Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers

Actions of plant Argonautes: predictable or unpredictable?

Argonaute (AGO) proteins are the key effector of RNA-induced silencing complex (RISC). Land plants typically encode numerous AGO proteins, and they can be typically divided into two major functional groups based on the species of their housed small RNAs (sRNAs). One group of AGOs, guided by 24-nucleotide (nt) sRNAs, canonically function in nuclei to implement transcriptional gene silencing (TGS), whereas the other group of AGOs, guided by 21-nt sRNAs, act in the cytoplasm to fulfill posttranscriptional gene silencing (PTGS). Many new discoveries have been recently made on functions and mechanisms of AGO proteins in plants, and some of the findings change our views on the conventional classification and roles of AGO proteins. In this review, we summarize our current knowledge of AGO proteins in plants.

Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops

Gene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylation. Comprehensive identification of Pol V subunit orthologs across the monocot radiation revealed a duplication of the largest two subunits within the grasses (Poaceae), including critical cereal crops. These paralogous Pol subunits display sequence conservation within catalytic domains, but their carboxy terminal domains differ in length and character of the Ago-binding platform, suggesting unique functional interactions. Phylogenetic analysis of the catalytic region indicates positive selection on one paralog following duplication, consistent with retention via neofunctionalization. Positive selection on residue pairs that are predicted to interact between subunits suggests that paralogous subunits have evolved specific assembly partners. Additional Pol subunits as well as Pol-interacting proteins also possess grass-specific paralogs, supporting the hypothesis that a novel Pol complex with distinct function has evolved in the grass family, Poaceae.

Uncovering key small RNAs associated with gametocidal action in wheat

Gametocidal (Gc) chromosomes can kill gametes that lack them by causing chromosomal breakage to ensure their preferential transmission, and they have been exploited in genetic breeding. The present study investigated the possible roles of small RNAs (sRNAs) in Gc action. By sequencing two small RNA libraries from the anthers of Triticum aestivum cv. Chinese Spring (CS) and the Chinese Spring-Gc 3C chromosome monosomic addition line (CS-3C), we identified 239 conserved and 72 putative novel miRNAs, including 135 differentially expressed miRNAs. These miRNAs were predicted to target multiple genes with various molecular functions relevant to the features of Gc action, including sterility and genome instability. The transgenic overexpression of miRNA, which was up-regulated in CS-3C, reduced rice fertility. The CS-3C line exhibited a genome-wide reduction in 24 nt siRNAs compared with that of the CS line, particularly in transposable element (TE) and repetitive DNA sequences. Corresponding to this reduction, the bisulfite sequencing analysis of four retro-TE sequences showed a decrease in CHH methylation, typical of RNA-directed DNA methylation (RdDM). These results demonstrate that both miRNA-directed regulation of gene expression and siRNA-directed DNA methylation of target TE loci could play a role in Gc action.

Comparative transcriptome analysis reveals that tricarboxylic acid cycle-related genes are associated with maize CMS-C fertility restoration

BACKGROUND

C-type cytoplasmic male sterility (CMS-C) is one of the three major types of cytoplasmic male sterility (CMS) in maize. Rf4 is a dominant restorer gene for CMS-C and has great value in hybrid maize breeding, but little information concerning its functional mechanism is known.

RESULTS

To reveal the functional mechanism of Rf4, we developed a pair of maize near-isogenic lines (NILs) for the Rf4 locus, which included a NIL_rf4 male-sterile line and a NIL_Rf4 male fertility-restored line. Genetic analysis and molecular marker detection indicated that the male fertility of NIL_Rf4 was controlled by Rf4. Whole-genome sequencing demonstrated genomic differences between the two NILs was clustered in the Rf4 mapping region. Unmapped reads of NILs were further assembled to uncover Rf4 candidates. RNA-Seq was then performed for the developing anthers of the NILs to identify critical genes and pathways associated with fertility restoration. A total of 7125 differentially expressed genes (DEGs) were identified. These DEGs were significantly enriched in 242 Gene Ontology (GO) categories, wherein 100 DEGs were involved in pollen tube development, pollen tube growth, pollen development, and gametophyte development. Homology analysis revealed 198 male fertility-related DEGs, and pathway enrichment analysis revealed that 58 DEGs were enriched in cell energy metabolism processes involved in glycolysis, the pentose phosphate pathway, and pyruvate metabolism. By querying the Plant Reactome Pathway database, we found that 14 of the DEGs were involved in the mitochondrial tricarboxylic acid (TCA) cycle and that most of them belonged to the isocitrate dehydrogenase (IDH) and oxoglutarate dehydrogenase (OGDH) enzyme complexes. Transcriptome sequencing and real-time quantitative PCR (qPCR) showed that all the above TCA cycle-related genes were up-regulated in NIL_Rf4. The results of our subsequent enzyme-linked immunosorbent assay (ELISA) experiments pointed out that the contents of both the IDH and OGDH enzymes accumulated more in the spikelets of NIL_Rf4 than in those of NIL_rf4.

CONCLUSION

The present research provides valuable genomic resources for deep insight into the molecular mechanism underlying CMS-C male fertility restoration. Importantly, our results indicated that genes involved in energy metabolism, especially some mitochondrial TCA cycle-related genes, were associated with maize CMS-C male fertility restoration.

Plant 24-nt reproductive phasiRNAs from intramolecular duplex mRNAs in diverse monocots

In grasses, two pathways that generate diverse and numerous 21-nt (premeiotic) and 24-nt (meiotic) phased siRNAs are highly enriched in anthers, the male reproductive organs. These "phasiRNAs" are analogous to mammalian piRNAs, yet their functions and evolutionary origins remain largely unknown. The 24-nt meiotic phasiRNAs have only been described in grasses, wherein their biogenesis is dependent on a specialized Dicer (DCL5). To assess how evolution gave rise to this pathway, we examined reproductive phasiRNA pathways in nongrass monocots: garden asparagus, daylily, and lily. The common ancestors of these species diverged approximately 115-117 million years ago (MYA). We found that premeiotic 21-nt and meiotic 24-nt phasiRNAs were abundant in all three species and displayed spatial localization and temporal dynamics similar to grasses. The miR2275-triggered pathway was also present, yielding 24-nt reproductive phasiRNAs, and thus originated more than 117 MYA. In asparagus, unlike in grasses, these siRNAs are largely derived from inverted repeats (IRs); analyses in lily identified thousands of precursor loci, and many were also predicted to form foldback substrates for Dicer processing. Additionally, reproductive phasiRNAs were present in female reproductive organs and thus may function in both male and female germinal development. These data describe several distinct mechanisms of production for 24-nt meiotic phasiRNAs and provide new insights into the evolution of reproductive phasiRNA pathways in monocots.

On plant defense signaling networks and early land plant evolution

All land plants must cope with phytopathogens. Algae face pathogens, too, and it is reasonable to assume that some of the strategies for dealing with pathogens evolved prior to the origin of embryophytes – plant terrestrialization simply changed the nature of the plant-pathogen interactions. Here we highlight that many potential components of the angiosperm defense toolkit are i) found in streptophyte algae and non-flowering embryophytes and ii) might be used in non-flowering plant defense as inferred from published experimental data. Nonetheless, the common signaling networks governing these defense responses appear to have become more intricate during embryophyte evolution. This includes the evolution of the antagonistic signaling pathways of jasmonic and salicylic acid, multiple independent expansions of resistance genes, and the evolution of resistance gene-regulating microRNAs. Future comparative studies will illuminate which modules of the streptophyte defense signaling network constitute the core and which constitute lineage- and/or environment-specific (peripheral) signaling circuits.

