MEIOTIC F-BOX Is Essential for Male Meiotic DNA Double-Strand Break Repair in Rice

Cytological observation and transcriptome analysis reveal that NTFR1 is a new tetraploid rice fertility gene using the tetraploid fertility-directed lines

Neo-tetraploid rice, a type of high-fertility tetraploid rice, is thought to be a useful material for utilizing its heterosis. However, the mechanism of its high fertility remains little known. Here, two tetraploid fertility-directed lines were generated and used to evaluate their variation on fertility charts. Cytological observations indicated that the low tetraploid fertility-directed lines (LFDL) exhibited a lower seed-setting ratio (12.64 %), pollen fertility (53.28 %), embryo sac fertility (85.71 %) while compared with the high tetraploid fertility-directed lines (HFDL). In addition, approximately 31.44 % and 48.13 % of chromosome lagging at Metaphase I and Metaphase II, and 33.33 % and 53.47 % of chromosome straggling at Anaphase I and Anaphase II were detected in the LFDL, respectively. Transcriptome analysis identified 911 differentially expressed genes (DEGs) in the HFDL compared with the LFDL. Among these DEGs, 202 meiosis-related or stage-specific genes exhibited significant down-regulation in HFDL compared with LFDL. Further, we selected NTFR1 as the candidate gene and verified its fertility phenotype in knock-out mutants, and detected a significant decrease in the seed-setting ratio, pollen viability, pollen fertility, and embryo sac fertility. This study provided a new fertility gene for tetraploid rice, and it may offer the fertility regulatory mechanisms in neo-tetraploid rice.

MORE FLORET1 Interacts with C-type Replication Protein A Complex and Regulates Male Meiosis in Rice

Meiosis plays a pivotal role in plant reproduction, which is also crucial for enhancing genetic diversity. Although the impact of MOF1 on floral organ development and its negative regulation of the key tapetal gene PKS2 have been established, the specific function of MOF1 in male meiotic process remains elusive. In this study, we identified two mutant lines of MOF1 in Nipponbare background. Compared to the wild-type controls, MOF1 mutations resulted in significant reductions in seed setting rate and pollen fertility, partially attributed to its defects in the formation of male meiotic bivalents. RNA-seq analyses and RT-qPCR assays revealed that loss-of-function mutation of MOF1 didn't alter expression levels of 60 known meiotic-regulated genes, suggesting that MOF1 may not function as a transcriptional factor in its meiotic regulation. Yeast two-hybrid and bimolecular fluorescence complementation assays demonstrated the protein-protein interactions among MOF1, RPA2c, RPA1c, as well as FAR1, among which RPA1c and RPA2c involved in meiotic bivalent formation. Furthermore, gene expression pattern analyses and subcellular localization studies indicated the co-expression among above interacted proteins in nucleus during anther development. Our findings provide a mechanistic insight into how MOF1 modulate male meiosis possibly through interactions with key meiotic proteins, facilitating a better understanding of male reproductive regulation.

The F box protein INHIBITOR FOR BROWN FURROWS 1 (IBF1) regulates flavonoid accumulation in rice hull by promoting degradation of chalcone synthase 1

Flavonoids are secondary metabolites of plants that play various roles in plants. The transcriptional level regulation of flavonoid synthesis in plants has been extensively studied, but research on the protein level of flavonoid synthesis in plants is still limited. In the present study, a brown hull mutant, bh2, was screened from an ethane methyl sulfonate (EMS)-induced bank from the seeds of the indica cultivar RH2B. The bh2 mutant exhibited a brown hull phenotype and higher levels of total flavonoids and anthocyanins compared with wild-type plants. We identified the gene INHIBITOR FOR BROWN FURROWS 1 (IBF1) in the bh2 mutant through MutMap analysis and subsequently cloned it. IBF1 encodes an F-box protein and is involved in the formation of an SCF (S-phase kinase-associated protein 1 [SKP1], Cullin, and F-box) complex with the Oryza sativa SKP1-like proteins OSK1/OSK20. Through yeast two-hybrid, bimolecular fluorescence complementation, and pull-down assays, the interaction of IBF1 with chalcone synthase 1 (CHS1) was confirmed. This interaction facilitated the degradation of CHS1 through the ubiquitin-26S proteasome system. The ibf1 chs1 double mutants exhibited normal hull color, restoring the phenotype of ibf1. Genetic analysis suggested that IBF1 regulates hull color in a CHS1-dependent manner. Collectively, our study suggests that IBF1 serves as a crucial negative regulator that controls flavonoid biosynthesis by mediating CHS1 degradation, thereby regulating hull color.

BcWRKY53 promotes chlorophyll biosynthesis and cold tolerance of non-heading Chinese cabbage under cold stress

WRKY transcription factors are widely involved in plant responses to biotic and abiotic stresses, including cold stress. However, they have not been well studied in the regulation of chlorophyll synthesis and cold tolerance. So it is meaningful to analyze the mechanism under cold stress in non-heading Chinese cabbage. Here, BcWRKY53, a transcriptional activator WRKY-III gene, was identified by a screen upstream of the key chlorophyll synthesis genes BcCHLH and BcGUN4. BcWRKY53 was localized in the cell nucleus and induced to a significant extent by cold treatment. Ectopic expression of BcWRKY53 in Arabidopsis not only increased the chlorophyll content under cold stress, but also improved the cold tolerance. After silencing of BcWRKY53, there was a decrease in chlorophyll content and an increase in cold sensitivity. BcWRKY53 could inhibit self-expression by binding W-boxes in its own promoter. In addition, histone deacetylase 9 (BcHDA9) interacted with BcWRKY53 to inhibit BcWRKY53-mediated transcriptional activation. When ectopically overexpressed, BcHDA9 negatively regulates chlorophyll content and cold tolerance under cold treatment. Taken together, this study demonstrated that the cold-inducible transcription factor BcWRKY53 positively regulates BcCHLH and BcGUN4 under the regulation of self-regulation and BcHDA9 interactions. In this way, BcWRKY53 is actively involved in chlorophyll synthesis and the establishment of cold tolerance, which providing practical theoretical support in molecular characterization of cold tolerance and variety selection of non-heading Chinese cabbage.

m6A demethylase OsALKBH5 is required for double-strand break formation and repair by affecting mRNA stability in rice meiosis

N6-methyladenosine (m6A) RNA modification is the most prevalent messenger RNA (mRNA) modification in eukaryotes and plays critical roles in the regulation of gene expression. m6A is a reversible RNA modification that is deposited by methyltransferases (writers) and removed by demethylases (erasers). The function of m6A erasers in plants is highly diversified and their roles in cereal crops, especially in reproductive development essential for crop yield, are largely unknown. Here, we demonstrate that rice OsALKBH5 acts as an m6A demethylase required for the normal progression of male meiosis. OsALKBH5 is a nucleo-cytoplasmic protein, highly enriched in rice anthers during meiosis, that associates with P-bodies and exon junction complexes, suggesting that it is involved in regulating mRNA processing and abundance. Mutations of OsALKBH5 cause reduced double-strand break (DSB) formation, severe defects in DSB repair, and delayed meiotic progression, leading to complete male sterility. Transcriptome analysis and m6A profiling indicate that OsALKBH5-mediated m6A demethylation stabilizes the mRNA level of multiple meiotic genes directly or indirectly, including several genes that regulate DSB formation and repair. Our study reveals the indispensable role of m6A metabolism in post-transcriptional regulation of meiotic progression in rice.

Sequence-based analysis of the rice CAMTA family: haplotype and network analyses

The calmodulin-binding transcription activator (CAMTA) family contributes to stress responses in many plant species. The Oryza sativa ssp. japonica genome harbors seven CAMTA genes; however, intraspecific variation and functional roles of this gene family have not been determined. Here, we comprehensively evaluated the structure and characteristics of the CAMTA genes in japonica rice using bioinformatics approaches and RT-qPCR. Within the CAMTA gene and promoter sequences, 527 single nucleotide polymorphisms were retrieved from 3,024 rice accessions. The CAMTA genes could be subdivided into 5-14 haplotypes. Association analyses between haplotypes and phenotypic traits, such as grain weight and salt stress parameters, identified phenotypic differences between rice subpopulations harboring different CAMTA haplotypes. Co-expression analyses and the identification of CAMTA-specific binding motifs revealed candidate genes regulated by CAMTA. A Gene Ontology functional enrichment analysis of 690 co-expressed genes revealed that CAMTA genes have key roles in defense responses. An interaction analysis identified 30 putative CAMTA interactors. Three genes were identified in co-expression and interaction network analyses, suggesting that they are potentially regulated by CAMTAs. Based on all information obtained together with the phenotypes of the CRISPR-Cas9 knockout mutant lines of three OskCAMTA genes generated, CAMTA1 likely plays important roles in the response to salt stress in rice. Overall, our findings suggest that the CAMTA gene family is involved in development and the salt stress response and reveal candidate target genes, providing a basis for further functional characterization.

