated with NPA or auxinole produced leaves with fewer perforations compared to their respective controls. Although NPA treatment was insufficient to completely alter vein patterning, NPA-treated leaves did have significantly more atypical areoles compared to control leaves. Events involved in perforation formation in lace plant leaves were altered following treatment with NPA, including anthocyanin production, reactive oxygen species (ROS) accumulation, and the release of mitochondrial cytochrome c.

CONCLUSIONS

Our results indicated that inhibition of auxin signaling disrupts several downstream features of the lace plant PCD signaling cascade and results in fewer or no perforations. Therefore, we concluded that auxin signaling is important for developmentally regulated PCD in lace plant leaves.

PERSISTENT TAPETAL CELL2 Is Required for Normal Tapetal Programmed Cell Death and Pollen Wall Patterning

The timely programmed cell death (PCD) of the tapetum, the innermost somatic anther cell layer in flowering plants, is critical for pollen development, including the deposition and patterning of the pollen wall. Although several genes involved in tapetal PCD and pollen wall development have been characterized, the underlying regulatory mechanism remains elusive. Here we report that PERSISTENT TAPETAL CELL2 (PTC2), which encodes an AT-hook nuclear localized protein in rice (Oryza sativa), is required for normal tapetal PCD and pollen wall development. The mutant ptc2 showed persistent tapetal cells and abnormal pollen wall patterning including absent nexine, collapsed bacula, and disordered tectum. The defective tapetal PCD phenotype of ptc2 was similar to that of a PCD delayed mutant, ptc1, in rice, while the abnormal pollen wall patterning resembled that of a pollen wall defective mutant, Transposable Element Silencing Via AT-Hook, in Arabidopsis (Arabidopsis thaliana). Levels of anther cutin monomers in ptc2 anthers were significantly reduced, as was expression of a series of lipid biosynthetic genes. PTC2 transcript and protein were shown to be present in the anther after meiosis, consistent with the observed phenotype. Based on these data, we propose a model explaining how PTC2 affects anther and pollen development. The characterization of PTC2 in tapetal PCD and pollen wall patterning expands our understanding of the regulatory network of male reproductive development in rice and will aid future breeding approaches.

A predicted NEDD8 conjugating enzyme gene identified as a Capsicum candidate Rf gene using bulk segregant RNA sequencing

Cytoplasmic male sterility (CMS) is an important tool for producing F₁ hybrids, which can exhibit heterosis. The companion system, restorer-of-fertility (Rf), is poorly understood at the molecular level and would be valuable in producing restorer lines for hybrid seed production. The identity of the Rf gene in Capsicum (pepper) is currently unclear. In this study, using bulked segregant RNA sequencing (BSR-seq), a strong candidate Rf gene, Capana06g002866, which is annotated as a NEDD8 conjugating enzyme E2, was identified. Capana06g002866 has an ORF of 555 bp in length encoding 184 amino acids; it can be cloned from F₁ plants from the hybridization of the CMS line 8A and restorer line R1 but is not found in CMS line 8A. With qRT-PCR validation, Capana06g002866 was found to be upregulated in restorer accessions compared to sterile accessions. The relative expression in flower buds increased with the developmental stage in F₁ plants, while the expression was very low in all flower bud stages of the CMS lines. These results provide new insights into the Rf gene in pepper and will be useful for other crops utilizing the CMS system.

Integrated Methylome and Transcriptome Analysis between the CMS-D2 Line ZBA and Its Maintainer Line ZB in Upland Cotton