Genome-wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice

Autotetraploid rice is a useful germplasm with high biomass production; however, low fertility is the main barrier in commercial utilization. In our previous study, differential expression of meiosis-related miRNAs was found to be involved in the pollen sterility of autotetraploid rice. However, genome-wide DNA variations and methylomes associated with low fertility of autotetraploid rice are still poorly understood. Here, we measured both global DNA variations and the methylome and compared them with the transcriptome during pollen development in autotetraploid rice by high-throughput sequencing. A total of 34416 SNPs, 6993 InDels, 1003 SVs and 25 CNVs were detected, and 11367 and 41117 differentially methylated regions showed hypermethylation and hypomethylation in 02428-4x. In total, 1110 genes displayed differentially expression in 02428-4x during meiosis, of these six harbored CNVs, including four upregulated genes with gain CNVs, such as LOC_Os11g38620. We identified 122 genes by comparing with the previous data that might be associated with low fertility during pollen development in 02428-4x. Of the 122 gens, 98 were displayed methylation and differential expression, including OsMADS98, CYP703A3 and OsABCG26. The downregulation of these three genes were confirmed by qPCR during meiosis of 02428-4x, which played pivotal roles in pollen fertility. These results indicate that the low fertility of autotetraploid rice is not only caused by the differential expression of genes involved in pollen development, but also by sequence variation and differential methylation, suggesting that the reason for pollen sterility in autotetraploid rice is complex and might be affected by multiple factors.

Expansion of Capsicum annuum fruit is linked to dynamic tissue-specific differential expression of miRNA and siRNA profiles

Small regulatory RNAs, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs) have emerged as important transcriptional and post-transcriptional regulators controlling a wide variety of physiological processes including fruit development. Data are, however, limited for their potential roles in developmental processes determining economically important traits of crops. The current study aimed to discover and characterize differentially expressed miRNAs and siRNAs in sweet pepper (Capsicum annuum) during fruit expansion. High-throughput sequencing was employed to determine the small regulatory RNA expression profiles in various fruit tissues, such as placenta, seed, and flesh at 28 and 40 days after anthesis. Comparative differential expression analyses of conserved, already described and our newly predicted pepper-specific miRNAs revealed that fruit expansion is accompanied by an increasing level of miRNA-mediated regulation of gene expression. Accordingly, ARGONAUTE1 protein, the primary executor of miRNA-mediated regulation, continuously accumulated to an extremely high level in the flesh. We also identified numerous pepper-specific, heterochromatin-associated 24-nt siRNAs (hetsiRNAs) which were extremely abundant in the seeds, as well as 21-nt and 24-nt phased siRNAs (phasiRNAs) that were expressed mainly in the placenta and the seeds. This work provides comprehensive tissue-specific miRNA and siRNA expression landscape for a developing pepper fruit. We identified several novel, abundantly expressing tissue- and pepper-specific small regulatory RNA species. Our data show that fruit expansion is associated with extensive changes in sRNA abundance, raising the possibility that manipulation of sRNA pathways may be employed to improve the quality and quantity of the pepper fruit.

Loss of RNA-Directed DNA Methylation in Maize Chromomethylase and DDM1-Type Nucleosome Remodeler Mutants

Plants make use of distinct types of DNA methylation characterized by their DNA methyltransferases and modes of regulation. One type, RNA-directed DNA methylation (RdDM), is guided by small interfering RNAs (siRNAs) to the edges of transposons that are close to genes, areas called mCHH islands in maize (Zea mays). Another type, chromomethylation, is guided by histone H3 lysine 9 methylation to heterochromatin across the genome. We examined DNA methylation and small RNA expression in plant tissues that were mutant for both copies of the genes encoding chromomethylases as well as mutants for both copies of the genes encoding DECREASED DNA METHYLATION1 (DDM1)-type nucleosome remodelers, which facilitate chromomethylation. Both sets of double mutants were nonviable but produced embryos and endosperm. RdDM was severely compromised in the double mutant embryos, both in terms of DNA methylation and siRNAs. Loss of 24-nucleotide siRNA from mCHH islands was coupled with a gain of 21-, 22-, and 24-nucleotide siRNAs in heterochromatin. These results reveal a requirement for both chromomethylation and DDM1-type nucleosome remodeling for RdDM in mCHH islands, which we hypothesize is due to dilution of RdDM components across the genome when heterochromatin is compromised.

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture

DNA methylation can contribute to the maintenance of genome integrity and regulation of gene expression. In most situations, DNA methylation patterns are inherited quite stably. However, changes in DNA methylation can occur at some loci as a result of tissue culture resulting in somaclonal variation. To investigate heritable epigenetic changes as a consequence of tissue culture, a sequence-capture bisulfite sequencing approach was implemented to monitor context-specific DNA methylation patterns in ∼15 Mb of the maize genome for a population of plants that had been regenerated from tissue culture. Plants that have been regenerated from tissue culture exhibit gains and losses of DNA methylation at a subset of genomic regions. There was evidence for a high rate of homozygous changes to DNA methylation levels that occur consistently in multiple independent tissue culture lines, suggesting that some loci are either targeted or hotspots for epigenetic variation. The consistent changes inherited following tissue culture include both gains and losses of DNA methylation and can affect CG, CHG, or both contexts within a region. Only a subset of the tissue culture changes observed in callus plants are observed in the primary regenerants, but the majority of DNA methylation changes present in primary regenerants are passed onto offspring. This study provides insights into the susceptibility of some loci and potential mechanisms that could contribute to altered DNA methylation and epigenetic state that occur during tissue culture in plant species.

Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon

BACKGROUND

MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. However, the watermelon miRNAs and phasiRNAs and their functions are not well explored.

RESULTS

Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, petals, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed using the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 127 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf.

CONCLUSIONS

The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon.

Transcriptome analysis reveals new microRNAs-mediated pathway involved in anther development in male sterile wheat

Background

337S is a novel bi-pole-photo-thermo-sensitive genic male sterile line in wheat, and sensitive to both long day length/high temperature and short day length/low temperature condition. Although the regulatory function of MicroRNAs (miRNAs) in reproductive development has been increasingly studied, their roles in pre-meiotic and meiotic cells formation of plants have not been clearly explored. Here, we explored the roles of miRNAs in regulating male sterility of 337S at short day length/low temperature condition.

Results

Small RNA sequencing and degradome analyses were employed to identify miRNAs and their targets in the 337S whose meiotic cells collapsed rapidly during male meiotic prophase, resulting in failure of meiosis at SL condition. A total of 102 unique miRNAs were detected. Noticeably, the largest miRNA family was MiR1122. The target CCR4-associated factor 1 (CAF1) of miR2275, a subunit of the Carbon Catabolite Repressed 4-Negative on TATA-less (CCR4-NOT) complex, contributes to the process of early meiosis, and was first identified here. Further studies showed that the expression of several pivotal anther-related miRNAs was altered in 337S at SL condition, especially tae-miR1127a, which may be related to male sterility of 337S. Here, we also identified a new member of SWI/SNF factors SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A, member 3-like 3 (SMARCA3L3) targeted by tae-miR1127a, whose function might be involved in faithful progression of meiosis in male reproductive cells.

Conclusion

The miRNA-target interactions of tae-miR2275-CAF1 and tae-miR1127a-SMARCA3L3 might be involved in regulating male fertility in 337S. Our results also implied that multiple roles for SMARCA3L3 and CAF1 in DNA repair and transcriptional regulation jointly orchestrated a tight and orderly system for maintaining chromatin and genome integrity during meiosis.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4727-5) contains supplementary material, which is available to authorized users.

