MiR529a modulates panicle architecture through regulating SQUAMOSA PROMOTER BINDING-LIKE genes in rice (Oryza sativa)

The role of Ancestral MicroRNAs in grass inflorescence development

Plant inflorescences are complex, highly diverse structures whose morphology is determined in meristems that form during reproductive development. Inflorescence structure influences flower formation, and consequently grain number, and yield in crops. Correct inflorescence and flower development require tight control of gene expression via complex interplay between regulatory networks. MicroRNAs (miRNAs) have emerged as fundamental modulators of gene expression at the transcriptional and/or post-transcriptional level in plant inflorescence development. First discovered more than three decades ago, miRNAs have proved to be revolutionary in advancing our mechanistic understanding of gene expression. This review highlights current knowledge of downstream target genes and pathways of some highly conserved miRNAs that regulate the maintenance, identity, and activity of inflorescence and floral meristems in economically and agriculturally important grass species, including rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare), and wheat (Triticum aestivum). Furthermore, we summarize emerging regulatory networks of miRNAs and their targets to suggest new avenues and strategies for application of miRNAs as a tool to enhance crop yield and performance.

Regulation of tillering and panicle branching in rice and wheat

Branching is a critical aspect of plant architecture that significantly impacts the yield and adaptability of staple cereal crops like rice and wheat. Cereal crops develop tillers during the vegetative stage and panicle or spike branches during the reproductive stage, respectively, both of which are significantly impacted by hormones and genetic factors. Tillering and panicle branching are closely interconnected and exhibit high environmental plasticity. Here, we summarize the recent progress in genetic, hormonal, and environmental factors regulation in the branching of rice and wheat. This review not only provides a comprehensive overview of the current knowledge on branching mechanisms in rice and wheat, but also explores the prospects for future research aimed at optimizing crop architecture for enhanced productivity.

miRNAs and genes as molecular regulators of rice grain morphology and yield

Rice is one of the most consumed crops worldwide and the genetic and molecular basis of its grain yield attributes are well understood. Various studies have identified different yield-related parameters in rice that are regulated by the microRNAs (miRNAs). MiRNAs are endogenous small non-coding RNAs that silence gene expression during or after transcription. They control a variety of biological or genetic activities in plants including growth, development and response to stress. In this review, we have summarized the available information on the genetic control of panicle architecture and grain yield (number and morphology) in rice. The miRNA nodes that are associated with their regulation are also described while focussing on the central role of miR156-SPL node to highlight the co-regulation of two master regulators that determine the fate of panicle development. Since abiotic stresses are known to negatively affect yield, the impact of abiotic stress induced alterations on the levels of these miRNAs are also discussed to highlight the potential of miRNAs for regulating crop yields.

Comparative analysis of SPL transcription factors from streptophyte algae and embryophytes reveals evolutionary trajectories of SPL family in streptophytes

SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode plant-specific transcription factors which are important regulators of diverse plant developmental processes. We took advantage of available genome sequences of streptophyte algae representatives to investigate the relationships of SPL genes between freshwater green algae and land plants. Our analysis showed that streptophyte algae, hornwort and liverwort genomes encode from one to four SPL genes which is the smallest set, in comparison to other land plants studied to date. Based on the phylogenetic analysis, four major SPL phylogenetic groups were distinguished with Group 3 and 4 being sister to Group 1 and 2. Comparative motif analysis revealed conserved protein motifs within each phylogenetic group and unique bryophyte-specific motifs within Group 1 which suggests lineage-specific protein speciation processes. Moreover, the gene structure analysis also indicated the specificity of each by identifying differences in exon-intron structures between the phylogenetic groups, suggesting their evolutionary divergence. Since current understanding of SPL genes mostly arises from seed plants, the presented comparative and phylogenetic analyzes from freshwater green algae and land plants provide new insights on the evolutionary trajectories of the SPL gene family in different classes of streptophytes.

Unraveling the transcriptional network regulated by miRNAs in blast-resistant and blast-susceptible rice genotypes during Magnaporthe oryzae interaction

The plant pathogen Magnaporthe oryzae poses a significant threat to global food security, and its management through the cultivation of resistant varieties and crop husbandry practices, including fungicidal sprays, has proven to be inadequate. To address this issue, we conducted small-RNA sequencing to identify the roles of miRNAs and their target genes in both resistant (PB1637) and susceptible (PB1) rice genotypes. We confirmed the expression of differentially expressed miRNAs using stem-loop qRT-PCR analysis and correlated them with rice patho-phenotypic and physio-biochemical responses. Our findings revealed several noteworthy differences between the resistant and susceptible genotypes. The resistant genotype exhibited reduced levels of total chlorophyll and carotenoids compared to the susceptible genotype. However, it showed increased levels of total protein, callose, H2O2, antioxidants, flavonoids, and total polyphenols. Additionally, among the defense-associated enzymes, guaiacol peroxidase and polyphenol oxidase responses were higher in the susceptible genotypes. In our comparative analysis, we identified 27 up-regulated and 43 down-regulated miRNAs in the resistant genotype, while the susceptible genotype exhibited 44 up-regulated and 62 down-regulated miRNAs. Furthermore, we discovered eight up-regulated and five down-regulated miRNAs shared between the resistant and susceptible genotypes. Notably, we also identified six novel miRNAs in the resistant genotype and eight novel miRNAs in the susceptible genotype. These novel miRNAs, namely Chr8_26996, Chr12_40110, and Chr12_41899, were found to negatively correlate with the expression of predicted target genes, including Cyt-P450 monooxygenase, serine carboxypeptidase, and zinc finger A20 domain-containing stress-associated protein, respectively. The results of our study on miRNA and transcriptional responses provide valuable insights for the development of future rice lines that are resistant to blast disease. By understanding the roles of specific miRNAs and their target genes in conferring resistance, we can enhance breeding strategies and improve crop management practices to ensure global food security.