DNA methylation is an important epigenetic modification involved in multiple biological processes. Altered methylation patterns have been reported to be associated with male sterility in some plants, but their role in cotton cytoplasmic male sterility (CMS) remains unclear. Here, integrated methylome and transcriptome analyses were conducted between the CMS-D2 line ZBA and its near-isogenic maintainer line ZB in upland cotton. More methylated cytosine sites (mCs) and higher methylation levels (MLs) were found among the three sequence contexts in ZB compared to ZBA. A total of 4568 differentially methylated regions (DMRs) and 2096 differentially methylated genes (DMGs) were identified. Among the differentially expressed genes (DEGs) associated with DMRs (DMEGs), 396 genes were upregulated and 281 genes were downregulated. A bioinformatics analysis of these DMEGs showed that hyper-DEGs were significantly enriched in the “oxidative phosphorylation” pathway. Further qRT-PCR validation indicated that these hypermethylated genes (encoding the subunits of mitochondrial electron transport chain (ETC) complexes I and V) were all significantly upregulated in ZB. Our biochemical data revealed a higher extent of H₂O₂ production but a lower level of adenosine triphosphate (ATP) synthesis in CMS-D2 line ZBA. On the basis of the above results, we propose that disrupted DNA methylation in ZBA may disrupt the homeostasis of reactive oxygen species (ROS) production and ATP synthesis in mitochondria, triggering a burst of ROS that is transferred to the nucleus to initiate programmed cell death (PCD) prematurely, ultimately leading to microspore abortion. This study illustrates the important role of DNA methylation in cotton CMS.

Pollen development in male sterile mangosteen (Garcinia mangostana L.) and male fertile seashore mangosteen (Garcinia celebica L.)

Mangosteen (Garcinia mangostana L.) is an economically important tropical fruit, yet the reproductive biology of this dioecious plant is complex. Male trees are not known, and female trees have sterile anthers leading to apomixis. We hypothesized that pollen abortion in mangosteen is due to altered tapetum activity during microgametogenesis. Developmental events at the cellular and sub-cellular levels during pollen development in G. mangostana were therefore examined and compared with seashore mangosteen (G. celebica L.), a closely related species with fertile anthers. In G. mangostana, the microspore mother cell had disorganized cytoplasm, including lack of Golgi apparatus and its vesicles, as well as abnormal callose wall accumulation. Globular droplets, which resembled orbicules or Ubisch bodies, were abundant in the locule, including pre-Ubisch bodies found along the tapetal plasma membrane. The tapetum of G. mangostana underwent cell death earlier than the fertile G. celebica, and during the premature death, the mitochondria had dramatically altered shapes. Low accumulation of starch in collapsed microspore mother cells and tetrad cell remnants also suggested that altered cell metabolism is related to pollen abortion in mangosteen. The present results demonstrate the importance of coordinated development between the tapetum and microspores in pollen development and provide new insights into male sterility in mangosteen (G. mangostana).

Comparative development of staminate and pistillate flowers in the dioecious cactus Opuntia robusta

PCD role in unisexual flowers. The developmental processes underlying the transition from hermaphroditism to unisexuality are key to understanding variation and evolution of floral structure and function. A detailed examination of the cytological and histological patterns involved in pollen and ovule development of staminate and pistillate flowers in the dioecious Opuntia robusta was undertaken, and the potential involvement of programmed cell death in the abortion of the sex whorls was explored. Flowers initiated development as hermaphrodites and became functionally unisexual by anthesis. Female individuals have pistillate flowers with a conspicuous stigma, functional ovary, collapsed stamens and no pollen grains. Male individuals have staminate flowers, with large yellow anthers, abundant pollen grains, underdeveloped stigma, style and an ovary that rarely produced ovules. In pistillate flowers, anther abortion resulted from the premature degradation of the tapetum by PCD, followed by irregular deposition of callose wall around the microsporocytes, and finally by microspore degradation. In staminate flowers, the stigma could support pollen germination; however, the ovaries were reduced, with evidence of placental arrest and ovule abortion through PCD, when ovules were present. We demonstrate that PCD is recruited in both pistillate and staminate flower development; however, it occurs at different times of floral development. This study contributes to the understanding of the nature of the O. robusta breeding system and identifies developmental landmarks that contribute to sexual determination in Cactaceae.

Relationship between loss of desiccation tolerance and programmed cell death (PCD) in mung bean (Vigna radiata) seeds