GLUTAMYL-tRNA SYNTHETASE 1 deficiency confers thermosensitive male sterility in rice by affecting reactive oxygen species homeostasis

Temperature is one of the key environmental factors influencing crop fertility and yield. Understanding how plants sense and respond to temperature changes is, therefore, crucial for improving agricultural production. In this study, we characterized a temperature-sensitive male sterile mutant in rice (Oryza sativa), glutamyl-tRNA synthetase 1-2 (ers1-2), that shows reduced fertility at high temperatures and restored fertility at low temperatures. Mutation of ERS1 resulted in severely delayed pollen development and meiotic progression at high temperatures, eventually leading to male sterility. Moreover, meiosis-specific events, including synapsis and crossover formation, were also delayed in ers1-2 compared with the wild type. However, these defects were all mitigated by growing ers1-2 at low temperatures. Transcriptome analysis and measurement of ascorbate, glutathione, and hydrogen peroxide (H2O2) contents revealed that the delayed meiotic progression and male sterility in ers1-2 were strongly associated with changes in reactive oxygen species (ROS) homeostasis. At high temperatures, ers1-2 exhibited decreased accumulation of ROS scavengers and overaccumulation of ROS. In contrast, at low temperatures, the antioxidant system of ROS was more active, and ROS contents were lower. These data suggest that ROS homeostasis in ers1-2 is disrupted at high temperatures but restored at low temperatures. We speculate that ERS1 dysfunction leads to changes in ROS homeostasis under different conditions, resulting in delayed or rescued meiotic progression and thermosensitive male fertility. ers1-2 may hold great potential as a thermosensitive material for crop heterosis breeding.

BcSRC2 interacts with BcAPX4 to increase ascorbic acid content for responding ABA signaling and drought stress in pak choi

As a reducing substance, ascorbic acid functioned well in abiotic and biotic stress. However, the regulatory mechanism of drought resistance is rarely known in pak choi. Here we found a gene BcSRC2 containing a C2 domain that responds to ABA signal and drought regulation in pak choi. Silencing of BcSRC2 reduces ascorbic acid content and drought resistance of pak choi. In Arabidopsis, BcSRC2 overexpression promotes ascorbic acid accumulation and increases drought tolerance. Meanwhile, transcriptome analysis between WT and BcSRC2-overexpressing pak choi suggests that ascorbic acid-related genes are regulated. BcSRC2 interacts with BcAPX4 and inhibit APX activity in vitro and in vivo, increasing the ascorbic acid content. We also found that drought stress increases ABA content, which reduces the expression of BcMYB30. BcMYB30 bound to the promoter of BcSRC2 and reduced its expression. Overall, our results suggest that a regulatory module, BcMYB30-BcSRC2-BcAPX4, plays a central role in increasing ascorbic acid content for responding ABA-mediated drought regulation in pak choi.

ETHYLENE RESPONSE FACTOR 070 inhibits flowering in Pak-choi by indirectly impairing BcLEAFY expression

APETALA2/ethylene responsive factors respond to ethylene and participate in many biological and physiological processes, such as plant morphogenesis, stress resistance, and hormone signal transduction. Ethylene responsive factor 070 (BcERF070) is important in flowering. However, the underlying molecular mechanisms of BcERF070 in floral transition in response to ethylene signaling have not been fully characterized. Herein, we explored the function of BcERF070 in Pak-choi [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. Ethylene treatment induced BcERF070 expression and delayed flowering in Pak-choi. Silencing of BcERF070 induced flowering in Pak-choi. BcERF070 interacted with major latex protein-like 328 (BcMLP328), which forms a complex with helix-loop-helix protein 30 (BcbHLH30) to enhance the transcriptional activity of BcbHLH30 on LEAFY (BcLFY), ultimately promoting flowering. However, BcERF070 impaired the BcMLP328-BcbHLH30 complex activation of LEAFY (BcLFY), ultimately inhibiting flowering in Pak-choi. BcERF070 directly promoted the expression of the flowering inhibitor gene B-box 29 (BcBBX29) and delayed flowering by reducing FLOWERING LOCUS T (BcFT) expression. These results suggest that BcERF070 mediates ethylene-reduced flowering by impairing the BcMLP328-BcbHLH30 complex activation of BcLFY and by directly promoting the gene expression of the flowering inhibition factor BcBBX29 to repress BcFT expression. The findings contribute to understanding the molecular mechanisms underlying floral transition in response to ethylene in plants.

Structural Variants and Speciation: Multiple Processes at Play

Research on the genomic architecture of speciation has increasingly revealed the importance of structural variants (SVs) that affect the presence, abundance, position, and/or direction of a nucleotide sequence. SVs include large chromosomal rearrangements such as fusion/fissions and inversions and translocations, as well as smaller variants such as duplications, insertions, and deletions (CNVs). Although we have ample evidence that SVs play a key role in speciation, the underlying mechanisms differ depending on the type and length of the SV, as well as the ecological, demographic, and historical context. We review predictions and empirical evidence for classic processes such as underdominance due to meiotic aberrations and the coupling effect of recombination suppression before exploring how recent sequencing methodologies illuminate the prevalence and diversity of SVs. We discuss specific properties of SVs and their impact throughout the genome, highlighting that multiple processes are at play, and possibly interacting, in the relationship between SVs and speciation.

SCFRMF mediates degradation of the meiosis-specific recombinase DMC1

Meiotic recombination requires the specific RecA homolog DMC1 recombinase to stabilize strand exchange intermediates in most eukaryotes. Normal DMC1 levels are crucial for its function, yet the regulatory mechanisms of DMC1 stability are unknown in any organism. Here, we show that the degradation of Arabidopsis DMC1 by the 26S proteasome depends on F-box proteins RMF1/2-mediated ubiquitination. Furthermore, RMF1/2 interact with the Skp1 ortholog ASK1 to form the ubiquitin ligase complex SCFRMF1/2. Genetic analyses demonstrate that RMF1/2, ASK1 and DMC1 act in the same pathway downstream of SPO11-1 dependent meiotic DNA double strand break formation and that the proper removal of DMC1 is crucial for meiotic crossover formation. Moreover, six DMC1 lysine residues were identified as important for its ubiquitination but not its interaction with RMF1/2. Our results reveal mechanistic insights into how the stability of a key meiotic recombinase that is broadly conserved in eukaryotes is regulated.

The F-box protein SHORT PRIMARY ROOT modulates primary root meristem activity by targeting SEUSS-LIKE protein for degradation in rice

Root meristem activity is essential for root morphogenesis and adaptation, but the molecular mechanism regulating root meristem activity is not fully understood. Here, we identify an F-box family E3 ubiquitin ligase named SHORT PRIMARY ROOT (SHPR) that regulates primary root (PR) meristem activity and cell proliferation in rice. SHPR loss-of-function mutations impair PR elongation in rice. SHPR is involved in the formation of an SCF complex with the Oryza sativa SKP1-like protein OSK1/20. We show that SHPR interacts with Oryza sativa SEUSS-LIKE (OsSLK) in the nucleus and is required for OsSLK polyubiquitination and degradation by the ubiquitin 26S-proteasome system (UPS). Transgenic plants overexpressing OsSLK display a shorter PR phenotype, which is similar to the SHPR loss-of-function mutants. Genetic analysis suggests that SHPR promotes PR elongation in an OsSLK-dependent manner. Collectively, our study establishes SHPR as an E3 ubiquitin ligase that targets OsSLK for degradation, and uncovers a protein ubiquitination pathway as a mechanism for modulating root meristem activity in rice.