Revitalizing miRNAs mediated agronomical advantageous traits improvement in rice

One of the key enigmas in conventional and modern crop improvement programmes is how to introduce beneficial traits without any penalty impairment. Rice (Oryza sativa L.), among the essential staple food crops grown and utilized worldwide, needs to improve genotypes in multifaceted ways. With the global view to feed ten billion under the climatic perturbation, only a potent functional master regulator can withstand with hope for the next green revolution and food security. miRNAs are such, miniature, fine tuners for crop improvement and provide a value addition in emerging technologies, namely large-scale genotyping, phenotyping, genome editing, marker-assisted selection, and genomic selection, to make rice production feasible. There has been surplus research output generated since the last decade on miRNAs in rice, however, recent functional knowledge is limited to reaping the benefits for conventional and modern improvements in rice to avoid ambiguity and redundancy in the generated data. Here, we present the latest functional understanding of miRNAs in rice. In addition, their biogenesis, intra- and inter-kingdom signaling and communication, implication of amiRNAs, and consequences upon integration with CRISPR-Cas9. Further, highlights refer to the application of miRNAs for rice agronomical trait improvements, broadly classified into three functional domains. The majority of functionally established miRNAs are responsible for growth and development, followed by biotic and abiotic stresses. Tabular cataloguing reveals and highlights two multifaceted modules that were extensively studied. These belong to miRNA families 156 and 396, orchestrate multifarious aspects of advantageous agronomical traits. Moreover, updated and exhaustive functional aspects of different supplemental miRNA modules that would strengthen rice improvement are also being discussed.

Genome-Wide Identification and Expression Analysis of the SPL Gene Family in Three Orchids

SPL transcription factors regulate important processes such as plant growth and development, metabolic regulation, and abiotic stress. They play crucial roles in the development of flower organs. However, little is known about the characteristics and functions of the SPLs in the Orchidaceae. In this study, Cymbidium goeringii Rchb. f., Dendrobium chrysotoxum Lindl., and Gastrodia elata BI. were used as research objects. The SPL gene family of these orchids was analyzed on a genome-wide scale, and their physicochemical properties, phylogenetic relationships, gene structures, and expression patterns were studied. Transcriptome and qRT-PCR methods were combined to investigate the regulatory effect of SPLs on the development of flower organs during the flowering process (bud, initial bloom, and full bloom). This study identifies a total of 43 SPLs from C. goeringii (16), D. chrysotoxum (17), and G. elata (10) and divides them into eight subfamilies according to the phylogenetic tree. Most SPL proteins contained conserved SBP domains and complex gene structures; half of the genes had introns longer than 10 kb. The largest number and variety of cis-acting elements associated with light reactions were enriched, accounting for about 45% of the total (444/985); 13/43 SPLs contain response elements of miRNA156. GO enrichment analysis showed that the functions of most SPLs were mainly enriched in the development of plant flower organs and stems. In addition, expression patterns and qRT-PCR analysis suggested the involvement of SPL genes in the regulation of flower organ development in orchids. There was little change in the expression of the CgoSPL in C. goeringii, but DchSPL9 and GelSPL2 showed significant expression during the flowering process of D. chrysotoxum and G. elata, respectively. In summary, this paper provides a reference for exploring the regulation of the SPL gene family in orchids.

OsNAR2.1 induced endogenous nitrogen concentration variation affects transcriptional expression of miRNAs in rice

The studies of rice nitrogen concentration on the expression of miRNA so far are mostly limited to the exogenous nitrogen, leaving the effect of endogenous nitrogen largely unexplored. OsNAR2.1 is a high-affinity nitrate transporter partner protein which plays a central role in nitrate absorption and translocation in rice. The expression of OsNAR2.1 could influence the concentration of the endogenous nitrogen in rice. We showed that the expression and production of miRNA in rice can be influenced by manipulating the endogenous nitrogen concentration via OsNAR2.1 transgenic lines. The small RNA content, particularly 24 nucleotides small RNA, expressed differently in two transgenic rice lines (nitrogen efficient line with overexpression of OsNAR2.1 (Ov199), nitrogen-inefficient line with knockdown OsNAR2.1 by RNAi (RNAi)) compared to the wild-type (NP). Comparative hierarchical clustering expression pattern analysis revealed that the expression profiles of mature miRNA in both transgenic lines were different from NP. Several previously unidentified miRNAs were identified to be differentially expressed under different nitrogen concentrations, namely miR1874, miR5150, chr3-36147, chr4-27017 and chr5-21745. In conclusion, our findings suggest that the level of endogenous nitrogen concentration variation by overexpression or knockdown OsNAR2.1 could mediate the expression pattern and intensity of miRNA in rice, which is of high potential to be used in molecular breeding to improve the rice responses towards nitrogen utilization.

Comprehensive analyses of the SPL transcription factor family in Paulownia fortunei and their responses to biotic and abiotic stresses

To study the molecular characteristics, phylogenetic evolution, and gene functions of the SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes in Paulownia fortunei, a whole genome sequence analysis was carried out, and a total of 23 PfSPL genes were identified. Tandem duplication and fragment replication were the main patterns of gene expansion in the PfSPL family. Phylogenetic analysis showed that the 23 identified PfSPLs formed seven subgroups, and the structures of the proteins in the same subgroup were similar. Functional analysis indicated that PfSPL11 may regulate flowering, PfSPL5 was involved in gibberellin signaling, PfSPL1/4/23 regulated branching, and PfSPL9/16/18 were related to pathogen resistance. Yeast one hybrid technology confirmed that PfSPL4 and PfSP23 can bind to the promoter of PfTCPa. The transcriptome analysis indicated that PfSPL10 was sensitive to both drought and salt stress. Ten PfSPLs that responded to phytoplasma infection were identified. Molecular docking showed that PfSPL10 and PfSPL 4/5/9/10/11/13 formed active pockets in the conserved SBP domain that could bind methyl methane sulfonate (MMS) and rifampicin (Rif) through stable hydrogen bonds, respectively. This study provides a basis for further studies on the functions of the PfSPL transcription factor family, and for genetic improvement and breeding of trees resistant to PaWB disease.