Biogenesis and regulatory hierarchy of phased small interfering RNAs in plants

Several varieties of small RNAs including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are generated in plants to regulate development, genome stability and response to adverse environments. Phased siRNA (phasiRNA) is a type of secondary siRNA that is processed from a miRNA-mediated cleavage of RNA transcripts, increasing silencing efficiency or simultaneously suppressing multiple target genes. Trans-acting siRNAs (ta-siRNAs) are a particular class of phasiRNA produced from noncoding transcripts that silence targets in trans. It was originally thought that 'one-hit' and 'two-hit' models were essential for processing distinct TAS precursors; however, a single hit event was recently shown to be sufficient at triggering all types of ta-siRNAs. This review discusses the findings about biogenesis, targeting modes and regulatory networks of plant ta-siRNAs. We also summarize recent advances in the generation of other phasiRNAs and their possible biological benefits to plants.

Epigenetic reprogramming during spermatogenesis and male factor infertility

Infertility is an often devastating diagnosis encountered by around one in six couples who are trying to conceive. Moving away from the long-held belief that infertility is primarily a female issue, it is now recognised that half, if not more, of these cases may be due to male factors. Recent evidence has suggested that epigenetic abnormalities in chromatin dynamics, DNA methylation or sperm-borne RNAs may contribute to male infertility. In light of advances in deep sequencing technologies, researchers have been able to increase the coverage and depth of sequencing results, which in turn has allowed more comprehensive analyses of spermatozoa chromatin dynamics and methylomes and enabled the discovery of new subsets of sperm RNAs. This review examines the most current literature related to epigenetic processes in the male germline and the associations of aberrant modifications with fertility and development.

Despacito: the slow evolutionary changes in plant microRNAs

MicroRNAs (miRNAs) are key regulators of gene expression. A handful of miRNAs are broadly conserved in land plants, while the majority are lineage specific; this review describes the processes by which new miRNAs are hypothesized to have emerged. Two major models describe miRNA origins, firstly, de novo emergence via inverted duplication of target gene fragments, and secondly, the expansion and neofunctionalization of existing miRNA families. The occasional acquisition of target sites by previously un-targeted genes adds further dynamism to the process by which miRNAs may shift roles during evolution. Additional factors guiding miRNA evolution include functional constraints on their length and the importance of precursor conservation that is observed in regions above or below the mature miRNA duplex; these regions represent recognition sites for components of biogenesis machinery and direct precursor processing. Insights into the mechanisms of miRNA emergence and divergence are important for understanding plant genome evolution and the impact of miRNA regulatory networks.

Coupling of microRNA-directed phased small interfering RNA generation from long noncoding genes with alternative splicing and alternative polyadenylation in small RNA-mediated gene silencing

MicroRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs) play vital regulatory roles in plant growth and development. Little is known about these small RNAs in litchi (Litchi chinensis), an economically important fruit crop widely cultivated in Southeast Asia. We profiled the litchi small RNA population with various deep-sequencing techniques and in-depth bioinformatic analyses. The genome-wide identification of miRNAs, their target genes, and phasiRNA-generating (PHAS) genes/loci showed that the function of miR482/2118 has expanded, relative to its canonical function. We also discovered that, for 29 PHAS loci, miRNA-mediated phasiRNA production was coupled with alternative splicing (AS) and alternative polyadenylation (APA). Most of these loci encoded long noncoding RNAs. An miR482/2118 targeted locus gave rise to four main transcript isoforms through AS/APA, and diverse phasiRNAs generated from these isoforms appeared to target long terminal repeat (LTR) retrotransposons and other unrelated genes. This coupling enables phasiRNA production from different exons of noncoding PHAS genes and yields diverse phasiRNA populations, both broadening and altering the range of downstream phasiRNA-regulated genes. Our results reveal the diversity of miRNA and phasiRNA in litchi, and demonstrate AS/APA as a new layer of regulation in small RNA-mediated gene silencing.

Genetic and molecular characterization of photoperiod and thermo-sensitive male sterility in rice

A review on photoperiod and temperature-sensitive genic male sterility in rice. Male sterility in plants, facilitating the development of hybrid crops, has made great contribution to crop productivity worldwide. Environment-sensitive genic male sterility (EGMS), including photoperiod-sensitive genic male sterility (PGMS) and temperature-sensitive genic male sterility (TGMS), has provided a special class of germplasms for the breeding of "two-line" hybrids in several crops. In rice, the finding of the PGMS NK58S mutant in 1973 started the journey of research and breeding of two-line hybrids. Genetic and molecular characterization of these germplasms demonstrated diverse genes and molecular mechanisms of male sterility regulation. Two loci identified from NK58S, PMS1 and PMS3, both encode long noncoding RNAs. A major TGMS locus, TMS5, found in the TGMS line Annong S-1, encodes an RNase Z. A reverse PGMS mutant carbon starved anther encodes an R2R3 MYB transcription factor. Breeding efforts in the last three decades have resulted in hundreds of EGMS lines and two-line hybrids released to rice production, which have greatly elevated the yield potential and grain quality of rice varieties. The enhanced molecular understanding will offer new strategies for the development of EGMS lines thus further improving two-line hybrid breeding of rice as well as other crops.

Small RNA pathways responsible for non-cell-autonomous regulation of plant reproduction

In angiosperms, germline precursors and germ cells are always attached to or engulfed within somatic companion cells until just before fertilization. This is because sperm and egg cells develop as part of the multicellular gametophyte. Thus, the non-cell-autonomous regulation by somatic companions plays important roles in efficient reproduction, in addition to the cell-autonomous regulation. Epigenetic silencing of transposable elements is one of the central events by which the germline transmits the error-free genome to the next generation. This review focuses on small RNA-mediated epigenetic regulation of meiosis, spore formation and pollen development. Besides microRNA (miRNA) and small interfering RNA (siRNA), animals express PIWI-interacting RNA (piRNA), a germline-specific class of small RNAs. Plants lack piRNA-like RNAs and, instead, express unique classes of small RNAs: trans-acting siRNA (tasiRNA) and phased secondary siRNA (phasiRNA). Especially in grass species, 21- and 24-nucleotide phasiRNAs are abundant in anthers during premeiosis and meiosis. This review also describes recent progress in reproductive phasiRNA research.

EAT1 transcription factor, a non-cell-autonomous regulator of pollen production, activates meiotic small RNA biogenesis in rice anther tapetum

The 24-nucleotides (nt) phased secondary small interfering RNA (phasiRNA) is a unique class of plant small RNAs abundantly expressed in monocot anthers at early meiosis. Previously, 44 intergenic regions were identified as the loci for longer precursor RNAs of 24-nt phasiRNAs (24-PHASs) in the rice genome. However, the regulatory mechanism that determines spatiotemporal expression of these RNAs has remained elusive. ETERNAL TAPETUM1 (EAT1) is a basic-helix-loop-helix (bHLH) transcription factor indispensable for induction of programmed cell death (PCD) in postmeiotic anther tapetum, the somatic nursery for pollen production. In this study, EAT1-dependent non-cell-autonomous regulation of male meiosis was evidenced from microscopic observation of the eat1 mutant, in which meiosis with aberrantly decondensed chromosomes was retarded but accomplished somehow, eventually resulting in abortive microspores due to an aberrant tapetal PCD. EAT1 protein accumulated in tapetal-cell nuclei at early meiosis and postmeiotic microspore stages. Meiotic EAT1 promoted transcription of 24-PHAS RNAs at 101 loci, and importantly, also activated DICER-LIKE5 (DCL5, previous DCL3b in rice) mRNA transcription that is required for processing of double-stranded 24-PHASs into 24-nt lengths. From the results of the chromatin-immunoprecipitation and transient expression analyses, another tapetum-expressing bHLH protein, TDR INTERACTING PROTEIN2 (TIP2), was suggested to be involved in meiotic small-RNA biogenesis. The transient assay also demonstrated that UNDEVELOPED TAPETUM1 (UDT1)/bHLH164 is a potential interacting partner of both EAT1 and TIP2 during early meiosis. This study indicates that EAT1 is one of key regulators triggering meiotic phasiRNA biogenesis in anther tapetum, and that other bHLH proteins, TIP2 and UDT1, also play some important roles in this process. Spatiotemporal expression control of these bHLH proteins is a clue to orchestrate precise meiosis progression and subsequent pollen production non-cell-autonomously.