The coordinated regulation of early meiotic stages is dominated by non-coding RNAs and stage-specific transcription in wheat

Reproductive success hinges on precisely coordinated meiosis, yet our understanding of how structural rearrangements of chromatin and phase transitions during meiosis are transcriptionally regulated is limited. In crop plants, detailed analysis of the meiotic transcriptome could identify regulatory genes and epigenetic regulators that can be targeted to increase recombination rates and broaden genetic variation, as well as provide a resource for comparison among eukaryotes of different taxa to answer outstanding questions about meiosis. We conducted a meiotic stage-specific analysis of messenger RNA (mRNA), small non-coding RNA (sncRNA), and long intervening/intergenic non-coding RNA (lincRNA) in wheat (Triticum aestivum L.) and revealed novel mechanisms of meiotic transcriptional regulation and meiosis-specific transcripts. Amidst general repression of mRNA expression, significant enrichment of ncRNAs was identified during prophase I relative to vegetative cells. The core meiotic transcriptome was comprised of 9309 meiosis-specific transcripts, 48 134 previously unannotated meiotic transcripts, and many known and novel ncRNAs differentially expressed at specific stages. The abundant meiotic sncRNAs controlled the reprogramming of central metabolic pathways by targeting genes involved in photosynthesis, glycolysis, hormone biosynthesis, and cellular homeostasis, and lincRNAs enhanced the expression of nearby genes. Alternative splicing was not evident in this polyploid species, but isoforms were switched at phase transitions. The novel, stage-specific regulatory controls uncovered here challenge the conventional understanding of this crucial biological process and provide a new resource of requisite knowledge for those aiming to directly modulate meiosis to improve crop plants. The wheat meiosis transcriptome dataset can be queried for genes of interest using an eFP browser located at https://bar.utoronto.ca/efp_wheat/cgi-bin/efpWeb.cgi?dataSource=Wheat_Meiosis.

OsPRD2 is essential for double-strand break formation, but not spindle assembly during rice meiosis

Meiotic recombination starts with the programmed formation of double-strand breaks (DSB) in DNA, which are catalyzed by SPO11, a type II topoisomerase that is evolutionarily conserved, and several other accessary proteins. Homologs of MEIOSIS INHIBITOR 4 (MEI4/REC24/PRD2) are proteins that are also essential for the generation of meiotic DSBs in budding yeast, mice and Arabidopsis thaliana. In Arabidopsis, the protein ARABIDOPSIS THALIANA PUTATIVE RECOMBINATION INITIATION DEFECTS 2/MULTIPOLAR SPINDLE 1 (AtPRD2/MPS1) has been shown to have additional roles in spindle assembly, indicating a functional diversification. Here we characterize the role of the rice MEI4/PRD2 homolog in meiosis. The osprd2 mutant was completely male and female sterile. In male meiocytes of osprd2, no γH2AX foci were detected and twenty-four univalents were produced at diakinesis, suggesting that OsPRD2 is essential for DSB generation. OsPRD2 showed a dynamic localization during meiosis. For instance, OsPRD2 foci first appeared as discrete signals across chromosome at leptotene, and then became confined to the centromeres during zygotene, suggesting that they might be involved in assembly of the spindle. However we did not observe any obvious aberrant morphologies in neither the organization of the bipolar spindle nor in the orientation of the kinetochore in the mutant. These findings suggest that in rice PRD2 might not be required for spindle assembly and organization, as it does in Arabidopsis. Taken together our results indicate that plant MEI4/PRD2 homologs do play a conserved role in the formation of meiotic DSBs in DNA, but that their involvement in bipolar spindle assembly is rather species-specific.

Stomatal Development and Gene Expression in Rice Florets

Stomata play a fundamental role in modulating the exchange of gases between plants and the atmosphere. These microscopic structures form in high numbers on the leaf epidermis and are also present on flowers. Although leaf stomata are well studied, little attention has been paid to the development or function of floral stomata. Here, we characterize in detail the spatial distribution and development of the floral stomata of the indica rice variety IR64. We show that stomatal complexes are present at low density on specific areas of the lemma, palea and anthers and are morphologically different compared to stomata found on leaves. We reveal that in the bract-like organs, stomatal development follows the same cell lineage transitions as in rice leaves and demonstrate that the overexpression of the stomatal development regulators OsEPFL9-1 and OsEPF1 leads to dramatic changes in stomatal density in rice floral organs, producing lemma with approximately twice as many stomata (OsEPFL9-1_oe) or lemma where stomata are practically absent (OsEPF1_oe). Transcriptomic analysis of developing florets also indicates that the cellular transitions during the development of floral stomata are regulated by the same genetic network used in rice leaves. Finally, although we were unable to detect an impact on plant reproduction linked to changes in the density of floral stomata, we report alterations in global gene expression in lines overexpressing OsEPF1 and discuss how our results reflect on the possible role(s) of floral stomata.

Emerging roles of the ubiquitin-proteasome pathway in enhancing crop yield by optimizing seed agronomic traits

Ubiquitin-proteasome pathway has the potential to modulate crop productivity by influencing agronomic traits. Being sessile, the plant often uses the ubiquitin-proteasome pathway to maintain the stability of different regulatory proteins to survive in an ever-changing environment. The ubiquitin system influences plant reproduction, growth, development, responses to the environment, and processes that control critical agronomic traits. E3 ligases are the major players in this pathway, and they are responsible for recognizing and tagging the targets/substrates. Plants have a variety of E3 ubiquitin ligases, whose functions have been studied extensively, ranging from plant growth to defense strategies. Here we summarize three agronomic traits influenced by ubiquitination: seed size and weight, seed germination, and accessory plant agronomic traits particularly panicle architecture, tillering in rice, and tassels branch number in maize. This review article highlights some recent progress on how the ubiquitin system influences the stability/modification of proteins that determine seed agronomic properties like size, weight, germination and filling, and ultimately agricultural productivity and quality. Further research into the molecular basis of the aforementioned processes might lead to the identification of genes that could be modified or selected for crop development. Likewise, we also propose advances and future perspectives in this regard.

An F-box protein ACOZ1 functions in crossover formation by ensuring proper chromosome compaction during maize meiosis

Meiosis is an essential reproductive process to create new genetic variation. During early meiosis, higher order chromosome organization creates a platform for meiotic processes to ensure the accuracy of recombination and chromosome segregation. However, little is known about the regulatory mechanisms underlying dynamic chromosome organization in plant meiosis. Here, we describe abnormal chromosome organization in zygotene1 (ACOZ1), which encodes a canonical F-box protein in maize. In acoz1 mutant meiocytes, chromosomes maintain a leptotene-like state and never compact to a zygotene-like configuration. Telomere bouquet formation and homologous pairing are also distorted and installation of synaptonemal complex ZYP1 protein is slightly defective. Loading of early recombination proteins RAD51 and DMC1 is unaffected, indicating that ACOZ1 is not required for double strand break formation or repair. However, crossover formation is severely disturbed. The ACOZ1 protein localizes on the boundary of chromatin, rather directly to chromosomes. Furthermore, we identified that ACOZ1 interacts with SKP1 through its C-terminus, revealing that it acts as a subunit of the SCF E3 ubiquitin/SUMO ligase complex. Overall, our results suggest that ACOZ1 functions independently from the core meiotic recombination pathway to influence crossover formation by controlling chromosome compaction during maize meiosis.

Review: Exploring possible approaches using ubiquitylation and sumoylation pathways in modifying plant stress tolerance

Ubiquitin and similar proteins, such as SUMO, are utilized by plants to modify target proteins to rapidly change their stability and activity in cells. This review will provide an overview of these crucial protein interactions with a focus on ubiquitylation and sumoylation in plants and how they contribute to stress tolerance. The work will also explore possibilities to use these highly conserved pathways for novel approaches to generate more robust crop plants better fit to cope with abiotic and biotic stress situations.