Identification of Alfalfa SPL gene family and expression analysis under biotic and abiotic stresses

The SQUAMOSA promoter binding-like protein (SPL) is a specific transcription factor that affects plant growth and development. The SPL gene family has been explored in various plants, but information about these genes in alfalfa is limited. This study, based on the whole genome data of alfalfa SPL, the fundamental physicochemical properties, phylogenetic evolution, gene structure, cis-acting elements, and gene expression of members of the MsSPL gene family were analyzed by bioinformatics methods. We identified 82 SPL sequences in the alfalfa, which were annotated into 23 genes, including 7 (30.43%) genes with four alleles, 10 (43.47%) with three, 3 (13.04%) with two, 3 (13.04%) with one allele. These SPL genes were divided into six groups, that are constructed from A. thaliana, M. truncatula and alfalfa. Chromosomal localization of the identified SPL genes showed arbitary distribution. The subcellular localization predictions showed that all MsSPL proteins were located in the nucleus. A total of 71 pairs of duplicated genes were identified, and segmental duplication mainly contributed to the expansion of the MsSPL gene family. Analysis of the Ka/Ks ratios indicated that paralogs of the MsSPL gene family principally underwent purifying selection. Protein-protein interaction analysis of MsSPL proteins were performed to predict their roles in potential regulatory networks. Twelve cis-acting elements including phytohormone and stress elements were detected in the regions of MsSPL genes. We further analyzed that the MsSPLs had apparent responses to abiotic stresses such as drought and salt and the biotic stress of methyl jasmonate. These results provide comprehensive information on the MsSPL gene family in alfalfa and lay a solid foundation for elucidating the biological functions of MsSPLs. This study also provides valuable on the regulation mechanism and function of MsSPLs in response to biotic and abiotic stresses.

Non-coding RNAs fine-tune the balance between plant growth and abiotic stress tolerance

To survive in adverse environmental conditions, plants have evolved sophisticated genetic and epigenetic regulatory mechanisms to balance their growth and abiotic stress tolerance. An increasing number of non-coding RNAs (ncRNAs), including small RNAs (sRNAs) and long non-coding RNAs (lncRNAs) have been identified as essential regulators which enable plants to coordinate multiple aspects of growth and responses to environmental stresses through modulating the expression of target genes at both the transcriptional and posttranscriptional levels. In this review, we summarize recent advances in understanding ncRNAs-mediated prioritization towards plant growth or tolerance to abiotic stresses, especially to cold, heat, drought and salt stresses. We highlight the diverse roles of evolutionally conserved microRNAs (miRNAs) and small interfering RNAs (siRNAs), and the underlying phytohormone-based signaling crosstalk in regulating the balance between plant growth and abiotic stress tolerance. We also review current discoveries regarding the potential roles of ncRNAs in stress memory in plants, which offer their descendants the potential for better fitness. Future ncRNAs-based breeding strategies are proposed to optimize the balance between growth and stress tolerance to maximize crop yield under the changing climate.

Osa-miR1320 targets the ERF transcription factor OsERF096 to regulate cold tolerance via JA-mediated signaling

MicroRNAs play key roles in abiotic stress response. Rice (Oryza sativa L.) miR1320 is a species-specific miRNA that contributes to miR168-regulated immunity. However, it is still unknown whether miR1320 is involved in rice response to abiotic stress. In this study, we illustrated that the miR1320 precursor generated two mature miR1320s, miR1320-3p, and miR1320-5p, and they both displayed decreased expression under cold stress. Genetic evidence showed that miR1320 overexpression resulted in increased cold tolerance, while miR1320 knock down (KD) reduced cold tolerance. Furthermore, an APETALA2/ethylene-responsive factor (ERF) transcription factor OsERF096 was identified as a target of miR1320 via 5'-RACE and dual luciferase assays. OsERF096 expression was altered by miR1320 overexpression and KD and exhibited an opposite pattern to that of miR1320 in different tissues and under cold stress. Consistently, OsERF096 negatively regulated cold stress tolerance. Furthermore, we suggested that OsERF096 could bind to the GCC and DRE cis-elements and act as a transcriptional activator in the nucleus. Based on RNA-sequencing and targeted metabolomics assays, we found that OsERF096 modified hormone content and signaling pathways. Finally, phenotypic and reverse transcription-quantitative PCR assays showed that jasmonic acid (JA) methyl ester application recovered the cold-sensitive phenotype and JA-activated expression of three Dehydration Responsive Element Binding genes in the OsERF096-OE line. Taken together, our results strongly suggest that the miR1320-OsERF096 module regulates cold tolerance by repressing the JA-mediated cold signaling pathway.

Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica)

BACKGROUND

Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human health. However, research on the foxtail millet SPL (SQUAMOSA PROMOTER BINDING-LIKE) gene family is limited.  RESULTS: In this study, a total of 18 SPL genes were identified for the comprehensive analysis of the whole genome of foxtail millet. These SiSPL genes were divided into seven subfamilies (I, II, III, V, VI, VII, and VIII) according to the classification of the Arabidopsis thaliana SPL gene family. Structural analysis of the SiSPL genes showed that the number of introns in subfamilies I and II were much larger than others, and the promoter regions of SiSPL genes were rich in different cis-acting elements. Among the 18 SiSPL genes, nine genes had putative binding sites with foxtail millet miR156. No tandem duplication events were found between the SiSPL genes, but four pairs of segmental duplications were detected. The SiSPL genes expression were detected in different tissues, which was generally highly expressed in seeds development process, especially SiSPL6 and SiSPL16, which deserve further study. The results of the expression levels of SiSPL genes under eight types of abiotic stresses showed that many stress responsive genes, especially SiSPL9, SiSPL10, and SiSPL16, were highly expressed under multiple stresses, which deserves further attention.