Phased secondary small interfering RNAs in Panaxnotoginseng

Background

Recent results demonstrated that either non-coding or coding genes generate phased secondary small interfering RNAs (phasiRNAs) guided by specific miRNAs. Till now, there is no studies for phasiRNAs in Panax notoginseng (Burk.) F.H. Chen (P. notoginseng), an important traditional Chinese herbal medicinal plant species.

Methods

Here we performed a genome-wide discovery of phasiRNAs and its host PHAS loci in P. notoginseng by analyzing small RNA sequencing profiles. Degradome sequencing profile was used to identify the trigger miRNAs of these phasiRNAs and potential targets of phasiRNAs. We also used RLM 5’-RACE to validate some of the identified phasiRNA targets.

Results

After analyzing 24 small RNA sequencing profiles of P. notoginseng, 204 and 90 PHAS loci that encoded 21 and 24 nucleotide (nt) phasiRNAs, respectively, were identified. Furthermore, we found that phasiRNAs produced from some pentatricopeptide repeat-contain (PPR) genes target another layer of PPR genes as validated by both the degradome sequencing profile and RLM 5’-RACE analysis. We also found that miR171 with 21 nt triggers the generations of 21 nt phasiRNAs from its conserved targets.

Conclusions

We validated that some phasiRNAs generated from PPRs and TASL genes are functional by targeting other PPRs in trans. These results provide the first set of PHAS loci and phasiRNAs in P. notoginseng, and enhance our understanding of PHAS in plants.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-4331-0) contains supplementary material, which is available to authorized users.

AGO18b negatively regulates determinacy of spikelet meristems on the tassel central spike in maize

The maize tassel represents an indeterminate male inflorescence. The number of primordia that a given inflorescence meristem produces is related to its determinacy, i.e., capacity for continued meristem activity. Transcription factors (TFs) controlling determinacy in tassel axillary meristems are well studied in maize, and small RNAs are known to influence tassel development by repressing targets, including tassel-related TFs. As core components of the RNA-inducible silence complex (RISC), Argonaute (AGO) proteins are required for small RNA-mediated repression. Here, we characterized the biological function of AGO18b, a tassel-enriched AGO. The abundance of AGO18b transcripts gradually increased during tassel development from inception to gametogenesis and were enriched in the inflorescence meristem and axillary meristems of the tassel. Repressing AGO18b expression resulted in more spikelets, which contributed to a longer central spike of the tassel. Additionally, the transcripts of several HD-ZIP III TFs that were canonical targets of microRNA166 (miR166) accumulated in the AGO18b-repressed lines. We propose that AGO18b is a negative regulator of the determinacy of inflorescence and axillary meristems, and that it acts by interacting with the miR166-HD-ZIP III TF regulatory pathway.

Plant small RNAs: the essential epigenetic regulators of gene expression for salt-stress responses and tolerance

Saline environment cues distort the plant growth, development and crop yield. Epigenetics has emerged as one of the prime themes in plant functional genomics for molecular-stress-physiology research, as copious studies have provided new visions into the epigenetic control of stress adaptations. The epigenetic control is associated with the regulation of the expression of stress-related genes which also comprises many steady alterations inherited in next cellular generation as stress memory. These epigenetic amendments also implicate induction of small RNA (sRNA)-mediated fine-tuning of transcriptional and post-transcriptional regulations of gene expression. These tiny (19-24 nt) RNA species, particularly microRNAs (miRNAs) besides endogenous small interfering RNA (siRNA) have emerged as important responsive entities for epigenetic modulation of salt-stress effects on plants. There is a recent upsurge in development of tools and databases useful for prediction, identification and validation of small RNAs (sRNAs) and their target messenger RNAs (mRNAs). Therefore, these small but key regulatory molecules have received a wide attention in post-genomic era as potential targets for engineering stress tolerance in major glycophytic crops, though it is yet to be explored optimally. This review aims to provide critical updates on plant sRNAs as key epigenetic regulators of plant salt-stress responses, their target prediction and validation, computational tools and databases available for plant small RNAs, besides discussing their roles in salt-stress regulatory networks and adaptive mechanisms in plants, with special emphasis on their exploration for engineering salinity tolerance in plants.

Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction

DNA methylation and histone modifications are epigenetic changes on a DNA molecule that alter the three-dimensional (3D) structure locally as well as globally, impacting chromatin looping and packaging on a larger scale. Epigenetic marks thus inform higher-order chromosome organization and placement in the nucleus. Conventional epigenetic marks are joined by chromatin modifiers like cohesins, condensins and membrane-anchoring complexes to support particularly 3D chromosome organization. The most popular consequences of epigenetic modifications are gene expression changes, but chromatin modifications have implications beyond this, particularly in actively dividing cells and during sexual reproduction. In this opinion paper, we will focus on epigenetic mechanisms and chromatin modifications during meiosis as part of plant sexual reproduction where 3D management of chromosomes and re-organization of chromatin are defining features and prime tasks in reproductive cells, not limited to modulating gene expression. Meiotic chromosome organization, pairing and synapsis of homologous chromosomes as well as distribution of meiotic double-strand breaks and resulting crossovers are presumably highly influenced by epigenetic mechanisms. Special mobile small RNAs have been described in anthers, where these so-called phasiRNAs seem to direct DNA methylation in meiotic cells. Intriguingly, many of the mentioned developmental processes make use of epigenetic changes and small RNAs in a manner other than gene expression changes. Widening our approaches and opening our mind to thinking three-dimensionally regarding epigenetics in plant development holds high promise for new discoveries and could give us a boost for further knowledge.

Molecular Control of Male Fertility for Crop Hybrid Breeding

In many plant species, male-sterile female lines with cytoplasmic male sterility (CMS) or nuclear-controlled environment-sensitive genic male sterility (EGMS) have long been used to efficiently produce hybrids that harness hybrid vigor or heterosis. However, the underlying molecular mechanisms for these applications have only recently been uncovered in a few species. We provide here an update on the understanding of cytoplasmic-nuclear communication based on the discovery of mitochondrial CMS genes and their corresponding nuclear fertility determinants. Recent findings that uncover diverse mechanisms such as epigenetic, transcriptional, and post-transcriptional controls of EGMS by temperature and photoperiod signals are also reviewed. Furthermore, translational research that applies basic knowledge of plant male fertility control to hybrid seed production practice is highlighted.