SCF ubiquitin E3 ligase regulates DNA double-strand breaks in early meiotic recombination

Homeostasis of meiotic DNA double strand breaks (DSB) is critical for germline genome integrity and homologous recombination. Here we demonstrate an essential role for SKP1, a constitutive subunit of the SCF (SKP1-Cullin-F-box) ubiquitin E3 ligase, in early meiotic processes. SKP1 restrains accumulation of HORMAD1 and the pre-DSB complex (IHO1-REC114-MEI4) on the chromosome axis in meiotic germ cells. Loss of SKP1 prior to meiosis leads to aberrant localization of DSB repair proteins and a failure in synapsis initiation in meiosis of both males and females. Furthermore, SKP1 is crucial for sister chromatid cohesion during the pre-meiotic S-phase. Mechanistically, FBXO47, a meiosis-specific F-box protein, interacts with SKP1 and HORMAD1 and targets HORMAD1 for polyubiquitination and degradation in HEK293T cells. Our results support a model wherein the SCF ubiquitin E3 ligase prevents hyperactive DSB formation through proteasome-mediated degradation of HORMAD1 and subsequent modulation of the pre-DSB complex during meiosis.

Natural variation in WHITE-CORE RATE 1 regulates redox homeostasis in rice endosperm to affect grain quality

Grain chalkiness reduces the quality of rice (Oryza sativa) and is a highly undesirable trait for breeding and marketing. However, the underlying molecular cause of chalkiness remains largely unknown. Here, we cloned the F-box gene WHITE-CORE RATE 1 (WCR1), which negatively regulates grain chalkiness and improves grain quality in rice. A functional A/G variation in the promoter region of WCR1 generates the alleles WCR1A and WCR1G, which originated from tropical japonica and wild rice Oryza rufipogon, respectively. OsDOF17 is a transcriptional activator that binds to the AAAAG cis-element in the WCR1A promoter. WCR1 positively affects the transcription of the metallothionein gene MT2b and interacts with MT2b to inhibit its 26S proteasome-mediated degradation, leading to decreased reactive oxygen species production and delayed programmed cell death in rice endosperm. This, in turn, leads to reduced chalkiness. Our findings uncover a molecular mechanism underlying rice chalkiness and identify the promising natural variant WCR1A, with application potential for rice breeding.

FBXO47 is essential for preventing the synaptonemal complex from premature disassembly in mouse male meiosis

Meiotic prophase I is a prolonged G2 phase that ensures the completion of numerous meiosis-specific chromosome events. During meiotic prophase I, homologous chromosomes undergo synapsis to facilitate meiotic recombination yielding crossovers. It remains largely elusive how homolog synapsis is temporally maintained and destabilized during meiotic prophase I. Here we show that FBXO47 is the stabilizer of the synaptonemal complex during male meiotic prophase I. Disruption of FBXO47 shows severe impact on homologous chromosome synapsis, meiotic recombination, and XY body formation, leading to male infertility. Notably, in the absence of FBXO47, although once homologous chromosomes are synapsed, the synaptonemal complex is precociously disassembled before progressing beyond pachytene. Remarkably, Fbxo47 KO spermatocytes remain in an earlier stage of meiotic prophase I and lack crossovers, despite apparently exhibiting diplotene-like chromosome morphology. We propose that FBXO47 plays a crucial role in preventing the synaptonemal complex from premature disassembly during cell cycle progression of meiotic prophase I.

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FBXO47 is a stabilizer of the synaptonemal complex during male meiotic prophase

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FBXO47 KO shows precocious disassembly of the synaptonemal complex

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FBXO47 may function independently of SCF E3 ligase to maintain homolog synapsis

GIpred: a computational tool for prediction of GIGANTEA proteins using machine learning algorithm

In plants, GIGANTEA (GI) protein plays different biological functions including carbon and sucrose metabolism, cell wall deposition, transpiration and hypocotyl elongation. This suggests that GI is an important class of proteins. So far, the resource-intensive experimental methods have been mostly utilized for identification of GI proteins. Thus, we made an attempt in this study to develop a computational model for fast and accurate prediction of GI proteins. Ten different supervised learning algorithms i.e., SVM, RF, JRIP, J48, LMT, IBK, NB, PART, BAGG and LGB were employed for prediction, where the amino acid composition (AAC), FASGAI features and physico-chemical (PHYC) properties were used as numerical inputs for the learning algorithms. Higher accuracies i.e., 96.75% of AUC-ROC and 86.7% of AUC-PR were observed for SVM coupled with AAC + PHYC feature combination, while evaluated with five-fold cross validation. With leave-one-out cross validation, 97.29% of AUC-ROC and 87.89% of AUC-PR were respectively achieved. While the performance of the model was evaluated with an independent dataset of 18 GI sequences, 17 were observed as correctly predicted. We have also performed proteome-wide identification of GI proteins in wheat, followed by functional annotation using Gene Ontology terms. A prediction server "GIpred" is freely accessible at http://cabgrid.res.in:8080/gipred/ for proteome-wide recognition of GI proteins.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01130-6.

RNA N6-methyladenosine modification promotes auxin biosynthesis required for male meiosis in rice

N⁶-methyladenosine (m⁶A) RNA modification confers an essential layer of gene regulation in living organisms, including plants; yet, the underlying mechanisms of its deposition on specific target mRNAs involved in key plant developmental processes are so far unknown. Here, we show that a core component of the rice m⁶A methyltransferase complex, OsFIP37, is recruited by an RNA-binding protein, OsFIP37-associated protein 1 (OsFAP1), to mediate m⁶A RNA modification on an auxin biosynthesis gene, OsYUCCA3, during microsporogenesis. This stabilizes OsYUCCA3 mRNA and promotes local auxin biosynthesis in anthers during male meiosis, which is essential for meiotic division and subsequent pollen development in rice. Loss of function of OsFAP1 causes dissociation of OsFIP37 with OsYUCCA3 and the resulting abolished m⁶A deposition on OsYUCCA3. Our findings reveal that OsFAP1-dependent m⁶A deposition on OsYUCCA3 by OsFIP37 constitutes a hitherto unknown link between RNA modification and hormonal control of male meiosis in plant reproductive development.

Gibberellins orchestrate panicle architecture mediated by DELLA-KNOX signalling in rice

Panicle architecture is a key determinant of grain yield in cereals, but the mechanisms governing panicle morphogenesis and organ development remain elusive. Here, we have identified a quantitative trait locus (qPA1) associated with panicle architecture using chromosome segment substitution lines from parents Nipponbare and 9311. The panicle length, branch number and grain number of Nipponbare were significantly higher than CSSL-9. Through map-based cloning and complementation tests, we confirmed that qPA1 was identical to SD1 (Semi Dwarf1), which encodes a gibberellin 20-oxidase enzyme participating in gibberellic acid (GA) biosynthesis. Transcript analysis revealed that SD1 was widely expressed during early panicle development. Analysis of sd1/osga20ox2 and gnp1/ osga20ox1 single and double mutants revealed that the two paralogous enzymes have non-redundant functions during panicle development, likely due to differences in spatiotemporal expression; GNP1 expression under control of the SD1 promoter could rescue the sd1 phenotype. The DELLA protein SLR1, a component of the GA signalling pathway, accumulated more highly in sd1 plants. We have demonstrated that SLR1 physically interacts with the meristem identity class I KNOTTED1-LIKE HOMEOBOX (KNOX) protein OSH1 to repress OSH1-mediated activation of downstream genes related to panicle development, providing a mechanistic link between gibberellin and panicle architecture morphogenesis.

Fanconi anemia ortholog FANCM regulates meiotic crossover distribution in plants

Meiotic recombination increases genetic diversity and manipulation of its frequency and distribution holds great promise in crop breeding. In Arabidopsis thaliana, FANCM (a homolog of mammalian Fanconi anemia complementation group M) suppresses recombination and its function seems conserved in other species including the rosids Brassica spp. and pea (Pisum sativum), and the monocot rice (Oryza sativa). To examine the role of FANCM during meiotic recombination in lettuce (Lactuca sativa, an asterid), we characterized the function of lettuce LsFANCM and found that it can functionally substitute for AtFANCM in transgenic Arabidopsis plants. Moreover, three independent CRISPR/Cas9-edited lettuce Lsfancm mutants showed reduced pollen viability and seed setting. Unexpectedly, analyses of chromosome behavior revealed that 77.8% of Lsfancm meiocytes exhibited univalents. The normal formation of double-strand breaks in DNA and the discontinuous assembly of synaptonemal complex in Lsfancm mutants supports the hypothesis that LsFANCM might be dispensable for the initiation of meiotic recombination but required for normal synapsis. Furthermore, the frequency of lettuce HEI10 (Human Enhancer of Invasion 10) foci, a marker for Class-I crossovers (COs), was similar between wild-type (WT) and Lsfancm. Strikingly, the distribution of LsHEI10 foci and chiasmata in Lsfancm meiotic chromosomes was markedly different from the WT. A similar alteration in the distribution of Class-I COs was also observed in the Arabidopsis Atfancm mutant. Taken together, these results demonstrate that FANCM is important for shaping the distribution of meiotic Class-I COs in plants, and reveal an evolutionarily divergent role for FANCM in meiotic bivalent formation between Arabidopsis and lettuce.