CONCLUSIONS

In this research, 18 SPL genes were identified in foxtail millet, and their phylogenetic relationships, gene structural features, duplication events, gene expression and potential roles in foxtail millet development were studied. The findings provide a new perspective for the mining of the excellent SiSPL gene and the molecular breeding of foxtail millet.

Osa-miR535 targets SQUAMOSA promoter binding protein-like 4 to regulate blast disease resistance in rice

Many rice microRNAs have been identified as fine-tuning factors in the regulation of agronomic traits and immunity. Among them, Osa-miR535 targets SQUAMOSA promoter binding protein-like 14 (OsSPL14) to positively regulate tillers but negatively regulate yield and immunity. Here, we uncovered that Osa-miR535 targets another SPL gene, OsSPL4, to suppress rice immunity against Magnaporthe oryzae. Overexpression of Osa-miR535 significantly decreased the accumulation of the fusion protein SPL4_TBS -YFP that contains the target site of Osa-miR535 in OsSPL4. Consistently, Osa-miR535 mediated the cleavage of OsSPL4 mRNA between the 10th and 11th base pair of the predicted binding site at the 3' untranslated region. Transgenic rice lines overexpressing OsSPL4 (OXSPL4) displayed enhanced blast disease resistance accompanied by enhanced immune responses, including increased expression of defense-relative genes and up-accumulated H₂ O₂ . By contrast, the knockout mutant osspl4 exhibited susceptibility. Moreover, OsSPL4 binds to the promoter of GH3.2, an indole-3-acetic acid-amido synthetase, and promotes its expression. Together, these data indicate that Os-miR535 targets OsSPL4 and OsSPL4-GH3.2, which may parallel the OsSPL14-WRKY45 module in rice blast disease resistance.

Distinct Evolutionary Profiles and Functions of microRNA156 and microRNA529 in Land Plants

MicroRNA156 (miR156) and miR529 have high sequence similarity and recognize overlapping sites in the same target genes, SQUAMOSA promoter binding protein-like (SPL or SBP box) genes, making it difficult to accurately distinguish their roles in regulatory networks that affect numerous biological functions. Here, we collected data about miR156 and miR529 family members from representative land plants and performed sequence comparisons, phylogenetic analysis, small RNA sequencing, and parallel analysis of RNA ends (PARE) analysis to dissect their evolutionary and functional differences. Although miR156 and miR529 are highly similar, there are differences in their mismatch-sensitive regions, which are essential for target recognition. In land plants, miR156 precursors are conserved mainly within the hairpin region, whereas miR529 precursors are conserved outside the hairpin region, including both the 5’ and 3’ arms. Phylogenetic analysis showed that MIR156 and MIR529 evolved independently, through divergent evolutionary patterns. The two genes also exhibit different expression patterns, with MIR529 preferentially expressed in reproductive tissues and MIR156 in other tissues. PARE analysis revealed that miR156 and miR529 possess specific targets in addition to common targets in maize, pointing to functional differences between them. Based on our findings, we developed a method for the rapid identification of miR529 and miR156 family members and uncovered the evolutionary divergence of these families, providing insights into their different regulatory roles in plant growth and development.

Bract suppression regulated by the miR156/529-SPLs-NL1-PLA1 module is required for the transition from vegetative to reproductive branching in rice

Reproductive transition of grasses is characterized by switching the pattern of lateral branches, featuring the suppression of outgrowth of the subtending leaves (bracts) and rapid formation of higher-order branches in the inflorescence (panicle). However, the molecular mechanisms underlying such changes remain largely unknown. Here, we show that bract suppression is required for the reproductive branching in rice. We identified a pathway involving the intrinsic time ruler microRNA156/529, their targets SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes, NECK LEAF1 (NL1), and PLASTOCHRON1 (PLA1), which regulates the bract outgrowth and thus affects the pattern switch between vegetative and reproductive branching. Suppression of the bract results in global reprogramming of transcriptome and chromatin accessibility following the reproductive transition, while these processes are largely dysregulated in the mutants of these genes. These discoveries contribute to our understanding of the dynamic plant architecture and provide novel insights for improving crop yields.

Genome-wide analysis of microRNA156 and its targets, the genes encoding SQUAMOSA promoter-binding protein-like (SPL) transcription factors, in the grass family Poaceae

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play an important role in post-transcriptional gene regulation in plants and animals by targeting messenger RNAs (mRNAs) for cleavage or repressing translation of specific mRNAs. The first miRNA identified in plants, miRNA156 (miR156), targets the SQUAMOSA promoter-binding protein-like (SPL) transcription factors, which play critical roles in plant phase transition, flower and plant architecture, and fruit development. We identified multiple copies of MIR156 and SPL in the rice, Brachypodium, sorghum, maize, and foxtail millet genomes. Sequence and chromosomal synteny analysis showed that both MIR156s and SPLs are conserved across species in the grass family. Analysis of expression data of the SPLs in eleven juvenile and adult rice tissues revealed that four non-miR156-targeted genes were highly expressed and three miR156-targeted genes were only slightly expressed in all tissues/developmental stages. The remaining SPLs were highly expressed in the juvenile stage, but their expression was lower in the adult stage. It has been proposed that under strong selective pressure, non-miR156-targeted mRNA may be able to re-structure to form a miRNA-responsive element. In our analysis, some non-miR156-targeted SPLs (SPL5/8/10) had gene structure and gene expression patterns similar to those of miR156-targeted genes, suggesting that they could diversify into miR156-targeted genes. DNA methylation profiles of SPLs and MIR156s in different rice tissues showed diverse methylation patterns, and hypomethylation of non-CG sites was observed in rice endosperm. Our findings suggested that MIR156s and SPLs had different origination and evolutionary mechanisms: the SPLs appear to have resulted from vertical evolution, whereas MIR156s appear to have resulted from strong evolutionary selection on mature sequences.

