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DNA-dependent RNA polymerases (Pols) transfer the genetic information stored in genomic DNA to RNA in all organisms. In eukaryotes, the typical products of nuclear Pol I, Pol II, and Pol III are ribosomal RNAs, mRNAs, and transfer RNAs, respectively. Intriguingly, plants possess two additional Pols, Pol IV and Pol V, which produce small RNAs and long noncoding RNAs, respectively, mainly for silencing transposable elements. The five plant Pols share some subunits, but their distinct functions stem from unique subunits that interact with specific regulatory factors in their transcription cycles. Here, we summarize recent advances in our understanding of plant nucleus-localized Pols, including their evolution, function, structures, and transcription cycles. This review explores the evolution, structure, and functions in transcription of nucleus-localized DNA-dependent RNA polymerases in plants. [ABSTRACT FROM AUTHOR]

A major threat to rice production is the disease epidemics caused by insect-borne viruses that emerge and re-emerge with undefined origins. It is well known that some human viruses have zoonotic origins from wild animals. However, it remains unknown whether native plants host uncharacterized endemic viruses with spillover potential to rice (Oryza sativa) as emerging pathogens. Here, we discovered rice tiller inhibition virus (RTIV), a novel RNA virus species, from colonies of Asian wild rice (O. rufipogon) in a genetic reserve by metagenomic sequencing. We identified the specific aphid vector that is able to transmit RTIV and found that RTIV would cause low-tillering disease in rice cultivar after transmission. We further demonstrated that an infectious molecular clone of RTIV initiated systemic infection and causes low-tillering disease in an elite rice variety after Agrobacterium-mediated inoculation or stable plant transformation, and RTIV can also be transmitted from transgenic rice plant through its aphid vector to cause disease. Finally, global transcriptome analysis indicated that RTIV may disturb defense and tillering pathway to cause low tillering disease in rice cultivar. Thus, our results show that new rice viral pathogens can emerge from native habitats, and RTIV, a rare aphid-transmitted rice viral pathogen from native wild rice, can threaten the production of rice cultivar after spillover. Author summary: Emerging and re-emerging dangerous viruses cause epidemics or pandemics to threaten human and economically important crops and animals. Some of the most dangerous human viruses have zoonotic origins from wild animals. Native plants may also host new endemic viruses that can spread to cause epidemics in cultivated rice, one of the most important staple plants in the world. In the research, we discovered Rice tiller inhibition virus (RTIV), a new insect-borne positive-strand RNA virus, from Asian wild rice plants through metagenomic sequencing, and demonstrated that RTIV could be transmitted by a wide-distributed specific species of aphids to cultivated rice and inhibited tillering, an important agronomic trait of rice plants. We further rescued RTIV by developing infectious clone and confirmed that it can be a dangerous aphid-transmitted viral pathogen of cultivated rice plants. Thus, not only a rare aphid-transmitted viral pathogen of rice plants was discovered in the research, our findings also indicate that novel pathogenic viruses could spread out from native plants to threaten important crop plants. [ABSTRACT FROM AUTHOR]

RNA polymerase IV-dependent siRNAs, usually 24 nt in length, function in the RNA-directed DNA methylation that is responsible for de novo methylation in plants. We analyzed 24 nt siRNAs in inflorescences and found that among the 20,200 24 nt siRNA clusters, the top 0.81% highly expressed clusters accounted for more than 68% of the 24 nt siRNA reads in inflorescences. We named the highly expressed siRNAs as billionaire siRNAs (bill-siRNAs) and the less-expressed siRNAs as pauper siRNAs (pau-siRNAs). The bill-siRNAs in inflorescences are mainly derived from the ovary. Female gametes produced more bill-siRNAs than male gametes. In embryos and seedlings developed from fertilized egg cells, the bill-siRNAs from gametes disappeared. The endosperm, which develops from the fertilized central cell, also contained no bill-siRNAs from gametes but did contain newly and highly expressed siRNAs produced in different regions. In contrast, bill-siRNAs from the ovaries were maintained in the seed coat. The biosynthesis of bill-siRNAs in various tissues and cells is dependent on OsRDR2 (RNA-dependent RNA polymerase 2) and Pol IV (DNA-dependent RNA polymerase IV). Similar to the pau-siRNAs, the first base of bill-siRNAs is enriched at adenine, and bill-siRNAs can direct DNA methylation in various tissues. [ABSTRACT FROM AUTHOR]