Ubiquitination in Plant Meiosis: Recent Advances and High Throughput Methods

Meiosis is a specialized cell division which is essential to sexual reproduction. The success of this highly ordered process involves the timely activation, interaction, movement, and removal of many proteins. Ubiquitination is an extraordinarily diverse post-translational modification with a regulatory role in almost all cellular processes. During meiosis, ubiquitin localizes to chromatin and the expression of genes related to ubiquitination appears to be enhanced. This may be due to extensive protein turnover mediated by proteasomal degradation. However, degradation is not the only substrate fate conferred by ubiquitination which may also mediate, for example, the activation of key transcription factors. In plant meiosis, the specific roles of several components of the ubiquitination cascade-particularly SCF complex proteins, the APC/C, and HEI10-have been partially characterized indicating diverse roles in chromosome segregation, recombination, and synapsis. Nonetheless, these components remain comparatively poorly understood to their counterparts in other processes and in other eukaryotes. In this review, we present an overview of our understanding of the role of ubiquitination in plant meiosis, highlighting recent advances, remaining challenges, and high throughput methods which may be used to overcome them.

The Landscape of the Genomic Distribution and the Expression of the F-Box Genes Unveil Genome Plasticity in Hexaploid Wheat during Grain Development and in Response to Heat and Drought Stress

FBX proteins are subunits of the SCF complex (Skp1-cullin-FBX) belonging to the E3 ligase family, which is involved in the ubiquitin-proteasome 26S (UPS) pathway responsible for the post-translational protein turnover. By targeting, in a selective manner, key regulatory proteins for ubiquitination and 26S proteasome degradation, FBX proteins play a major role in plant responses to diverse developmental and stress conditions. Although studies on the genomic organization of the FBX gene family in various species have been reported, knowledge related to bread wheat (Triticum aestivum) is scarce and needs to be broadened. Using the latest assembly of the wheat genome, we identified 3670 TaFBX genes distributed non-homogeneously within the three subgenomes (A, B and D) and between the 21 chromosomes, establishing it as one of the richest gene families among plant species. Based on the presence of the five different chromosomal regions previously identified, the present study focused on the genomic distribution of the TaFBX family and the identification of differentially expressed genes during the embryogenesis stages and in response to heat and drought stress. Most of the time, when comparing the expected number of genes (taking into account the formal gene distribution on the entire wheat genome), the TaFBX family harbors a different pattern at the various stratum of observation (subgenome, chromosome, chromosomal regions). We report here that the local gene expansion of the TaFBX family must be the consequence of multiple and complex events, including tandem and small-scale duplications. Regarding the differentially expressed TaFBX genes, while the majority of the genes are localized in the distal chromosomal regions (R1 and R3), differentially expressed genes are more present in the interstitial regions (R2a and R2b) than expected, which could be an indication of the preservation of major genes in those specific chromosomal regions.

Exploiting Genic Male Sterility in Rice: From Molecular Dissection to Breeding Applications

Rice (Oryza sativa L.) occupies a very salient and indispensable status among cereal crops, as its vast production is used to feed nearly half of the world's population. Male sterile plants are the fundamental breeding materials needed for specific propagation in order to meet the elevated current food demands. The development of the rice varieties with desired traits has become the ultimate need of the time. Genic male sterility is a predominant system that is vastly deployed and exploited for crop improvement. Hence, the identification of new genetic elements and the cognizance of the underlying regulatory networks affecting male sterility in rice are crucial to harness heterosis and ensure global food security. Over the years, a variety of genomics studies have uncovered numerous mechanisms regulating male sterility in rice, which provided a deeper and wider understanding on the complex molecular basis of anther and pollen development. The recent advances in genomics and the emergence of multiple biotechnological methods have revolutionized the field of rice breeding. In this review, we have briefly documented the recent evolution, exploration, and exploitation of genic male sterility to the improvement of rice crop production. Furthermore, this review describes future perspectives with focus on state-of-the-art developments in the engineering of male sterility to overcome issues associated with male sterility-mediated rice breeding to address the current challenges. Finally, we provide our perspectives on diversified studies regarding the identification and characterization of genic male sterility genes, the development of new biotechnology-based male sterility systems, and their integrated applications for hybrid rice breeding.

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I

In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental and genetic factors. To gain insights into this specialized reproductive development program we used short- and long-read RNA-sequencing (RNA-seq) to study the temporal dynamics of transcript abundance in immuno-cytologically staged barley (Hordeum vulgare) anthers and meiocytes. We show that the most significant transcriptional changes in anthers occur at the transition from pre-meiosis to leptotene-zygotene, which is followed by increasingly stable transcript abundance throughout prophase I into metaphase I-tetrad. Our analysis reveals that the pre-meiotic anthers are enriched in long non-coding RNAs (lncRNAs) and that entry to meiosis is characterized by their robust and significant down regulation. Intriguingly, only 24% of a collection of putative meiotic gene orthologs showed differential transcript abundance in at least one stage or tissue comparison. Argonautes, E3 ubiquitin ligases, and lys48 specific de-ubiquitinating enzymes were enriched in prophase I meiocyte samples. These developmental, time-resolved transcriptomes demonstrate remarkable stability in transcript abundance in meiocytes throughout prophase I after the initial and substantial reprogramming at meiosis entry and the complexity of the regulatory networks involved in early meiotic processes.

Rice OsBRCA2 Is Required for DNA Double-Strand Break Repair in Meiotic Cells

The mammalian BREAST CANCER 2 (BRCA2) gene is a tumor suppressor that plays a crucial role in DNA repair and homologous recombination (HR). Here, we report the identification and characterization of OsBRCA2, the rice orthologue of human BRCA2. Osbrca2 mutant plants exhibit normal vegetative growth but experience complete male and female sterility as a consequence of severe meiotic defects. Pairing, synapsis and recombination are impaired in osbrca2 male meiocytes, leading to chromosome entanglements and fragmentation. In the absence of OsBRCA2, localization to the meiotic chromosome axes of the strand-invasion proteins OsRAD51 and OsDMC1 is severely reduced and in vitro OsBRCA2 directly interacts with OsRAD51 and OsDMC1. These results indicate that OsBRCA2 is essential for facilitating the loading of OsRAD51 and OsDMC1 onto resected ends of programmed double-strand breaks (DSB) during meiosis to promote single-end invasions of homologous chromosomes and accurate recombination. In addition, treatment of osbrca2-1 seedlings with mitomycin C (MMC) led to hypersensitivity. As MMC is a genotoxic agent that creates DNA lesions in the somatic cells that can only be repaired by HR, these results suggest that OsBRCA2 has a conserved role in DSB repair and HR in rice.

Transcriptome and Gene Editing Analyses Reveal MOF1a Defect Alters the Expression of Genes Associated with Tapetum Development and Chromosome Behavior at Meiosis Stage Resulting in Low Pollen Fertility of Tetraploid Rice

Autotetraploid rice is a useful rice germplasm for polyploid rice breeding. However, low fertility limits its commercial production. A neo-tetraploid rice with high fertility was developed from the progenies of crossing between autotetraploid lines by our research group. Our previous study showed that a myeloblastosis (MYB) transcription factor, MOF1, might be associated with the pollen development in tetraploid rice. However, little information is available about its role in pollen development in tetraploid rice. Here, we identified a new haplotype of MOF1 from neo-tetraploid rice and marked it as MOF1a. Transcriptome and qRT-PCR analysis demonstrated that MOF1a highly expressed in anthers, and displayed differential expression in neo-tetraploid rice compared to tetraploid rice line with low pollen fertility. The mutant (mof1a) of MOF1a, which was generated by CRISPR/Cas9 knockout in neo-tetraploid rice, showed low pollen fertility, and also exhibited abnormal tapetum and middle layer development, and defective chromosome behaviors during meiosis. A total of 13 tapetal related genes were found to be up-regulated in meiotic anthers of MOF1a compared with wild type plants by RNA-seq analysis, including CYP703A3, PTC1, and OsABCG26, which had been demonstrated to affect tapetal development. Moreover, 335 meiosis-related genes displayed differential expression patterns at same stage, including nine important meiosis-related genes, such as metallothionein OsMT1a. These results demonstrated that MOF1a plays an important role in pollen development and provides a foundation for understanding the molecular mechanism underlying MOF1a in reproduction of tetraploid rice.