Rice-specific Argonaute 17 controls reproductive growth and yield-associated phenotypes

This manuscript describes the functions of an Argonaute protein named AGO17 in rice. AGO17 is required for the development of rice reproductive tissues. Argonaute (AGO) proteins are a well-conserved multigene family of regulators mediating gene silencing across eukaryotes. Monocot plants have additional members of AGO, the functions of which are poorly understood. Among the non-dicot AGO1 clade members in monocots, AGO17 expresses highly in reproductive tissues. Here we show that overexpression of Oryza sativa indica AGO17 in rice resulted in robust growth and increased yield, whereas its silencing resulted in reduced panicle length, less fertility, and poor growth. Small (s)RNA transcriptome analysis revealed misregulation of several miRNAs and other categories of sRNAs in silenced and overexpression lines, in agreement with its likely competition with other AGO1 clade members. Targets of differentially expressed miRNAs included previously unreported target RNAs coding for proteins involved in development, phase transition, and transport. Our results indicate a distinctive role for OsAGO17 in rice reproductive development that could be harnessed to improve yield.

MiR529a controls plant height, tiller number, panicle architecture and grain size by regulating SPL target genes in rice (Oryza sativa L.)

Rice is one of the most important food crops in the world. Breeding high-yield, multi-resistant and high-quality varieties has always been the goal of rice breeding. Rice tiller, panicle architecture and grain size are the constituent factors of yield, which are regulated by both genetic and environmental factors, including miRNAs, transcription factors, and downstream target genes. Previous studies have shown that SPL (SQUAMOSA PROMOTER BINDING-LIKE) transcription factors can control rice tiller, panicle architecture and grain size, which were regulated by miR156, miR529 and miR535. In this study, we obtained miR529a target mimicry (miR529a-MIMIC) transgenic plants to investigate plant phenotypes, physiological and molecular characteristics together with miR529a overexpression (miR529a-OE) and wild type (WT) to explore the function of miR529a and its SPL target genes in rice. We found that OsSPL2, OsSPL17 and OsSPL18 at seedling stage were regulated by miR529a, but there had complicated mechanism to control plant height. OsSPL2, OsSPL16, OsSPL17 and SPL18 at tillering stage were regulated by miR529a to control plant height and tiller number. And panicle architecture and grain size were controlled by miR529a through altering the expression of all five target genes OsSPL2, OsSPL7, OsSPL14, OsSPL16, OsSPL17 and OsSPL18. Our study suggested that miR529a might control rice growth and development by regulating different SPL target genes at different stages, which could provide a new method to improve rice yield by regulating miR529a and its SPL target genes.

Characterization of Squamosa-Promoter Binding Protein-Box Family Genes Reveals the Critical Role of MsSPL20 in Alfalfa Flowering Time Regulation

SQUAMOSA Promoter-binding protein-Like (SPL) genes affect a broad range of plant biological processes and show potential application in crop improvement by genetic modification. As the most widely planted forage crop in the world, biomass and abiotic stresses tolerance are important breeding targets for alfalfa (Medicago sativa L.). Nevertheless, the systematic analysis of SPL genes in alfalfa genome remains lacking. In the present study, we characterized 22 putative non-redundant SPL genes in alfalfa genome and uncovered the abundant structural variation among MsSPL genes. The phylogenetic analysis of plant SPL proteins separated them into 10 clades and clade J was an alfalfa-specific clade, suggesting SPL genes in alfalfa might have experienced gene duplication and functional differentiation within the genome. Meanwhile, 11 MsSPL genes with perfect matches to miRNA response elements (MREs) could be degraded by miR156, and the cleavage sites were gene specific. In addition, we investigated the temporal and spatial expression patterns of MsSPL genes and their expression patterns in response to multiple treatments, characterizing candidate SPL genes in alfalfa development and abiotic stress tolerant regulation. More importantly, overexpression of the alfalfa-specific SPL gene (MsSPL20) showed stable delayed flowering time, as well as increased biomass. Further studies indicated that MsSPL20 delayed flowering time by regulating the expression of genes involved in floret development, including HD3A, FTIP1, TEM1, and HST1. Together, our findings provide valuable information for future research and utilization of SPL genes in alfalfa and elucidate a possibly alfalfa-specific flowering time regulation, thereby supplying candidate genes for alfalfa molecular-assisted breeding.

Photocontrol of Axillary Bud Outgrowth by MicroRNAs: Current State-of-the-Art and Novel Perspectives Gained From the Rosebush Model

Shoot branching is highly dependent on environmental factors. While many species show some light dependence for branching, the rosebush shows a strict requirement for light to allow branching, making this species an excellent model to further understand how light impinges on branching. Here, in the first part, we provide a review of the current understanding of how light may modulate the complex regulatory network of endogenous factors like hormones (SL, IAA, CK, GA, and ABA), nutrients (sugar and nitrogen), and ROS to control branching. We review the regulatory contribution of microRNAs (miRNAs) to branching in different species, highlighting the action of such evolutionarily conserved factors. We underline some possible pathways by which light may modulate miRNA-dependent regulation of branching. In the second part, we exploit the strict light dependence of rosebush for branching to identify putative miRNAs that could contribute to the photocontrol of branching. For this, we first performed a profiling of the miRNAs expressed in early light-induced rosebush buds and next tested whether they were predicted to target recognized regulators of branching. Thus, we identified seven miRNAs (miR156, miR159, miR164, miR166, miR399, miR477, and miR8175) that could target nine genes (CKX1/6, EXPA3, MAX4, CYCD3;1, SUSY, 6PFK, APX1, and RBOHB1). Because these genes are affecting branching through different hormonal or metabolic pathways and because expression of some of these genes is photoregulated, our bioinformatic analysis suggests that miRNAs may trigger a rearrangement of the regulatory network to modulate branching in response to light environment.