Mung bean (Vigna radiata), an important legume crop, has the property of desiccation tolerance (DT), which is lost in the final stage of germination (preimbibition, 18 h-24 h). We compared parameters related to the programmed cell death (PCD) of mung bean seeds before and after dehydration at different imbibition stages through various detection methods. The results of Evans blue and TTC staining methods showed that the dehydration process could lead to cell death. The results of optical and subcellular morphology showed that PCD occurred after dehydration. The destruction of DNA integrity and the activity changes in caspase and total nuclease in mung bean seeds after dehydration treatment indicated that the loss of desiccation tolerance was related to PCD. Dehydration resulted in the destruction of the mitochondrial structure, reversal of the membrane potential, and the entrance of cytochrome C into the cytoplasm. These processes all indicate that the mitochondrial apoptosis pathway was the main form of dehydration-induced PCD. The results of cytoplasmic Ca2+ concentration showed that Ca2+ signaling also played a role in inducing PCD, with the upstream signal being dehydration-induced changes in water potential and the downstream signal being the ROS and mitochondrial PT channel, according to the order in which these signals happened. The mitochondrial apoptosis pathway can be considered the main mechanism of dehydration-induced PCD based on our analysis of the sequence of major events in PCD. The main processes include dehydration induction, changes in Ca2+ and mitochondrial respiratory electron transport, the reversal of mitochondrial membrane potential induced by ROS and Ca2+, and the transmission and execution of PCD downstream signals induced by cytochrome C release.

Identification of Differentially Expressed miRNAs between a Wheat K-type Cytoplasmic Male Sterility Line and Its Near-Isogenic Restorer Line

K-type cytoplasmic male sterility (KCMS) lines were ideal material for three-line hybrid wheat system due to the major role in hybrid wheat production. In this study, the morphology of developing microspore and mature pollen was compared between a KCMS line and its near-isogenic restorer line (KCMS-NIL). The most striking difference is that the microspore was unable to develop into tricellular pollen in the KCMS line. MicroRNA plays vital roles in flowering and gametophyte development. Small RNA sequencing identified a total of 274 known and 401 novel miRNAs differentially expressed between two lines or two developmental stages. Most of miRNAs with high abundance were differentially expressed at the uninucleate stage, and their expression level recovered or remained at the binucleate stage. Further degradome sequencing identified target genes which were mainly enriched in transcription regulation, phytohormone signaling and RNA degradation pathways. Combining with the transcriptome data, a correlation was found between the abnormal anther development, such as postmeiotic mitosis cessation, deformative pollen wall and the chromosome condensation of the vegetative cell, and the alterations in the related miRNA and their targets expression profiles. According to the correlation and pathway analysis, we propose a hypothetic miRNA-mediated network for the control of KCMS restoration.

Metabolomics Studies on Cytoplasmic Male Sterility during Flower Bud Development in Soybean

Abnormal reactive oxygen species (ROS) may mediate cytoplasmic male sterility (CMS). To observe the effect of ROS on soybean CMS, metabolite content and antioxidant enzyme activity in the flower buds between soybean N8855-derived CMS line and its maintainer were compared. Of the 612 metabolites identified, a total of 74 metabolites were significantly differentiated in flower buds between CMS line and its maintainer. The differential metabolites involved 32 differential flavonoids, 13 differential phenolamides, and 1 differential oxidized glutathione (GSSG) belonging to a non-enzymatic ROS scavenging system. We observed lower levels of flavonoids and antioxidant enzyme activities in flower buds of the CMS line than in its maintainer. Our results suggest that deficiencies of enzymatic and non-enzymatic ROS scavenging systems in soybean CMS line cannot eliminate ROS in anthers effectively, excessive accumulation of ROS triggered programmed cell death and ultimately resulted in pollen abortion of soybean CMS line.

Selfish Mitonuclear Conflict

Mitochondria, a nearly ubiquitous feature of eukaryotes, are derived from an ancient symbiosis. Despite billions of years of cooperative coevolution - in what is arguably the most important mutualism in the history of life - the persistence of mitochondrial genomes also creates conditions for genetic conflict with the nucleus. Because mitochondrial genomes are present in numerous copies per cell, they are subject to both within- and among-organism levels of selection. Accordingly, 'selfish' genotypes that increase their own proliferation can rise to high frequencies even if they decrease organismal fitness. It has been argued that uniparental (often maternal) inheritance of cytoplasmic genomes evolved to curtail such selfish replication by minimizing within-individual variation and, hence, within-individual selection. However, uniparental inheritance creates conditions for cytonuclear conflict over sex determination and sex ratio, as well as conditions for sexual antagonism when mitochondrial variants increase transmission by enhancing maternal fitness but have the side-effect of being harmful to males (i.e., 'mother's curse'). Here, we review recent advances in understanding selfish replication and sexual antagonism in the evolution of mitochondrial genomes and the mechanisms that suppress selfish interactions, drawing parallels and contrasts with other organelles (plastids) and bacterial endosymbionts that arose more recently. Although cytonuclear conflict is widespread across eukaryotes, it can be cryptic due to nuclear suppression, highly variable, and lineage-specific, reflecting the diverse biology of eukaryotes and the varying architectures of their cytoplasmic genomes.