Method for the Large-Scale Identification of phasiRNAs in Brachypodium distachyon

Postranscriptional regulation has been widely shown to be regulated by several classes of small non-coding RNAs; most abundantly, microRNAs, which have been shown to be the first dominant class and has been widely characterized as post-transcriptional regulators. In addition to microRNAs, triggered by miRNAs, transcripts called as PHAS (or TAS) generate abundant class of small RNAs in 21-nt manner, which is a pattern formed by DICER-LIKE 4 (DCL4) processing. Although PHAS can be identified by aligning transcripts to reported PHAS in other species, the most sensitive and accurate way to discovery them is by mapping of the smallRNAs taking into account the transcript coordinates. Here, we describe a workflow that can be used for the identification PHAS and corresponding phasiRNAs in Brachypodium distachyon using publically availabe smallRNAs datasets.

The 'how' and 'where' of plant microRNAs

Contents 1002 I. 1002 II. 1007 III. 1010 IV. 1013 1013 References 1013 SUMMARY: MicroRNAs (miRNAs) are small non-coding RNAs, of typically 20-24 nt, that regulate gene expression post-transcriptionally through sequence complementarity. Since the identification of the first miRNA, lin-4, in the nematode Caenorhabditis elegans in 1993, thousands of miRNAs have been discovered in animals and plants, and their regulatory roles in numerous biological processes have been uncovered. In plants, research efforts have established the major molecular framework of miRNA biogenesis and modes of action, and are beginning to elucidate the mechanisms of miRNA degradation. Studies have implicated restricted and surprising subcellular locations in which miRNA biogenesis or activity takes place. In this article, we summarize the current knowledge on how plant miRNAs are made and degraded, and how they repress target gene expression. We discuss not only the players involved in these processes, but also the subcellular sites in which these processes are known or implicated to take place. We hope to raise awareness that the cell biology of miRNAs holds the key to a full understanding of these enigmatic molecules.

Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs

The next-generation sequencing (NGS) technology has revolutionized our previous understanding of the plant genomes, relying on its innate advantages, such as high throughput and deep sequencing depth. In addition to the protein-coding gene loci, massive transcription signals have been detected within intergenic or intragenic regions. Most of these signals belong to non-coding ones, considering their weak protein-coding potential. Generally, these transcripts could be divided into long non-coding RNAs and small non-coding RNAs (sRNAs) based on their sequence length. In addition to the well-known microRNAs (miRNAs), many plant endogenous sRNAs were collectively referred to as small interfering RNAs. However, an increasing number of unclassified sRNA species are being discovered by NGS. The high heterogeneity of these novel sRNAs greatly hampered the mechanistic studies, especially on the clear description of their biogenesis and action pathways. Fortunately, public databases, bioinformatics softwares and NGS datasets are increasingly available for plant sRNA research. Here, by summarizing these valuable resources, we proposed a general workflow to decipher the RDR (RNA-dependent RNA polymerase)- and DCL (Dicer-like)-dependent biogenesis pathways, and the Argonaute-mediated action modes (such as target cleavages and chromatin modifications) for specific sRNA species in plants. Taken together, we hope that by summarizing a list of the public resources, this work will facilitate the plant biologists to perform classification and functional characterization of the interesting sRNA species.

Grass phasiRNAs and male fertility

Recent studies have indicated that a special type of small noncoding RNAs, phased small-interfering RNAs (phasiRNAs) play crucial roles in many cellular processes of plant development. PhasiRNAs are generated from long RNA precursors at intervals of 21 or 24 nt in plants, and they are produced from both protein-coding gene and long noncoding RNA genes. Different from those in eudicots, grass phasiRNAs include a special class of small RNAs that are specifically expressed in reproductive organs. These grass phasiRNAs are associated with gametogenesis, especially with anther development and male fertility. In this review, we summarized current knowledge on these small noncoding RNAs in male germ cells and their possible biological functions and mechanisms in grass species.

miR3954 is a trigger of phasiRNAs that affects flowering time in citrus

In plant, a few 22-nt miRNAs direct cleavages of their targets and trigger the biogenesis of phased small interfering RNAs (phasiRNAs) in plant. In this study, we characterized a miRNA triggering phasiRNAs generation, miR3954, and explored its downstream target genes and potential function. Our results demonstrated that miR3954 showed specific expression in the flowers of citrus species, and it targeted a NAC transcription factor (Cs7 g22460) and two non-coding RNA transcripts (lncRNAs, Cs1 g09600 and Cs1 g09635). The production of phasiRNAs was detected from transcripts targeted by miR3954, and was further verified in both sequencing data and transient expression experiments. PhasiRNAs derived from the two lncRNAs targeted not only miR3954-targeted NAC gene but also additional NAC homologous genes. No homologous genes of these two lncRNAs were found in plants other than citrus species, implying that this miR3954-lncRNAs-phasiRNAs-NAC pathway is likely citrus-specific. Transgenic analysis indicated that the miR3954-overexpressing lines showed decreased transcripts of lncRNA, elevated abundance of phasiRNAs and reduced expression of NAC genes. Interestingly, the overexpression of miR3954 leads to early flowering in citrus plants. In summary, our results illustrated a model of the regulatory network of miR3954-lncRNA-phasiRNAs-NAC, which may be functionally involved in flowering in citrus.

Long noncoding RNAs in the model species Brachypodium distachyon

Eukaryotic genomes are pervasively transcribed and only a small portion of the transcribed sequences belongs to protein coding genes. High-throughput sequencing technology contributed to consolidate this perspective, allowing the identification of numerous noncoding RNAs with key roles in biological processes. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nt with limited phylogenetic conservation, expressed at low levels and characterized by tissue/organ specific expression profiles. Although a large set of lncRNAs has been identified, the functional roles of lncRNAs are only beginning to be recognized and the molecular mechanism of lncRNA-mediated gene regulation remains largely unexplored, particularly in plants where their annotation and characterization are still incomplete. Using public and proprietary poly-(A)+ RNA-seq data as well as a collection of full length ESTs from several organs, developmental stages and stress conditions in three Brachypodium distachyon inbred lines, we describe the identification and the main features of thousands lncRNAs. Here we provide a genome-wide characterization of lncRNAs, highlighting their intraspecies conservation and describing their expression patterns among several organs/tissues and stress conditions. This work represents a fundamental resource to deepen our knowledge on long noncoding RNAs in C3 cereals, allowing the Brachypodium community to exploit these results in future research programs.

Conservation and divergence of small RNA pathways and microRNAs in land plants

Background

As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. However, both small RNAs themselves and small RNA pathways are not well characterized in other land plants such as lycophytes and ferns, preventing a comprehensive evolutionary perspective on small RNAs in land plants.

Results

Using 25 representatives from major lineages of lycophytes and ferns, most of which lack sequenced genomes, we characterized small RNAs and small RNA pathways in these plants. We identified homologs of DICER-LIKE (DCL), ARGONAUTE (AGO), and other genes involved in small RNA pathways, predicted over 2600 conserved microRNA (miRNA) candidates, and performed phylogenetic analyses on small RNA pathways as well as miRNAs. Pathways underlying miRNA biogenesis, degradation, and activity were established in the common ancestor of land plants, but the 24-nucleotide siRNA pathway that guides DNA methylation is incomplete in sister species of seed plants, especially lycophytes. We show that the functional diversification of key gene families such as DCL and AGO as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered a conserved AGO subfamily absent in angiosperms.

Conclusions

Our phylogenetic analyses of miRNAs in bryophytes, lycophytes, ferns, and angiosperms refine the time-of-origin for conserved miRNA families as well as small RNA machinery in land plants.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1291-2) contains supplementary material, which is available to authorized users.