OsSPL9 Regulates Grain Number and Grain Yield in Rice

Rice grain yield consists of several key components, including tiller number, grain number per panicle (GNP), and grain weight. Among them, GNP is mainly determined by panicle branches and spikelet formation. In this study, we identified a gene affecting GNP and grain yield, OsSPL9, which encodes SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family proteins. The mutation of OsSPL9 significantly reduced secondary branches and GNP. OsSPL9 was highly expressed in the early developing young panicles, consistent with its function of regulating panicle development. By combining expression analysis and dual-luciferase assays, we further confirmed that OsSPL9 directly activates the expression of RCN1 (rice TERMINAL FLOWER 1/CENTRORADIALIS homolog) in the early developing young panicle to regulate the panicle branches and GNP. Haplotype analysis showed that Hap3 and Hap4 of OsSPL9 might be favorable haplotypes contributing to high GNP in rice. These results provide new insights on high grain number breeding in rice.

CRISPR-based assessment of genomic structure in the conserved SQUAMOSA promoter-binding-like gene clusters in rice

Although SQUAMOSA promoter-binding-like (SPL) transcription factors are important regulators of development in rice (Oryza sativa), prior assessments of the SPL family have been limited to single genes. A functional comparison across the full gene family in standardized genetic backgrounds has not been reported previously. Here, we demonstrate that the SPL gene family in rice is enriched due to the most recent whole genome duplication (WGD). Notably, 10 of 19 rice SPL genes (52%) cluster in four units that have persisted for at least 50 million years. We show that SPL gene grouping and retention following WGD is widespread in angiosperms, suggesting the conservatism and importance of this gene arrangement. We used Cas9 editing to generate transformation lines for all 19 SPL genes in a common set of backgrounds, and found that knockouts of 14 SPL genes exhibited defects in plant height, 10 exhibited defects in panicle size, and nine had altered grain lengths. We observed subfunctionalization of genes in the paleoduplicated pairs, but little evidence of neofunctionalization. Expression of OsSPL3 was negatively correlated with that of its closest neighbor in its synteny group, OsSPL4, and its sister paired gene, OsSPL12, in the opposing group. Nucleotide diversity was lower in eight of the nine singleton genes in domesticated rice, relative to wild rice, whereas the reverse was true for the paired genes. Together, these results provide functional information on eight previously unexamined OsSPL family members and suggest that paleoduplicate pair redundancy benefits plant survival and innovation.

Altering Plant Architecture to Improve Performance and Resistance

High-stress resistance and yield are major goals in crop cultivation, which can be addressed by modifying plant architecture. Significant progress has been made in recent years to understand how plant architecture is controlled under various growth conditions, recognizing the central role phytohormones play in response to environmental stresses. miRNAs, transcription factors, and other associated proteins regulate plant architecture, mainly via the modulation of hormone homeostasis and signaling. To generate crop plants of ideal architecture, we propose simultaneous editing of multiple genes involved in the regulatory networks associated with plant architecture as a feasible strategy. This strategy can help to address the need to increase grain yield and/or stress resistance under the pressures of the ever-increasing world population and climate change.

OsmiR535, a Potential Genetic Editing Target for Drought and Salinity Stress Tolerance in Oryza sativa

OsmiR535 belongs to the miR156/miR529/miR535 superfamily, a highly conserved miRNA family in plants. OsmiR535 is involved in regulating the cold-stress response, modulating plant development, and determining panicle architecture and grain length. However, the role that OsmiR535 plays in plant responses to drought and salinity are elusive. In the current study, molecular and genetic engineering techniques were used to elucidate the possible role of OsmiR535 in response to NaCl, PEG(Poly ethylene glycol), ABA(Abscisic acid), and dehydration stresses. Our results showed that OsmiR535 is induced under stressed conditions as compared to control. With transgenic and CRISPR/Cas9 knockout system techniques, our results verified that either inhibition or knockout of OsmiR535 in rice could enhance the tolerance of plants to NaCl, ABA, dehydration and PEG stresses. In addition, the overexpression of OsmiR535 significantly reduced the survival rate of rice seedlings during PEG and dehydration post-stress recovery. Our results demonstrated that OsmiR535 negatively regulates the stress response in rice. Moreover, our practical application of CRISPR/Cas9 mediated genome editing created a homozygous 5 bp deletion in the coding sequence of OsmiR535, demonstrating that OsmiR535 could be a useful genetic editing target for drought and salinity tolerance and a new marker for molecular breeding of Oryza sativa.