3D Imaging of Tapetal Mitochondria Suggests the Importance of Mitochondrial Fission in Pollen Growth

Mitochondrial fission occurs frequently in plant cells, but its biological significance is poorly understood because mutants specifically impaired in mitochondrial fission do not show obvious defects in vegetative growth. Here, we revealed that the production of viable pollen was reduced in mutants lacking one of the three main proteins involved in mitochondrial fission in Arabidopsis (Arabidopsis thaliana), DYNAMIN-RELATED PROTEIN3A (DRP3A)/Arabidopsis DYNAMIN-LIKE PROTEIN2A, DRP3B, and ELONGATED MITOCHONDRIA1 (ELM1). In drp3b and elm1, young microspores contained an abnormal number of nuclei, and mature pollen had aberrant accumulation of lipids in their coat and an irregular pollen outer wall. Because the formation of the pollen wall and coat is mainly associated with tapetal function, we used 3D imaging to quantify geometric and textural features of cells and mitochondria in the tapetum at different stages, using isolated single tapetal cells in which the in vivo morphology and volume of cells and mitochondria were preserved. Tapetal cells and their mitochondria changed in the volume and morphology at different developmental stages. Defective mitochondrial fission in the elm1 and drp3b mutants caused changes in mitochondrial status, including mitochondrial elongation, abnormal mitochondrial ultrastructure, a decrease in cross-sectional area, and a slight alteration of mitochondrial distribution, as well as a large reduction in mitochondrial density. Our studies suggest that mitochondrial fission is required for proper mitochondrial status in the tapetum and possibly in pollen as well and therefore plays an important role for the production of viable pollen.

Abnormal tapetum development and energy metabolism associated with sterility in SaNa-1A CMS of Brassica napus L

Abnormal tapetum degradation and anther development in cytoplasmic male sterility SaNa-1A are the main reasons for the anther abortion. SaNa-1A is a novel cytoplasmic male sterility (CMS) line of Brassica napus derived from somatic hybrids of B. napus-Sinapis alba, and SaNa-1B is the corresponding maintainer line. Ultrastructural comparison between developing anthers of sterile and maintainer lines revealed abnormal subcellular structure of pollen mother cells (PMCs) in the CMS line. The PMC volume and size of nucleus and nucleolus in the CMS line were smaller than those in the maintainer line. The abnormal tapetum cell development and delayed tapetum degradation inhibited microspore development. Finally, anther abortion in the CMS line occurred. Physiological and biochemical analyses of developing anthers and mitochondria revealed that over-accumulation of reactive oxygen species (ROS) in the SaNa-1A and deficiency in antioxidant enzyme system aggravated the oxidization of membrane lipids, resulting in malondialdehyde (MDA) accumulation in anthers. High MDA content in the CMS line was toxic to the cells. ROS accumulation in SaNa-1A also affected anther development. Abnormal structure and function of terminal oxidase, which participates in the electron transport chain of mitochondrial membrane, were observed and affected the activity of cytochrome c oxidase and F₁F₀-ATPase, which inhibited ATP biosynthesis. Proline deficiency in SaNa-1A also affected anther development. Few hybridization signals of programmed cell death (PCD) in tetrads of SaNa-1A were identified using TdT-mediated dUTP Nick-End Labeling assay. PCD was not obvious in tapetum cells of SaNa-1A until the unicellular stage. These results validated the cytological differences mentioned above, and proved that abnormal tapetum degradation and anther development in SaNa-1A were the main reasons for the anther abortion.

Metabolomic characterization of sunflower leaf allows discriminating genotype groups or stress levels with a minimal set of metabolic markers

INTRODUCTION

Plant and crop metabolomic analyses may be used to study metabolism across genetic and environmental diversity. Complementary analytical strategies are useful for investigating metabolic changes and searching for biomarkers of response or performance.