Role of small RNAs in epigenetic reprogramming during plant sexual reproduction

Sexual reproduction, the formation of a new individual from specialized reproductive cells after fertilization, involves the precise orchestration of different developmental and genomic processes. These processes are to a large extent governed by small RNAs (sRNAs) that either belong to the class of micro RNAs (miRNAs) or small-interfering RNAs (siRNAs). The latter are derived from transposable elements (TEs) and involved in genome defense and transgenerational inheritance of heterochromatin identity, ensuring genome stability. Remarkably, male and female gametophytes employ sRNAs to ensure reproductive success, but the underlying processes of their formation and action differ. Here, we review current advances in the field concerning the roles of sRNAs during flowering plant (angiosperm) reproduction and pinpoint where further research is required to solve open questions.

Mutations in Argonaute5 Illuminate Epistatic Interactions of the K1 and I Loci Leading to Saddle Seed Color Patterns in Glycine max

The soybean (Glycine max) seed coat has distinctive, genetically programmed patterns of pigmentation, and the recessive k1 mutation can epistatically overcome the dominant I and ii alleles, which inhibit seed color by producing small interfering RNAs (siRNAs) targeting chalcone synthase (CHS) mRNAs. Small RNA sequencing of dissected regions of immature seed coats demonstrated that CHS siRNA levels cause the patterns produced by the ii and ik alleles of the I locus, which restrict pigment to the hilum or saddle region of the seed coat, respectively. To identify the K1 locus, we compared RNA-seq data from dissected regions of two Clark isolines having similar saddle phenotypes mediated by CHS siRNAs but different genotypes (homozygous ik K1 versus homozygous ii k1). By examining differentially expressed genes, mapping information, and genome resequencing, we identified a 129-bp deletion in Glyma.11G190900 encoding Argonaute5 (AGO5), a member of the Argonaute family. Amplicon sequencing of several independent saddle pattern mutants from different genetic backgrounds revealed independent lesions affecting AGO5, thus establishing Glyma.11G190900 as the K1 locus. Nonfunctional AGO5 from k1 alleles leads to altered distributions of CHS siRNAs, thus explaining how the k1 mutation reverses the phenotype of the seed coat regions from yellow to pigmented, even in the presence of the normally dominant I or ii alleles.

Analysis of small RNAs revealed differential expressions during pollen and embryo sac development in autotetraploid rice

Background

Partial pollen and embryo sac sterilities are the two main reasons for low fertility in autotetraploid rice. Our previous study revealed that small RNAs changes may associate with pollen fertility in autotetraploid rice. However, knowledge on comparative analysis between the development of pollen and embryo sac by small RNAs in autotetraploid rice is still unknown. In the present study, WE-CLSM (whole-mount eosin B-staining confocal laser scanning microscopy) and high-throughput sequencing technology was employed to examine the cytological variations and to analyze small RNAs changes during pollen and embryo sac development in autotetraploid rice compared with its diploid counterpart.

Results

A total of 321 and 368 differentially expressed miRNAs (DEM) were detected during pollen and embryo sac development in autotetraploid rice, respectively. Gene Ontology enrichment analysis on the targets of DEM associated with embryo sac and pollen development revealed 30 prominent functional gene classes, such as cell differentiation and signal transduction during embryo sac development, while only 7 prominent functional gene classes, such as flower development and transcription factor activity, were detected during pollen development in autotetraploid rice. The expression levels of 39 DEM, which revealed interaction with meiosis-related genes, showed opposite expression patterns during pollen and embryo sac development. Of these DEM, osa-miR1436_L + 3_1ss5CT and osa-miR167h-3p were associated with the female meiosis, while osa-miR159a.1 and osa-MIR159a-p5 were related with the male meiosis. 21 nt-phasiRNAs were detected during both pollen and embryo sac development, while 24 nt-phasiRNAs were found only in pollen development, which displayed down-regulation in autotetraploid compared to diploid rice and their spatial-temporal expression patterns were similar to osa-miR2275d. 24 nt TEs-siRNAs were found to be up-regulated in embryo sac but down-regulated in pollen development.

Conclusion

The above results not only provide the small RNAs changes during four landmark stages of pollen and embryo sac development in autotetraploid rice but also have identified specifically expressed miRNAs, especially meiosis-related miRNAs, pollen-specific-24 nt-phasiRNAs and TEs-siRNAs in autotetraploid rice. Together, these findings provide a foundation for understanding the effect of polyploidy on small RNAs expression patterns during pollen and embryo sac development that may lead to different abnormalities in autotetraploid rice.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3526-8) contains supplementary material, which is available to authorized users.

Epigenetic processes in flowering plant reproduction

Seeds provide up to 70% of the energy intake of the human population, emphasizing the relevance of understanding the genetic and epigenetic mechanisms controlling seed formation. In flowering plants, seeds are the product of a double fertilization event, leading to the formation of the embryo and the endosperm surrounded by maternal tissues. Analogous to mammals, plants undergo extensive epigenetic reprogramming during both gamete formation and early seed development, a process that is supposed to be required to enforce silencing of transposable elements and thus to maintain genome stability. Global changes of DNA methylation, histone modifications, and small RNAs are closely associated with epigenome programming during plant reproduction. Here, we review current knowledge on chromatin changes occurring during sporogenesis and gametogenesis, as well as early seed development in major flowering plant models.

An Agrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize

CRISPR/Cas9 is a powerful genome editing tool in many organisms, including a number of monocots and dicots. Although the design and application of CRISPR/Cas9 is simpler compared to other nuclease-based genome editing tools, optimization requires the consideration of the DNA delivery and tissue regeneration methods for a particular species to achieve accuracy and efficiency. Here, we describe a public sector system, ISU Maize CRISPR, utilizing Agrobacterium-delivered CRISPR/Cas9 for high-frequency targeted mutagenesis in maize. This system consists of an Escherichia coli cloning vector and an Agrobacterium binary vector. It can be used to clone up to four guide RNAs for single or multiplex gene targeting. We evaluated this system for its mutagenesis frequency and heritability using four maize genes in two duplicated pairs: Argonaute 18 (ZmAgo18a and ZmAgo18b) and dihydroflavonol 4-reductase or anthocyaninless genes (a1 and a4). T0 transgenic events carrying mono- or diallelic mutations of one locus and various combinations of allelic mutations of two loci occurred at rates over 70% mutants per transgenic events in both Hi-II and B104 genotypes. Through genetic segregation, null segregants carrying only the desired mutant alleles without the CRISPR transgene could be generated in T1 progeny. Inheritance of an active CRISPR/Cas9 transgene leads to additional target-specific mutations in subsequent generations. Duplex infection of immature embryos by mixing two individual Agrobacterium strains harbouring different Cas9/gRNA modules can be performed for improved cost efficiency. Together, the findings demonstrate that the ISU Maize CRISPR platform is an effective and robust tool to targeted mutagenesis in maize.

An Agrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize

CRISPR/Cas9 is a powerful genome editing tool in many organisms, including a number of monocots and dicots. Although the design and application of CRISPR/Cas9 is simpler compared to other nuclease-based genome editing tools, optimization requires the consideration of the DNA delivery and tissue regeneration methods for a particular species to achieve accuracy and efficiency. Here, we describe a public sector system, ISU Maize CRISPR, utilizing Agrobacterium-delivered CRISPR/Cas9 for high-frequency targeted mutagenesis in maize. This system consists of an Escherichia coli cloning vector and an Agrobacterium binary vector. It can be used to clone up to four guide RNAs for single or multiplex gene targeting. We evaluated this system for its mutagenesis frequency and heritability using four maize genes in two duplicated pairs: Argonaute 18 (ZmAgo18a and ZmAgo18b) and dihydroflavonol 4-reductase or anthocyaninless genes (a1 and a4). T₀ transgenic events carrying mono- or diallelic mutations of one locus and various combinations of allelic mutations of two loci occurred at rates over 70% mutants per transgenic events in both Hi-II and B104 genotypes. Through genetic segregation, null segregants carrying only the desired mutant alleles without the CRISPR transgene could be generated in T₁ progeny. Inheritance of an active CRISPR/Cas9 transgene leads to additional target-specific mutations in subsequent generations. Duplex infection of immature embryos by mixing two individual Agrobacterium strains harbouring different Cas9/gRNA modules can be performed for improved cost efficiency. Together, the findings demonstrate that the ISU Maize CRISPR platform is an effective and robust tool to targeted mutagenesis in maize.

MATRILINEAL, a sperm-specific phospholipase, triggers maize haploid induction

Sexual reproduction in flowering plants involves double fertilization, the union of two sperm from pollen with two sex cells in the female embryo sac. Modern plant breeders increasingly seek to circumvent this process to produce doubled haploid individuals, which derive from the chromosome-doubled cells of the haploid gametophyte. Doubled haploid production fixes recombinant haploid genomes in inbred lines, shaving years off the breeding process. Costly, genotype-dependent tissue culture methods are used in many crops, while seed-based in vivo doubled haploid systems are rare in nature and difficult to manage in breeding programmes. The multi-billion-dollar maize hybrid seed business, however, is supported by industrial doubled haploid pipelines using intraspecific crosses to in vivo haploid inducer males derived from Stock 6, first reported in 1959 (ref. 5), followed by colchicine treatment. Despite decades of use, the mode of action remains controversial. Here we establish, through fine mapping, genome sequencing, genetic complementation, and gene editing, that haploid induction in maize (Zea mays) is triggered by a frame-shift mutation in MATRILINEAL (MTL), a pollen-specific phospholipase, and that novel edits in MTL lead to a 6.7% haploid induction rate (the percentage of haploid progeny versus total progeny). Wild-type MTL protein localizes exclusively to sperm cytoplasm, and pollen RNA-sequence profiling identifies a suite of pollen-specific genes overexpressed during haploid induction, some of which may mediate the formation of haploid seed. These findings highlight the importance of male gamete cytoplasmic components to reproductive success and male genome transmittance. Given the conservation of MTL in the cereals, this discovery may enable development of in vivo haploid induction systems to accelerate breeding in crop plants.

Signatures of selection and host-adapted gene expression of the Phytophthora infestans RNA silencing suppressor PSR2

Phytophthora infestans is a devastating pathogen in agricultural systems. Recently, an RNA silencing suppressor (PSR2, 'Phytophthora suppressor of RNA silencing 2') has been described in P. infestans. PSR2 has been shown to increase the virulence of Phytophthora pathogens on their hosts. This gene is one of the few effectors present in many economically important Phytophthora species. In this study, we investigated: (i) the evolutionary history of PSR2 within and between species of Phytophthora; and (ii) the interaction between sequence variation, gene expression and virulence. In P. infestans, the highest PiPSR2 expression was correlated with decreased symptom expression. The highest gene expression was observed in the biotrophic phase of the pathogen, suggesting that PSR2 is important during early infection. Protein sequence conservation was negatively correlated with host range, suggesting host range as a driver of PSR2 evolution. Within species, we detected elevated amino acid variation, as observed for other effectors; however, the frequency spectrum of the mutations was inconsistent with strong balancing selection. This evolutionary pattern may be related to the conservation of the host target(s) of PSR2 and the absence of known corresponding R genes. In summary, our study indicates that PSR2 is a conserved effector that acts as a master switch to modify plant gene regulation early during infection for the pathogen's benefit. The conservation of PSR2 and its important role in virulence make it a promising target for pathogen management.

Biogenesis of diverse plant phasiRNAs involves an miRNA-trigger and Dicer-processing

It has been almost 30 years since RNA interference (RNAi) was shown to silence genes via double-stranded RNAs (dsRNAs) in Caenorhabditis elegans (Fire et al. 1998). 20-30-nucleotide (nt) small non-coding RNAs are a key element of the RNAi machinery. Recently, phased small interfering RNAs (phasiRNAs), small RNAs that are generated from a long RNA precursor at intervals of 21 to 26-nt, have been identified in plants and animals. In Drosophila, phasiRNAs are generated by the endonuclease, Zucchini (Zuc), in germlines. These phasiRNAs, known as one of PIWI-interacting RNAs (piRNAs), mainly repress transposable elements. Similarly, reproduction-specific phasiRNAs have been identified in the family Poaceae, although DICER LIKE (DCL) protein-dependent phasiRNA biogenesis in rice is distinct from piRNA biogenesis in animals. In plants, phasiRNA biogenesis is initiated when 22-nt microRNAs (miRNAs) cleave single-stranded target RNAs. Subsequently, RNA-dependent RNA polymerase (RDR) forms dsRNAs from the cleaved RNAs, and dsRNAs are further processed by DCLs into 21 to 24-nt phasiRNAs. Finally, the phasiRNAs are loaded to ARGONAUTE (AGO) proteins to induce RNA-silencing. There are diverse types of phasiRNA precursors and the miRNAs that trigger the biogenesis. Their expression patterns also differ among plant species, suggesting that species-specific combinations of these triggers dictate the spatio-temporal pattern of phasiRNA biogenesis during development, or in response to environmental stimuli.

PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice

Phased small-interfering RNAs (phasiRNAs) are a special class of small RNAs, which are generated in 21- or 24-nt intervals from transcripts of precursor RNAs. Although phasiRNAs have been found in a range of organisms, their biological functions in plants have yet to be uncovered. Here we show that phasiRNAs generated by the photopheriod-sensetive genic male sterility 1 (Pms1) locus were associated with photoperiod-sensitive male sterility (PSMS) in rice, a germplasm that started the two-line hybrid rice breeding. The Pms1 locus encodes a long-noncoding RNA PMS1T that was preferentially expressed in young panicles. PMS1T was targeted by miR2118 to produce 21-nt phasiRNAs that preferentially accumulated in the PSMS line under long-day conditions. A single nucleotide polymorphism in PMS1T nearby the miR2118 recognition site was critical for fertility change, likely leading to differential accumulation of the phasiRNAs. This result suggested possible roles of phasiRNAs in reproductive development of rice, demonstrating the potential importance of this RNA class as regulators in biological processes.

MS23, a master basic helix-loop-helix factor, regulates the specification and development of the tapetum in maize

Successful male gametogenesis involves orchestration of sequential gene regulation for somatic differentiation in pre-meiotic anthers. We report here the cloning of Male Sterile23 (Ms23), encoding an anther-specific predicted basic helix-loop-helix (bHLH) transcription factor required for tapetal differentiation; transcripts localize initially to the precursor secondary parietal cells then predominantly to daughter tapetal cells. In knockout ms23-ref mutant anthers, five instead of the normal four wall layers are observed. Microarray transcript profiling demonstrates a more severe developmental disruption in ms23-ref than in ms32 anthers, which possess a different bHLH defect. RNA-seq and proteomics data together with yeast two-hybrid assays suggest that MS23 along with MS32, bHLH122 and bHLH51 act sequentially as either homo- or heterodimers to choreograph tapetal development. Among them, MS23 is the earliest-acting factor, upstream of bHLH51 and bHLH122, controlling tapetal specification and maturation. By contrast, MS32 is constitutive and independently regulated and is required later than MS23 in tapetal differentiation.

miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species

BACKGROUND

Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African rice Oryza glaberrima and its wild relative Oryza barthii.