Exploring Heat-Response Mechanisms of MicroRNAs Based on Microarray Data of Rice Post-meiosis Panicle

To explore heat response mechanisms of mircoRNAs (miRNAs) in rice post-meiosis panicle, microarray analysis was performed on RNA isolated from rice post-meiosis panicles which were treated at 40°C for 0 min, 10 min, 20 min, 60 min, and 2 h. By integrating paired differentially expressed (DE) miRNAs and mRNA expression profiles, we found that the expression levels of 29 DE-miRNA families were negatively correlated to their 178 DE-target genes. Further analysis showed that the majority of miRNAs in 29 DE-miRNA families resisted the heat stress by downregulating their target genes and a time lag existed between expression of miRNAs and their target genes. Then, GO-Slim classification and functional identification of these 178 target genes showed that (1) miRNAs were mainly involved in a series of basic biological processes even under heat conditions; (2) some miRNAs might play important roles in the heat resistance (such as osa-miR164, osa-miR166, osa-miR169, osa-miR319, osa-miR390, osa-miR395, and osa-miR399); (3) osa-miR172 might play important roles in protecting the rice panicle under the heat stress, but osa-miR437, osa-miR418, osa-miR164, miR156, and miR529 might negatively affect rice fertility and panicle flower; and (4) osa-miR414 might inhibit the flowering gene expression by downregulation of LOC_Os 05g51830 to delay the heading of rice. Finally, a heat-induced miRNA-PPI (protein-protein interaction) network was constructed, and three miRNA coregulatory modules were discovered.

TaSPL13 regulates inflorescence architecture and development in transgenic wheat (Triticum aestivum L.)

The SQUAMOSA promoter-binding protein-like (SPL) proteins play vital roles in plant growth and development in rice (Oryza sative L.) and Arabidopsis thaliana (L.) Heynh. However, few studies regarding the SPL proteins have been reported in wheat. In this study, 56 TaSPLs were clustered into eight groups according to an OsSPL phylogenetic comparison analysis. The expression patterns of TaSPLs in different tissues were analysed by RNA-seq data, and partial results were confirmed by qRT-PCR. Based on the above results, genes such as TaSPL13 and TaSPL15 may be involved in spike or seed development in wheat. Multiple genes that regulate the inflorescence architecture of rice have been identified. Additionally, studies on the genes associated with spikelet development in wheat have been reported relatively rarely. Here, TaSPL13-2B was transferred into wheat cv. Bobwhite. Compared with the wild type, the transgenic lines showed significant increases in the number of florets and grains per spike, indicating that TaSPL13-2B could influence the floret development of wheat. TaSPL13-2B was transferred into rice cv. Nipponbare, which demonstrated that TaSPL13-2B can modify panicle architecture in transgenic rice, with significant increases in panicle length, the number and length of primary branches, and the number of secondary branches.

Loss of function of Oryza sativa Argonaute 18 induces male sterility and reduction in phased small RNAs

In this manuscript, we show that Oryza sativa indica Argonaute protein AGO18 is required for male gametophyte development likely to through a small RNA-mediated mechanism. Monocots have evolved unique gene silencing pathways due to the presence of unique members of Dicer-like and Argonaute (AGO) family members. Among the monocot AGO homologs, AGO18 occupies a unique position. Previous reports have implicated this protein in viral resistance as well as in gametogenesis, likely through its competition with AGO1 clade members for micro(mi)RNAs and other small (s)RNAs. Although expression of rice AGO18 in specific stages of male gametogenesis has been documented, its major functions in plant development remain poorly understood. Here, we show that Oryza sativa indica AGO18 is involved in male gametophyte development. Knockdown (KD) of AGO18 in transgenic rice lines resulted in stunted plants that are male sterile, whereas their carpels were functional. Transcriptome analysis revealed downregulation of several pollen development-associated genes in KD lines. sRNA sequencing in vegetative and reproductive tissues of KD lines indicated reduction of miRNAs and phased secondary sRNAs implicated in male gametophyte development. Our results indicate a distinct role for rice AGO18 in male fertility.

Genome-Wide Identification of lncRNAs Involved in Fertility Transition in the Photo-Thermosensitive Genic Male Sterile Rice Line Wuxiang S

Long non-coding RNAs (lncRNAs) act as universal regulators of various biological processes, but no genome-wide screening of lncRNAs involved in the fertility transition of the photo-thermosensitive genic male sterile (PTGMS) rice line has been reported. Here, we performed strand-specific RNA sequencing at three developmental stages of a novel PTGMS line Wuxiang S (WXS). A total of 3,948 lncRNAs were identified; 622 of these were detected as differentially expressed lncRNAs (DE-lncRNAs) between male-sterile WXS (WXS-S) and male-fertile WXS (WXS-F). A large proportion of lncRNAs differentially expressed at the stage of pollen mother cells meiosis, suggested that it may be the most critical stage for fertility transition of WXS. Furthermore, functional annotation of the cis- and trans- targets of DE-lncRNAs showed that 150 targets corresponding to 141 DE-lncRNAs were identified as involved in anther and pollen development. Moreover, computational analysis predicted 97 lncRNAs as precursors for 72 miRNAs, and 94 DE-lncRNAs as potential endogenous target mimics (eTMs) for 150 miRNAs. Finally, using the dual luciferase reporter assays, we demonstrated that two lncRNAs act as eTMs to regulate the expression of the SPL and GRF genes by competing for the shared osa-miR156 and osa-miR396, respectively. These genomic characteristics, differential expression, and interaction of lncRNAs with miRNAs and mRNAs contribute to our understanding of the roles of lncRNAs during the fertility transition in PTGMS rice lines.

The multiple roles of OsmiR535 in modulating plant height, panicle branching and grain shape

The miR156/miR529-SPL module acts a vital role in regulating plant growth and development. Though miR535 shows very high sequence identity to miR156 and miR529, it is still unknown whether miR535 could control plant growth and development. In this study, we performed the evolutionary analyses of miR535s in land plants and found that miR535s were less conserved than miR156s during evolution. In rice, miR535 expressed at a very low level during the vegetative growth but highly accumulated in young panicles, which is similar with OsmiR529, but opposite to OsmiR156. Expectedly, OsmiR535 overexpression in rice reduced plant height by decreasing the 1^st and 2^nd internode length. Furthermore, OsmiR535 overexpression imposed great influence in panicle architecture, such as more but shorter panicles, and fewer primary/secondary panicle branches. Moreover, OsmiR535 overexpression increased the grain length, but did not affect grain width. Through quantitative real-time PCR analyses, we further revealed that OsmiR535 overexpression repressed the expression of OsSPL7/12/16, as well as the OsSPLs downstream panicle related genes, including OsPIN1B, OsDEP1, OsLOG and OsSLR1. Taken together, our findings suggest that OsmiR535 multiply modulates plant height, panicle architecture and grain shape possibly by regulating OsSPLs genes in rice.