METHODS AND OBJECTIVES

The experimental material consisted in eight sunflower lines with two line status, four restorers (R, used as males) and four maintainers (B, corresponding to females) routinely used for sunflower hybrid varietal production, respectively to complement or maintain the cytoplasmic male sterility PET1. These lines were either irrigated at full soil capacity (WW) or submitted to drought stress (DS). Our aim was to combine targeted and non-targeted metabolomics to characterize sunflower leaf composition in order to investigate the effect of line status genotypes and environmental conditions and to find the best and smallest set of biomarkers for line status and stress response using a custom-made process of variables selection.

RESULTS

Five hundred and eighty-eight metabolic variables were measured by using complementary analytical methods such as 1H-NMR, MS-based profiles and targeted analyses of major metabolites. Based on statistical analyses, a limited number of markers were able to separate WW and DS samples in a more discriminant manner than previously published physiological data. Another metabolic marker set was able to discriminate line status.

CONCLUSION

This study underlines the potential of metabolic markers for discriminating genotype groups and environmental conditions. Their potential use for prediction is discussed.

Progressive programmed cell death inwards across the anther wall in male sterile flowers of the gynodioecious plant Plantago lanceolata

A cell death signal is perceived and responded to by epidermal cells first before being conveyed inwards across the anther wall in male sterile Plantago lanceolata flowers. In gynodioecious plants, floral phenotype is determined by an interplay between cytoplasmic male sterility (CMS)-promoting factors and fertility-restoring genes segregating in the nuclear background. Plantago lanceolata exhibits at least four different sterilizing cytoplasms. MS1, a "brown-anther" male sterile phenotype, segregates with a CMSI cytoplasm and a non-restoring nuclear background in P. lanceolata populations. The aim of this study was to investigate the cytology of early anther development in segregating hermaphrodite and male sterile flowers sharing the same CMSI cytoplasm, and to determine if the sterility phenotype correlates with any changes to the normal pattern of programmed cell death (PCD) that occurs during anther development. Cytology shows cellular abnormalities in all four anther wall layers (epidermis, endothecium, middle layer and tapetum), the persistence and enlargement of middle layer and tapetal cells, and the failure of microspore mother cells to complete meiosis in male sterile anthers. In these anthers, apoptotic-PCD occurs earlier than in fertile anthers and is detected in all four cell layers of the anther wall before the middle layer and tapetal cells become enlarged. PCD is separated spatially and temporally within the anther wall, occurring first in epidermal cells before extending radially to cells in the inner anther wall layers. This is the first evidence of a cell death signal being perceived and responded to by epidermal cells first before being conveyed inwards across the anther wall in male sterile plants.

Disassembly of dying cells in diverse organisms

Programmed cell death (PCD) is a conserved phenomenon in multicellular organisms required to maintain homeostasis. Among the regulated cell death pathways, apoptosis is a well-described form of PCD in mammalian cells. One of the characteristic features of apoptosis is the change in cellular morphology, often leading to the fragmentation of the cell into smaller membrane-bound vesicles through a process called apoptotic cell disassembly. Interestingly, some of these morphological changes and cell disassembly are also noted in cells of other organisms including plants, fungi and protists while undergoing 'apoptosis-like PCD'. This review will describe morphologic features leading to apoptotic cell disassembly, as well as its regulation and function in mammalian cells. The occurrence of cell disassembly during cell death in other organisms namely zebrafish, fly and worm, as well as in other eukaryotic cells will also be discussed.

Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement

Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient and historic contexts yielded high proportions of endogenous DNA, and although archaeological DNA was found to be highly degraded, it still provided sufficient coverage to analyze genetic changes over time. Shotgun sequencing data from specimens from the Eden's Bluff archaeological site in Arkansas yielded organellar DNA sequence from specimens up to 3,100 years old. Their sequences match those of modern cultivated sunflowers and are consistent with an early domestication bottleneck in this species. Our findings also suggest that recent breeding of sunflowers has led to a loss of genetic diversity that was present only a century ago in Native American landraces. These breeding episodes also left a profound signature on the mitochondrial and plastid haplotypes in cultivars, as two types were intentionally introduced from other Helianthus species for crop improvement. These findings gained from ancient and historic sunflower specimens underscore how future in-depth gene-based analyses can advance our understanding of the pace and targets of selection during the domestication of sunflower and other crop species.