Crop diseases are major factors responsible for substantial yield losses worldwide, which affects global food security. The use of resistance (R) genes is an effective and sustainable approach to controlling crop diseases. Here, we review recent advances on R gene studies in the major crops and related wild species. Current understanding of the molecular mechanisms underlying R gene activation and signaling, and susceptibility (S) gene-mediated resistance in crops are summarized and discussed. Furthermore, we propose some new strategies for R gene discovery, how to balance resistance and yield, and how to generate crops with broad-spectrum disease resistance. With the rapid development of new genome-editing technologies and the availability of increasing crop genome sequences, the goal of breeding next-generation crops with durable resistance to pathogens is achievable, and will be a key step toward increasing crop production in a sustainable way. In this perspective article, we summary recent progress on R gene isolation and the current understanding of the molecular mechanisms underlying R gene activation, and susceptibility (S) gene-mediated resistance in crops. Then we propose new strategies for R gene discovery, balancing resistance and yield in crop breeding toward improvement for disease resistance using new genome-editing technology. [ABSTRACT FROM AUTHOR]

Abstract Seed development in angiosperms requires a 2:1 maternal-to-paternal genome ratio (2m:1p) in the endosperm. When the ratio is disrupted, the seed development is impaired. Rice interploidy crosses result in endosperm failures, but the underlying molecular mechanisms remain unclear. Here, we report that the defective endosperm in rice interploidy crosses was associated with nonadditive expression of small RNAs and protein-coding genes. Interestingly, 24-nt small interfering RNAs were enriched in the 5′ and 3′ flanking sequences of nonadditively expressed genes in the interploidy crosses and were negatively associated with the expression of imprinted genes. Furthermore, some PRC2 family genes and DNA methylation-related genes including OsMET1b and OsCMT3a were upregulated in the 2×4 cross (pollinating a diploid "mother" with a tetraploid "father") but repressed in the reciprocal cross. These different epigenetic effects could lead to precocious or delayed cellularization during endosperm development. Notably, many endosperm-preferred genes, including starch metabolic and storage protein genes during grain filling, were found to be associated with DNA methylation or H3K27me3, which are repressed in both 2×4 and 4×2 crosses. WUSCHEL homeobox2 (WOX2) -like (WOX2L), an endosperm-preferred gene, was expressed specifically in the rice endosperm, in contrast to WOX2 expression in the Arabidopsis embryo. Disruption of WOX2L in transgenic rice by CRISPR/Cas9-mediated gene editing blocked starch and protein accumulation, resulting in seed abortion. In addition to gene repression, disrupting epigenetic process in the interploidy crosses also induced expression of stress-responsive genes. Thus, maintaining the 2m:1p genome ratio in the endosperm is essential for normal grain development in rice and other cereal crops. Interploidy crosses in rice disrupted expression of small RNAs, small RNA-associated genes including imprinted and endosperm-preferred genes, and epigenetic processes such as DNA and histone methylation, leading to abnormal cellularization during the grain-filling stage and, ultimately, endosperm failures and seed abortion. [ABSTRACT FROM AUTHOR]