OsSPL18 controls grain weight and grain number in rice

Grain weight and grain number are two important traits directly determining grain yield in rice. To date, a lot of genes related to grain weight and grain number have been identified; however, the regulatory mechanism underlying these genes remains largely unknown. In this study, we studied the biological function of OsSPL18 during grain and panicle development in rice. Knockout (KO) mutants of OsSPL18 exhibited reduced grain width and thickness, panicle length and grain number, but increased tiller number. Cytological analysis showed that OsSPL18 regulates the development of spikelet hulls by affecting cell proliferation. qRT-PCR and GUS staining analyses showed that OsSPL18 was highly expressed in developing young panicles and young spikelet hulls, in agreement with its function in regulating grain and panicle development. Transcriptional activation experiments indicated that OsSPL18 is a functional transcription factor with activation domains in both the N-terminus and C-terminus, and both activation domains are indispensable for its biological functions. Quantitative expression analysis showed that DEP1, a major grain number regulator, was significantly down-regulated in OsSPL18 KO lines. Both yeast one-hybrid and dual-luciferase (LUC) assays showed that OsSPL18 could bind to the DEP1 promoter, suggesting that OsSPL18 regulates panicle development by positively regulating the expression of DEP1. Sequence analysis showed that OsSPL18 contains the OsmiR156k complementary sequence in the third exon; 5' RLM-RACE experiments indicated that OsSPL18 could be cleaved by OsmiR156k. Taken together, our results uncovered a new OsmiR156k-OsSPL18-DEP1 pathway regulating grain number in rice.

Redox Balance-DDR-miRNA Triangle: Relevance in Genome Stability and Stress Responses in Plants

Plants are continuously faced with complex environmental conditions which can affect the oxidative metabolism and photosynthetic efficiency, thus leading to the over-production of reactive oxygen species (ROS). Over a certain threshold, ROS can damage DNA. DNA damage, unless repaired, can affect genome stability, thus interfering with cell survival and severely reducing crop productivity. A complex network of pathways involved in DNA damage response (DDR) needs to be activated in order to maintain genome integrity. The expression of specific genes belonging to these pathways can be used as indicators of oxidative DNA damage and effective DNA repair in plants subjected to stress conditions. Managing ROS levels by modulating their production and scavenging systems shifts the role of these compounds from toxic molecules to key messengers involved in plant tolerance acquisition. Oxidative and anti-oxidative signals normally move among the different cell compartments, including the nucleus, cytosol, and organelles. Nuclei are dynamically equipped with different redox systems, such as glutathione (GSH), thiol reductases, and redox regulated transcription factors (TFs). The nuclear redox network participates in the regulation of the DNA metabolism, in terms of transcriptional events, replication, and repair mechanisms. This mainly occurs through redox-dependent regulatory mechanisms comprising redox buffering and post-translational modifications, such as the thiol-disulphide switch, glutathionylation, and S-nitrosylation. The regulatory role of microRNAs (miRNAs) is also emerging for the maintenance of genome stability and the modulation of antioxidative machinery under adverse environmental conditions. In fact, redox systems and DDR pathways can be controlled at a post-transcriptional level by miRNAs. This review reports on the interconnections between the DDR pathways and redox balancing systems. It presents a new dynamic picture by taking into account the shared regulatory mechanism mediated by miRNAs in plant defense responses to stress.

Unravelling miRNA regulation in yield of rice (Oryza sativa) based on differential network model

Rice (Oryza sativa L.) is one of the essential staple food crops and tillering, panicle branching and grain filling are three important traits determining the grain yield. Although miRNAs have been reported being regulating yield, no study has systematically investigated how miRNAs differentially function in high and low yield rice, in particular at a network level. This abundance of data from high-throughput sequencing provides an effective solution for systematic identification of regulatory miRNAs using developed algorithms in plants. We here present a novel algorithm, Gene Co-expression Network differential edge-like transformation (GRN-DET), which can identify key regulatory miRNAs in plant development. Based on the small RNA and RNA-seq data, miRNA-gene-TF co-regulation networks were constructed for yield of rice. Using GRN-DET, the key regulatory miRNAs for rice yield were characterized by the differential expression variances of miRNAs and co-variances of miRNA-mRNA, including osa-miR171 and osa-miR1432. Phytohormone cross-talks (auxin and brassinosteroid) were also revealed by these co-expression networks for the yield of rice.

Genetic Regulation of Shoot Architecture

Shoot architecture is determined by the organization and activities of apical, axillary, intercalary, secondary, and inflorescence meristems and by the subsequent development of stems, leaves, shoot branches, and inflorescences. In this review, we discuss the unifying principles of hormonal and genetic control of shoot architecture including advances in our understanding of lateral branch outgrowth; control of stem elongation, thickness, and angle; and regulation of inflorescence development. We focus on recent progress made mainly in Arabidopsis thaliana, rice, pea, maize, and tomato, including the identification of new genes and mechanisms controlling shoot architecture. Key advances include elucidation of mechanisms by which strigolactones, auxins, and genes such as IDEAL PLANT ARCHITECTURE1 and TEOSINTE BRANCHED1 control shoot architecture. Knowledge now available provides a foundation for rational approaches to crop breeding and the generation of ideotypes with defined architectural features to improve performance and productivity.