RESULTS

Our RNA-seq analysis revealed a dramatic difference between the two species in the 21 nucleotide small RNA population, corresponding mainly to miR2118-triggered phased siRNAs. A detailed expression profiling during the panicle development of O. glaberrima and O. barthii using qRT-PCRs and in situ hybridization, confirmed a delayed expression of the phased siRNAs as well as their lncRNA precursors and regulators (miR2118 and MEL1 gene) in O. glaberrima compared to O. barthii. We provide evidence that the 21-nt phasiRNA pathway in rice is associated with male-gametogenesis but is initiated in spikelet meristems.

CONCLUSION

Differential expression of the miR2118-triggered 21-nt phasiRNA pathway between the two African rice species reflects differential rates of determinate fate acquisition of panicle meristems between the two species.

Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways

Dissection of the genetic pathways and mechanisms by which anther development occurs in grasses is crucial for both a basic understanding of plant development and for examining traits of agronomic importance such as male sterility. In rice, MULTIPLE SPOROCYTES1 (MSP1), a leucine-rich-repeat receptor kinase, plays an important role in anther development by limiting the number of sporocytes. OsTDL1a (a TPD1-like gene in rice) encodes a small protein that acts as a cofactor of MSP1 in the same regulatory pathway. In this study, we analyzed small RNA and mRNA changes in different stages of spikelets from wild-type rice, and from msp1 and ostdl1a mutants. Analysis of the small RNA data identified miRNAs demonstrating differential abundances. miR2275 was depleted in the two rice mutants; this miRNA is specifically enriched in anthers and functions to trigger the production of 24-nt phased secondary siRNAs (phasiRNAs) from PHAS loci. We observed that the 24-nt phasiRNAs as well as their precursor PHAS mRNAs were also depleted in the two mutants. An analysis of co-expression identified three Argonaute-encoding genes (OsAGO1d, OsAGO2b, and OsAGO18) that accumulate transcripts coordinately with phasiRNAs, suggesting a functional relationship. By mRNA in situ analysis, we demonstrated a strong correlation between the spatiotemporal pattern of these OsAGO transcripts and phasiRNA accumulations.

A wide reprogramming of histone H3 modifications during male meiosis I in rice is dependent on the Argonaute protein MEL1

The roles of epigenetic mechanisms, including small-RNA-mediated silencing, in plant meiosis largely remain unclear, despite their importance in plant reproduction. This study unveiled that rice chromosomes are reprogrammed during the premeiosis-to-meiosis transition in pollen mother cells (PMCs). This large-scale meiotic chromosome reprogramming (LMR) continued throughout meiosis I, during which time H3K9 dimethylation (H3K9me2) was increased, and H3K9 acetylation and H3S10 phosphorylation were broadly decreased, with an accompanying immunostaining pattern shift of RNA polymerase II. LMR was dependent on the rice Argonaute protein, MEIOSIS ARRESTED AT LEPTOTENE1 (MEL1), which is specifically expressed in germ cells prior to meiosis, because LMR was severely diminished in mel1 mutant anthers. Pivotal meiotic events, such as pre-synaptic centromere association, DNA double-strand break initiation and synapsis of homologous chromosomes, were also disrupted in this mutant. Interestingly, and as opposed to the LMR loss in most chromosomal regions, aberrant meiotic protein loading and hypermethylation of H3K9 emerged on the nucleolar organizing region in the mel1 PMCs. These results suggest that MEL1 plays important roles in epigenetic LMR to promote faithful homologous recombination and synapsis during rice meiosis.

The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them

High expression of plant nucleotide binding site leucine-rich repeat (NBS-LRR) defense genes is often lethal to plant cells, a phenotype perhaps associated with fitness costs. Plants implement several mechanisms to control the transcript level of NBS-LRR defense genes. As negative transcriptional regulators, diverse miRNAs target NBS-LRRs in eudicots and gymnosperms. To understand the evolutionary benefits of this miRNA-NBS-LRR regulatory system, we investigated the NBS-LRRs of 70 land plants, coupling this analysis with extensive small RNA data. A tight association between the diversity of NBS-LRRs and miRNAs was found. The miRNAs typically target highly duplicated NBS-LRRs In comparison, families of heterogeneous NBS-LRRs were rarely targeted by miRNAs in Poaceae and Brassicaceae genomes. We observed that duplicated NBS-LRRs from different gene families periodically gave birth to new miRNAs. Most of these newly emerged miRNAs target the same conserved, encoded protein motif of NBS-LRRs, consistent with a model of convergent evolution for these miRNAs. By assessing the interactions between miRNAs and NBS-LRRs, we found nucleotide diversity in the wobble position of the codons in the target site drives the diversification of miRNAs. Taken together, we propose a co-evolutionary model of plant NBS-LRRs and miRNAs hypothesizing how plants balance the benefits and costs of NBS-LRR defense genes.

Long non-coding RNAs are major contributors to transcriptome changes in sunflower meiocytes with different recombination rates

BACKGROUND

Meiosis is a form of specialized cell division that marks the transition from diploid meiocyte to haploid gamete, and provides an opportunity for genetic reassortment through recombination. Experimental data indicates that, relative to their wild ancestors, cultivated sunflower varieties show a higher recombination rate during meiosis. To better understand the molecular basis for this difference, we compared gene expression in male sunflower meiocytes in prophase I isolated from a domesticated line, a wild relative, and a F1 hybrid of the two.

RESULTS

Of the genes that showed differential expression between the wild and domesticated genotypes, 63.62 % could not be identified as protein-coding genes, and of these genes, 70.98 % passed stringent filters to be classified as long non-coding RNAs (lncRNAs). Compared to the sunflower somatic transcriptome, meiocytes express a higher proportion of lncRNAs, and the majority of genes with exclusive expression in meiocytes were lncRNAs. Around 40 % of the lncRNAs showed sequence similarity with small RNAs (sRNA), while 1.53 % were predicted to be sunflower natural antisense transcripts (NATs), and 9.18 % contained transposable elements (TE). We identified 6895 lncRNAs that are exclusively expressed in meiocytes, these lncRNAs appear to have higher conservation, a greater degree of differential expression, a higher proportion of sRNA similarity, and higher TE content relative to lncRNAs that are also expressed in the somatic transcriptome.

CONCLUSIONS

lncRNAs play important roles in plant meiosis and may participate in chromatin modification processes, although other regulatory functions cannot be excluded. lncRNAs could also be related to the different recombination rates seen for domesticated and wild sunflowers.

Pre-Meiotic Anther Development: Cell Fate Specification and Differentiation

Research into anther ontogeny has been an active and developing field, transitioning from a strictly lineage-based view of cellular differentiation events to a more complex understanding of cell fate specification. Here we describe the modern interpretation of pre-meiotic anther development, from the earliest cell specifications within the anther lobes through SPL/NZZ-, MSP1-, and MEL1-dependent pathways as well as the initial setup of the abaxial and adaxial axes and outgrowth of the anther lobes. We then continue with a look at the known information regarding further differentiation of the somatic layers of the anther (the epidermis, endothecium, middle layer, and tapetum), with an emphasis on male-sterile mutants identified as defective in somatic cell specification. We also describe the differences in developmental stages among species and use this information to discuss molecular studies that have analyzed transcriptome, proteome, and small-RNA information in the anther.