In vitro effects of androgen on testicular development by the AR-foxl3-rec8/fbxo47 axis in orange-spotted grouper (Epinephelus coioides)

In orange-spotted grouper, androgen can promote the development of testis and spermatogenesis, but the effect of androgen on testis development is unclear. Forkhead box L 3 (Foxl3) is important in the development of fish testis. Rec8 and fbxo47 are involved in meiosis, which impacts spermatogenesis. The present study investigated the plausible role of testis development through the Foxl3 transcriptional regulation of rec8 and fbxo47. The results of tissue distribution showed that rec8 and fbxo47 are highly expressed in gonad. In addition, the highest expression of foxl3, rec8, and fbxo47 was in the testis and intersex compared with the other stages of gonadal development, suggesting that foxl3, rec8, and fbxo47 are important in testis development. In addition, by using dual-luciferase assays, we found that the androgen can increase foxl3 promoter activity and Foxl3 can upregulate rec8 and fbxo47 promoter activity. Furthermore, the addition of β-testosterone significantly increased foxl3, rec8, and fbxo47 promoter activity. Together, these results suggest that foxl3 plays a decisive role in testis development by regulating the expression of rec8 or fbxo47 and imply that AR-foxl3-rec8/fbxo47 affects the testis development pathway.

foxl3, a sexual switch in germ cells, initiates two independent molecular pathways for commitment to oogenesis in medaka

Germ cells have the ability to differentiate into eggs and sperm and must determine their sexual fate. In vertebrates, the mechanism of commitment to oogenesis following the sexual fate decision in germ cells remains unknown. Forkhead-box protein L3 (foxl3) is a switch gene involved in the germline sexual fate decision in the teleost fish medaka (Oryzias latipes). Here, we show that foxl3 organizes two independent pathways of oogenesis regulated by REC8 meiotic recombination protein a (rec8a), a cohesin component, and F-box protein (FBP) 47 (fbxo47), a subunit of E3 ubiquitin ligase. In mutants of either gene, germ cells failed to undergo oogenesis but developed normally into sperm in testes. Disruption of rec8a resulted in arrest at a meiotic pachytenelike stage specifically in females, revealing a sexual difference in meiotic progression. Analyses of fbxo47 mutants showed that this gene regulates transcription factors that facilitate folliculogenesis: LIM homeobox 8 (lhx8b), factor in the germline α (figla), and newborn ovary homeobox (nobox). Interestingly, we found that the fbxo47 pathway ensures that germ cells do not deviate from an oogenic pathway until they reach diplotene stage. The mutant phenotypes together with the timing of their expression imply that germline feminization is established during early meiotic prophase I.

DWT1/DWL2 act together with OsPIP5K1 to regulate plant uniform growth in rice

Uniform growth of the main shoot and tillers significantly influences rice plant architecture and grain yield. The WUSCHEL-related homeobox transcription factor DWT1 is a key regulator of this important agronomic trait, disruption of which causes enhanced main shoot dominance and tiller dwarfism by an unknown mechanism. Here, we have used yeast-two-hybrid screening to identify OsPIP5K1, a member of the rice phosphatidylinositol-4-phosphate 5-kinase family, as a protein that interacts with DWT1. Cytological analyses confirmed that DWT1 induces accumulation of OsPIP5K1 and its product PI(4,5)P₂ , a phosphoinositide secondary messenger, in nuclear bodies. Mutation of OsPIP5K1 compounds the dwarf dwt1 phenotype but abolishes the main shoot dominance. Conversely, overexpression of OsPIP5K1 partially rescues dwt1 developmental defects. Furthermore, we showed that DWL2, the homologue of DWT1, is also able to interact with OsPIP5K1 and shares partial functional redundancy with DWT1 in controlling rice uniformity. Overall, our data suggest that nuclear localised OsPIP5K1 acts with DWT1 and/or DWL2 to coordinate the uniform growth of rice shoots, likely to be through nuclear phosphoinositide signals, and provides insights into the regulation of rice uniformity via a largely unexplored plant nuclear signalling pathway.

Signaling-mediated meiotic recombination in plants

Meiotic recombination provides genetic diversity in populations and ensures accurate homologous chromosome segregation for genome integrity. During meiosis, recombination processes, from DNA double strand breaks (DSBs) to crossover formation are tightly linked to higher order chromosome structure, including chromatid cohesion, axial element formation, homolog pairing and synapsis. The extensive studies on plant meiosis have revealed the important conserved roles for meiotic proteins in homologous recombination. Recent works have focused on elucidating the mechanistic basis of how meiotic proteins regulate recombination events via protein complex formation and modifications such as phosphorylation, ubiquitination, and SUMOylation. Here, we highlight recent advances on the signaling and modifications of meiotic proteins that mediate the formation of DSBs and crossovers in plants.

Overexpression of rice F-box protein OsFBX322 confers increased sensitivity to gamma irradiation in Arabidopsis

Ionizing radiation has a substantial effect on physiological and biochemical processes in plants via induction of transcriptional changes and diverse genetic alterations. Previous microarray analysis showed that rice OsFBX322, which encodes a rice F-box protein, was downregulated in response to three types of ionizing radiation: gamma irradiation, ion beams, and cosmic rays. In order to characterize the radiation-responsive genes in rice, OsFBX322 was selected for further analysis. OsFBX322 expression patterns in response to radiation were confirmed using quantitative RT-PCR. Transient expression of a GFP-OsFBX322 fusion protein in tobacco leaf epidermis indicated that OsFBX322 is localized to the nucleus. To determine the effect of OsFBX322 expression on radiation response, OsFBX322 was overexpressed in Arabidopsis. Transgenic overexpression lines were more sensitive to gamma irradiation than control plants. These results suggest that OsFBX322 plays a negative role in the defense response to radiation in plants. In addition, we obtained four co-expression genes of OsFBX322 by specific co-expression networks using the ARANCE. Quantitative RT-PCR showed that the four genes were also downregulated after exposure to the three types of radiation. These results imply that the co-expressed genes may serve as key regulators in the radiation response pathway in plants.

A Multiprotein Complex Regulates Interference-Sensitive Crossover Formation in Rice

In most eukaryotes, a set of conserved proteins that are collectively termed ZMM proteins (named for molecular zipper 1 [ZIP1], ZIP2, ZIP3, and ZIP4, MutS homologue 4 [MSH4] and MSH5, meiotic recombination 3, and sporulation 16 [SPO16] in yeast [Saccharomyces cerevisiae]) are essential for the formation of the majority of meiotic crossovers (COs). Recent reports indicated that ZIP2 acts together with SPO16 and ZIP4 to control CO formation through recognizing and stabilizing early recombination intermediates in budding yeast. However, whether this mechanism is conserved in plants is not clear. Here, we characterized the functions of SHORTAGE OF CHIASMATA 1 (OsSHOC1; ZIP2 ortholog) and PARTING DANCERS (OsPTD; SPO16 ortholog) and their interactions with other ZMM proteins in rice (Oryza sativa). We demonstrated that disruption of OsSHOC1 caused a reduction of CO numbers to ∼83% of wild-type CO numbers, whereas synapsis and early meiotic recombination steps were not affected. Furthermore, OsSHOC1 interacts with OsPTD, which is responsible for the same set of CO formations as OsSHOC1. In addition, OsSHOC1 and OsPTD are required for the normal loading of other ZMM proteins, and conversely, the localizations of OsSHOC1 and OsPTD were also affected by the absence of OsZIP4 and human enhancer of invasion 10 in rice (OsHEI10). OsSHOC1 interacts with OsZIP4 and OsMSH5, and OsPTD interacts with OsHEI10. Furthermore, bimolecular fluorescence complementation and yeast-three hybrid assays demonstrated that OsSHOC1, OsPTD, OsHEI10, and OsZIP4 were able to form various combinations of heterotrimers. Moreover, statistical and genetic analysis indicated that OsSHOC1 and OsPTD are epistatic to OsHEI10 and OsZIP4 in meiotic CO formation. Taken together, we propose that OsSHOC1, OsPTD, OsHEI10, and OsZIP4 form multiple protein complexes that have conserved functions in promoting class I CO formation.