Genetic imprinting refers to the unequal expression of paternal and maternal alleles of a gene in sexually reproducing organisms, including mammals and flowering plants. Although many imprinted genes have been identified in plants, the functions of these imprinted genes have remained largely uninvestigated., We report genome-wide analysis of gene expression, DNA methylation and small RNAs in the rice endosperm and functional tests of five imprinted genes during seed development using Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated gene9 (CRISPR/Cas9) gene editing technology., In the rice endosperm, we identified 162 maternally expressed genes (MEGs) and 95 paternally expressed genes (PEGs), which were associated with miniature inverted-repeat transposable elements, imprinted differentially methylated loci and some 21-22 small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs). Remarkably, one-third of MEGs and nearly one-half of PEGs were associated with grain yield quantitative trait loci. Most MEGs and some PEGs were expressed specifically in the endosperm. Disruption of two MEGs increased the amount of small starch granules and reduced grain and embryo size, whereas mutation of three PEGs reduced starch content and seed fertility., Our data indicate that both MEGs and PEGs in rice regulate nutrient metabolism and endosperm development, which optimize seed development and offspring fitness to facilitate parental-offspring coadaptation. These imprinted genes and mechanisms could be used to improve the grain yield of rice and other cereal crops. [ABSTRACT FROM AUTHOR]

Thymidine kinases ( TKs) are important components in the nucleotide salvage pathway. However, knowledge about plant TKs is quite limited. In this study, the molecular function of TKs in Arabidopsis thaliana was investigated., Two TKs were identified and named At TK1 and At TK2. Expression of both genes was ubiquitous, but AtTK1 was strongly expressed in high-proliferation tissues. AtTK1 was localized to the cytosol, whereas AtTK2 was localized to the mitochondria. Mutant analysis indicated that the two genes function coordinately to sustain normal plant development., Enzymatic assays showed that the two TK proteins shared similar catalytic specificity for pyrimidine nucleosides. They were able to complement an Escherichia coli strain lacking TK activity. 5′-Fluorodeoxyuridine (FdU) resistance and 5-ethynyl 2′-deoxyuridine (EdU) incorporation assays confirmed their activity in vivo. Furthermore, the tk mutant phenotype could be alleviated by nucleotide feeding, establishing that the biosynthesis of pyrimidine nucleotides was disrupted by the TK deficiency. Finally, both human and rice ( Oryza sativa) TKs were able to rescue the tk mutants, demonstrating the functional conservation of TKs across organisms., Taken together, our findings clarify the specialized function of two TKs in A. thaliana and establish that the salvage pathway mediated by the kinases is essential for plant growth and development. [ABSTRACT FROM AUTHOR]

Sugar metabolism and sugar signalling are not only critical for plant growth and development, but are also important for stress responses. However, how sugar homeostasis is involved in plant defence against pathogen attack in the model crop rice remains largely unknown. In this study, we observed that the grains of gif1, a loss-of-function mutant of the cell wall invertase gene GRAIN INCOMPLETE FILLING 1 ( GIF1), were hypersusceptible to postharvest fungal pathogens, with decreased levels of sugars and a thinner glume cell wall in comparison with the wild-type. Interestingly, constitutive expression of GIF1 enhanced resistance to both the rice bacterial pathogen Xanthomonas oryzae pv. oryzae and the fungal pathogen Magnaporthe oryzae. The GIF1-overexpressing ( GIF1- OE) plants accumulated higher levels of glucose, fructose and sucrose compared with the wild-type plants. More importantly, higher levels of callose were deposited in GIF1- OE plants during pathogen infection. Moreover, the cell wall was much thicker in the infection sites of the GIF1- OE plants when compared with the wild-type plants. We also found that defence-related genes were constitutively activated in the GIF1- OE plants. Taken together, our study reveals that sugar homeostasis mediated by GIF1 plays an important role in constitutive and induced physical and chemical defence. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented which discusses genome editing inplants.