Cytological and proteomic analyses of floral buds reveal an altered atlas of meiosis in autopolyploid Brassica rapa

Background

Polyploidy is considered as a basic event in plant speciation and evolution in nature, and the cytological and proteomic profilings of floral buds at meiosis (FAM) would definitely contribute to a better understanding of the polyploid-associated effects during plant reproduction cycle.

Results

Herein, the cytological investigations demonstrated that chromosome behaviors such as univalent and multivalent at prophase I, chaotic alignments at metaphase, aberrant segregation at telophase, were frequently observed during meiosis in autotetraploid Brassica rapa. The proteomic analysis showed a total of 562 differentially expressed proteins (DEPs) were identified in FAM between autotetraploid and diploid B. rapa. Notably, PARP2 and LIG1 related to base excision repair and BARD1 involved in recombination were significantly down-regulated in autotetraploid B. rapa, which indicated DNA repair pathway were more likely affected during meiosis in autotetraploid B. rapa. The functional analysis showed that DEPs assigned to “chromatin structure and dynamics”, “cell cycle control, cell division, chromosome partitioning” and “cytoskeleton” were preferentially up-regulated, which suggested a robust regulation of cell division in autotetraploid B. rapa. In combination with the floral RNA-seq data released, a number of DEPs were found positively correlated with their transcript abundance, but posttranslational modification of proteins might also play a role in regulating meiosis course after polyploidization.

Conclusions

In general, this study provides a detailed cytology and proteome landscape of FAM between diploid and autotetraploid B. rapa, which definitely affords us a better understanding of uniformity and discrepancy of meiosis at the plant reproductive stage before and after polyploidization.

Electronic supplementary material

The online version of this article (10.1186/s13578-019-0313-z) contains supplementary material, which is available to authorized users.

The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice

N⁶-Methyladenosine (m⁶A) RNA methylation plays important roles during development in different species. However, knowledge of m⁶A RNA methylation in monocots remains limited. In this study, we reported that OsFIP and OsMTA2 are the components of m⁶A RNA methyltransferase complex in rice and uncovered a previously unknown function of m⁶A RNA methylation in regulation of plant sporogenesis. Importantly, OsFIP is essential for rice male gametogenesis. Knocking out of OsFIP results in early degeneration of microspores at the vacuolated pollen stage and simultaneously causes abnormal meiosis in prophase I. We further analyzed the profile of rice m⁶A modification during sporogenesis in both WT and OsFIP loss-of-function plants, and identified a rice panicle specific m⁶A modification motif “UGWAMH”. Interestingly, we found that OsFIP directly mediates the m⁶A methylation of a set of threonine protease and NTPase mRNAs and is essential for their expression and/or splicing, which in turn regulates the progress of sporogenesis. Our findings revealed for the first time that OsFIP plays an indispensable role in plant early sporogenesis. This study also provides evidence for the different functions of the m⁶A RNA methyltransferase complex between rice and Arabidopsis.

N⁶-Methyladenosine (m⁶A) is the most abundant internal modification of eukaryotic mRNA, and m⁶A mRNA methylation affects almost every stage of mRNA metabolism. However, the components of the m⁶A methyltransferase complex and their functions in monocots are completely unknown. In this study, we identified the components of the m⁶A RNA methyltransferase complex in rice, and uncovered a hitherto unknown function of m⁶A RNA methylation in regulating early microspore apoptosis. We also systematically analyzed the characteristics of m⁶A modification during sporogenesis for the first time, and revealed the sporogenesis stage-specific distribution of m⁶A peaks along genes and the specific modification motif in rice, which are different from that of other species and other developmental stages. The target genes of m⁶A methyltransferase complex member OsFIP were also identified in this study. Given the important roles of posttranscriptional mRNA regulation in gene expression and sporogenesis in plants, the findings of this study should stimulate more studies exploring the role of plant m⁶A methyltransferase and other components.

Cytological and transcriptome analyses reveal abrupt gene expression for meiosis and saccharide metabolisms that associated with pollen abortion in autotetraploid rice

Autotetraploid rice is a useful germplasm that has four chromosome sets and strong biological advantages; however, low fertility limits its commercial utilization. Little information is available about the DNA variation and differential gene expressions associated with low fertility in autotetraploid rice. In the present study, 81 SNPs and 182 InDels were identified in T449 (an autotetraploid rice line with low fertility) compared to E249 (diploid counterpart) by whole-genome re-sequencing. We detected only three non-synonymous SNPs and six large-effect InDels, which were associated with three and six genes, respectively. A total of 75 meiosis-related differentially expressed genes were detected during the meiosis stage by transcriptome analysis, including OsMTOPVIB, which is essential for meiotic DSB formation, and OsMOF, which takes part in homologous chromosome pairing and synapsis. Approximately 20.69% lagging chromosome at metaphase I and 4.65% abnormal tetrad were observed in T449. Moreover, transcriptome analysis revealed down-regulation of a sucrose transporter (OsSUT5) and two monosaccharide transporters (OsMST1 and OsMST8) in T449 at the single microspore stage, and their expression levels were verified by qRT-PCR. Cytological observation of saccharide distribution showed abnormal accumulation of saccharides in T449 and the contents of fructose and glucose were markedly higher in T449 than E249 at the single microspore stage. Our results suggested that polyploidy not only induces abrupt expression changes in the meiosis-related genes that lead to abnormal chromosome behavior, but also causes changes in the saccharide distribution and expression patterns of saccharide-related genes, which jointly causes sterility in the autotetraploid rice.

Characterization and comparative expression analysis of CUL1 genes in rice

Cullin-RING E3 ubiquitin ligase (CRL) complex is known as the largest family of E3 ligases. The most widely characterized CRL, SCF complex (CRL1), utilizes CUL1 as a scaffold protein to assemble the complex components. To better understand CRL1-mediated cellular processes in rice, three CUL1 genes (OsCUL1s) were isolated in Oryza sativa. Although all OsCUL1 proteins exhibited high levels of amino acid similarities with each other, OsCUL1-3 had a somewhat distinct structure from OsCUL1-1 and OsCUL1-2. Basal expression levels of OsCUL1-3 were much lower than those of OsCUL1-1 and OsCUL1-2 in all selected samples, showing that OsCUL1-1 and OsCUL1-2 play predominant roles relative to OsCUL1-3 in rice. OsCUL1-1 and OsCUL1-2 genes were commonly upregulated in dry seeds and by ABA and salt/drought stresses, implying their involvement in ABA-mediated processes. These genes also showed similar expression patterns in response to various hormones and abiotic stresses, alluding to their functional redundancy. Expression of the OsCUL1-3 gene was also induced in dry seeds and by ABA-related salt and drought stresses, implying their participation in ABA responses. However, its expression pattern in response to hormones and abiotic stresses was somehow different from those of the OsCUL1-1 and OsCUL1-2 genes. Taken together, these findings suggest that the biological role and function of OsCUL1-3 may be distinct from those of OsCUL1-1 and OsCUL1-2. The results of expression analysis of OsCUL1 genes in this study will serve as a useful platform to better understand overlapping and distinct roles of OsCUL1 proteins and CRL1-mediated cellular processes in rice plants.

Cytomixis in plants: facts and doubts

The migration of nuclei between plant cells (cytomixis) is a mysterious cellular phenomenon frequently observable in the male meiosis of higher plants. Cytomixis attracts attention because of unknown cellular mechanisms underlying migration of nuclei and its potential evolutionary significance, since the genetic material is transferred between the cells that form pollen. Although cytomixis was discovered over a century ago, the advance in our understanding of this process has been rather insignificant because of methodological difficulties. The data that allowed for a new insight into this phenomenon were obtained by examining the migrating nuclei with electron and confocal laser microscopy, immunostaining, and fluorescence in situ hybridization. As has been shown, the chromatin migrating between cells is surrounded by an undamaged nuclear membrane. Such chromatin does not undergo heterochromatization and contains normal euchromatin markers. The condensation degree of the migrating chromatin corresponds to the current meiotic stage, and normal structures of synaptonemal complex are present in the migrating part of the nucleus. The cells involved in cytomixis lack any detectable morphological and molecular markers of programmed cell death. It has been shown that individual chromosomes and genomes (in the case of allopolyploids) have no predisposition to the migration between cells, i.e., parts of the nucleus are involved in cytomixis in a random manner. However, the fate of migrating chromatin after it has entered the recipient cell is still vague. A huge amount of indirect data suggests that migrating chromatin is incorporated into the nucleus of the recipient cell; nonetheless, the corresponding direct evidences are still absent. No specific markers of cytomictic chromatin have been yet discovered. Thus, the causes and consequences of cytomixis are still disputable. This review briefs the recent data on the relevant issues, describes the classical and modern methodological approaches to analysis of the intercellular migration of nuclei, and discusses the problems in cytomixis research and its prospects.

Affinity proteomics reveals extensive phosphorylation of the Brassica chromosome axis protein ASY1 and a network of associated proteins at prophase I of meiosis

During meiosis, the formation of crossovers (COs) generates genetic variation and provides physical links that are essential for accurate chromosome segregation. COs occur in the context of a proteinaceous chromosome axis. The transcriptomes and proteomes of anthers and meiocytes comprise several thousand genes and proteins, but because of the level of complexity relatively few have been functionally characterized. Our understanding of the physical and functional interactions between meiotic proteins is also limited. Here we use affinity proteomics to analyse the proteins that are associated with the meiotic chromosome axis protein, ASY1, in Brassica oleracea anthers and meiocytes. We show that during prophase I ASY1 and its interacting partner, ASY3, are extensively phosphorylated, and we precisely assign phosphorylation sites. We identify 589 proteins that co-immunoprecipitate with ASY1. These correspond to 492 Arabidopsis orthologues, over 90% of which form a coherent protein-protein interaction (PPI) network containing known and candidate meiotic proteins, including proteins more usually associated with other cellular processes such as DNA replication and proteolysis. Mutant analysis confirms that affinity proteomics is a viable strategy for revealing previously unknown meiotic proteins, and we show how the PPI network can be used to prioritise candidates for analysis. Finally, we identify another axis-associated protein with a role in meiotic recombination. Data are available via ProteomeXchange with identifier PXD006042.

Tackling Plant Meiosis: From Model Research to Crop Improvement

Genetic engineering and traditional plant breeding, which harnesses the natural genetic variation that arises during meiosis, will have key roles to improve crop varieties and thus deliver Food Security in the future. Meiosis, a specialized cell division producing haploid gametes to maintain somatic diploidy following their fusion, assures genetic variation by regulated genetic exchange through homologous recombination. However, meiotic recombination events are restricted in their total number and their distribution along chromosomes limiting allelic variations in breeding programs. Thus, modifying the number and distribution of meiotic recombination events has great potential to improve and accelerate plant breeding. In recent years much progress has been made in understanding meiotic progression and recombination in plants. Many genes and factors involved in these processes have been identified primarily in Arabidopsis thaliana but also more recently in crops such as Brassica, rice, barley, maize, or wheat. These advances put researchers in the position to translate acquired knowledge to various crops likely improving and accelerating breeding programs. However, although fundamental aspects of meiotic progression and recombination are conserved between species, differences in genome size and organization (due to repetitive DNA content and ploidy level) exist, particularly among plants, that likely account for differences in meiotic progression and recombination patterns found between species. Thus, tools and approaches are needed to better understand differences and similarities in meiotic progression and recombination among plants, to study fundamental aspects of meiosis in a variety of plants including crops and non-model species, and to transfer knowledge into crop species. In this article, we provide an overview of tools and approaches available to study plant meiosis, highlight new techniques, give examples of areas of future research and review distinct aspects of meiosis in non-model species.

The F-Box Protein ZYGO1 Mediates Bouquet Formation to Promote Homologous Pairing, Synapsis, and Recombination in Rice Meiosis

Telomere bouquet formation, a highly conserved meiotic event, plays an important role in homologous pairing and therefore progression of meiosis; however, the underlying molecular mechanism remains largely unknown. Here, we identified ZYGOTENE1 (ZYGO1), a novel F-box protein in rice (Oryza sativa), and verified its essential role in bouquet formation during early meiosis. In zygo1 mutants, zygotene chromosome aggregation and telomere clustering failed to occur. The suppressed telomere clustering in homologous pairing aberration in rice meiosis1 (pair1) zygo1 and rice completion of meiotic recombination (Oscom1) zygo1 double mutants, together with the altered localization of OsSAD1 (a SUN protein associated with the nuclear envelope) in zygo1, showed that ZYGO1 has a significant function in bouquet formation. In addition, the interaction between ZYGO1 and rice SKP1-like protein 1 suggested that ZYGO1 might modulate bouquet formation as a component of the SKP1-Cullin1-F-box complex. Although double-strand break formation and early recombination element installation occurred normally, zygo1 mutants showed defects in full-length pairing and synaptonemal complex assembly. Furthermore, crossover (CO) formation was disturbed, and foci of Human enhancer of invasion 10 were restricted to the partially synapsed chromosome regions, indicating that CO reduction might be caused by the failure of full-length chromosome alignment in zygo1 Therefore, we propose that ZYGO1 mediates bouquet formation to efficiently promote homolog pairing, synapsis, and CO formation in rice meiosis.

Prominent topologically associated domains differentiate global chromatin packing in rice from Arabidopsis

The non-random three-dimensional organization of genomes is critical for many cellular processes. Recently, analyses of genome-wide chromatin packing in the model dicot plant Arabidopsis thaliana have been reported ^1-4 . At a kilobase scale, the A. thaliana chromatin interaction network is highly correlated with a range of genomic and epigenomic features ^1-4 . Surprisingly, topologically associated domains (TADs), which appear to be a prevalent structural feature of genome packing in many animal species, are not prominent in the A. thaliana genome ^1,2,4-6 . Using a genome-wide chromatin conformation capture approach, Hi-C (ref. ⁷ ), we report high-resolution chromatin packing patterns of another model plant, rice. We unveil new structural features of chromatin organization at both chromosomal and local levels compared to A. thaliana, with thousands of distinct TADs that cover about a quarter of the rice genome. The rice TAD boundaries are associated with euchromatic epigenetic marks and active gene expression, and enriched with a sequence motif that can be recognized by plant-specific TCP proteins. In addition, we report chromosome decondensation in rice seedlings undergoing cold stress, despite local chromatin packing patterns remaining largely unchanged. The substantial variation found already in a comparison of two plant species suggests that chromatin organization in plants might be more diverse than in multicellular animals.

Bivalent Formation 1, a plant-conserved gene, encodes an OmpH/coiled-coil motif-containing protein required for meiotic recombination in rice

Meiosis is essential for eukaryotic sexual reproduction and plant fertility. In comparison with over 80 meiotic genes identified in Arabidopsis, there are only ~30 meiotic genes characterized in rice (Oryza sativa L.). Many genes involved in the regulation of meiotic progression remain to be determined. In this study, we identified a sterile rice mutant and cloned a new meiotic gene, OsBVF1 (Bivalent Formation 1) by map-based cloning. Molecular genetics and cytological approaches were carried out to address the function of OsBVF1 in meiosis. Phylogenetic analyses were used to study the evolution of OsBVF1 and its homologs in plant species. Here we showed that the bvf1 male meiocytes were defective in formation of meiotic double strand break, thereby resulting in a failure of bivalent formation in diakinesis and unequal chromosome segregation in anaphase I. The causal gene, OsBVF1, encodes a unique OmpH/coiled-coil motif-containing protein and its homologs are highly conserved in the plant kingdom and seem to be a single-copy gene in the majority of plant species. Our study demonstrates that OsBVF1 is a novel plant-conserved factor involved in meiotic recombination in rice, providing a new insight into understanding of meiotic progression regulation.