Calcium plays an important role in plant growth, development, and response to environmental stimuli. Copines are conserved plasma membrane-localized calcium-binding proteins which regulate plant immune responses and development. In this study, we found that copine proteins BON2 and BON3, the paralogs of BON1, physically interact with calcium pumps ACA8 and ACA10 in Arabidopsis. Notably, ACA9, the closest homologue of ACA8 and ACA10 functioning in pollen tube growth, interacts with all three copines. This is consistent with the protein–protein interactions between the two protein families, the aca8, aca10, aca8/aca10, bon1/2/3 mutants as well as aca9 mutant exhibited defects on pollen germination and seed production. Taken together, plasma membrane-localized interacting calcium pumps and copines coordinately control pollen tube growth, likely through manipulating calcium efflux. [ABSTRACT FROM AUTHOR]

DNA methylation is an important epigenetic mark that regulates the expression of genes and transposons. RNA-directed DNA methylation (RdDM) is the main molecular pathway responsible for de novo DNA methylation in plants. Although the mechanism of RdDM has been well studied in Arabidopsis (Arabidopsis thaliana), most mutations in RdDM genes cause no remarkable developmental defects in Arabidopsis. Here, we isolated and cloned Five Elements Mountain 1 (FEM1), which encodes RNA-dependent RNA polymerase 2 (OsRDR2) in rice (Oryza sativa). Mutation in OsRDR2 abolished the accumulation of 24-nt small interfering RNAs, and consequently substantially decreased genome-wide CHH (H = A, C, or T) methylation. Moreover, male and female reproductive development was disturbed, which led to sterility in osrdr2 mutants. We discovered that OsRDR2-dependent DNA methylation may regulate the expression of multiple key genes involved in stamen development, meiosis, and pollen viability. In wild-type (WT) plants but not in osrdr2 mutants, genome-wide CHH methylation levels were greater in panicles, stamens, and pistils than in seedlings. The global increase of CHH methylation in reproductive organs of the WT was mainly explained by the enhancement of RdDM activity, which includes OsRDR2 activity. Our results, which revealed a global increase in CHH methylation through enhancement of RdDM activity in reproductive organs, suggest a crucial role for OsRDR2 in the sexual reproduction of rice., (© American Society of Plant Biologists 2021. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

In plants, hybrid vigor is influenced by genetic and epigenetic mechanisms; however, the molecular pathways are poorly understood. We investigated the potential contributions of epigenetic regulators to heterosis in Arabidposis and found that the chromatin remodeler DECREASED DNA METHYLATION 1 (DDM1) affects early seedling growth heterosis in Col/C24 hybrids. ddm1 mutants showed impaired heterosis and increased expression of non-additively expressed genes related to salicylic acid metabolism. Interestingly, our data suggest that salicylic acid is a hormetic regulator of seedling growth heterosis, and that hybrid vigor arises from crosses that produce optimal salicylic acid levels. Although DNA methylation failed to correlate with differential non-additively expressed gene expression, we uncovered DDM1 as an epigenetic link between salicylic acid metabolism and heterosis, and propose that the endogenous salicylic acid levels of parental plants can be used to predict the heterotic outcome. Salicylic acid protects plants from pathogens and abiotic stress. Thus, our findings suggest that stress-induced hormesis, which has been associated with increased longevity in other organisms, may underlie specific hybrid vigor traits.

Gibberellins (GAs) form a group of important plant tetracyclic diterpenoid hormones that are involved in many aspects of plant growth and development. Emerging evidence implicates that GAs also play roles in stress responses. However, the role of GAs in biotic stress is largely unknown. Here, we report that knockout or overexpression of the Elongated uppermost internode (Eui) gene encoding a GA deactivating enzyme compromises or increases, respectively, disease resistance to bacterial blight (Xanthomonas oryzae pv. oyrzae) and rice blast (Magnaporthe oryzae). Exogenous application of GA(3) and the inhibitor of GA synthesis (uniconazol) could increase disease susceptibility and resistance, respectively, to bacterial blight. Similarly, uniconazol restored disease resistance of the eui mutant and GA(3) decreased disease resistance of the Eui overexpressors to bacterial blight. Therefore, the change of resistance attributes to GA levels. In consistency with this, the GA metabolism genes OsGA20ox2 and OsGA2ox1 were down-regulated during pathogen challenge. We also found that PR1a induction was enhanced but the SA level was decreased in the Eui overexpressor, while the JA level was reduced in the eui mutant. Together, our current study indicates that GAs play a negative role in rice basal disease resistance, with EUI as a positive modulator through regulating the level of bioactive GAs.