Rice Branching Research Articles

Overexpression of CsBRC, an F-box gene from Camellia sinensis, increased the plant branching in tobacco and rice.

Tea plant (Camellia sinensis [L.]) is one of the most important crops in China, and tea branch is an important agronomic trait that determines the yield of tea plant. In previous work focused on GWAS that detecting GWAS signals related to plant architecture through whole genome re-sequencing of ancient tea plants, a gene locus TEA 029928 significantly related to plant type was found. Sequence alignment results showed that this gene belonged to the F-box family. We named it CsBRC. CsBRC-GFP fusion proteins were mainly localized in the plasma membrane. By comparing the phenotypes of CsBRC transgenic tobacco and WT tobacco, it was found that the number of branches of transgenic tobacco was significantly higher than that of wild-type tobacco. Through RNA-seq analysis, it was found that CsBRC affects the branching development of plants by regulating the expression of genes related to brassinosteroid synthesis pathway in plants. In addition, overexpression of CsBRC in rice could increase tiller number, grain length and width, and 1,000-grain weight.

The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice.

The architecture of the rice inflorescence is an important determinant of crop yield. The length of the inflorescence and the number of branches are among the key factors determining the number of spikelets, and thus grains, that a plant will develop. In particular, the timing of the identity transition from indeterminate branch meristem to determinate spikelet meristem governs the complexity of the inflorescence. In this context, the ALOG gene TAWAWA1 (TAW1) has been shown to delay the transition to determinate spikelet development in Oryza sativa (rice). Recently, by combining precise laser microdissection of inflorescence meristems with RNA-seq, we observed that two ALOG genes, OsG1-like 1 (OsG1L1) and OsG1L2, have expression profiles similar to that of TAW1. Here, we report that osg1l1 and osg1l2 loss-of-function CRISPR mutants have similar phenotypes to the phenotype of the previously published taw1 mutant, suggesting that these genes might act on related pathways during inflorescence development. Transcriptome analysis of the osg1l2 mutant suggested interactions of OsG1L2 with other known inflorescence architecture regulators and the data sets were used for the construction of a gene regulatory network (GRN), proposing interactions among genes potentially involved in controlling inflorescence development in rice. In this GRN, we selected the homeodomain-leucine zipper transcription factor encoding the gene OsHOX14 for further characterization. The spatiotemporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of OsHOX14 suggests that the proposed GRN indeed serves as a valuable resource for the identification of new proteins involved in rice inflorescence development.

OsAAP15, an amino acid transporter in response to nitrogen concentration, mediates panicle branching and grain yield in rice

N is essential for plant architecture, particularly tillering. However, whether and how N mediates panicle branching and influences rice grain yield remains unclear. In order to identify genes and pathways associated with N-regulated panicle branching, we treated rice with different concentrations of N to determine the key genes by transcriptomic analysis and function verification. We measured panicle growth in response to N, and found that panicle branching benefits from 2 mM exogenous N, and 2–5 mM N is essential for vascular bundle, phloem, and xylem development in these branches. Interestingly, total N concentrations increased continuously with N 0–2 mM and decreased continuously with N 5–15 mM, whereas the concentrations of amino acids Tyr and Val increased continuously with N 0–15 mM in the panicle. Furthermore, N metabolism, phytohormone signal transduction, stress response, and photosynthesis pathways play important roles in response to nitrogen of regulating panicle branching. Altered expression of key N-response amino acid transporter gene OsAAP15 positively regulated panicle branching at low N concentrations, however, OsAAP15 negatively influenced it at high N concentrations. Overexpression of OsAAP15 in the field significantly increased primary and secondary branches, filled grain number, and grain yield by regulating the concentrations of amino acids Tyr and Val in the panicle. Taken together, OsAAP15, an amino acid transporter in response to nitrogen concentration, could mediate panicle branching and grain yield, and it may have applications in rice breeding to improve grain yield under extreme N concentrations.

Multifunctional chemical inhibitors of the florigen activationcomplex discovered by structure-based high-throughput screening.

Structure-based high-throughput screening of chemical compounds that target protein-protein interactions (PPIs) is a promising technology for gaining insight into how plant development is regulated, leading to many potential agricultural applications. At present, there are no examples of using high-throughput screening to identify chemicals that target plant transcriptional complexes, some of which are responsible for regulating multiple physiological functions. Florigen, a protein encoded by FLOWERING LOCUS T (FT), was initially identified as a molecule that promotes flowering and has since been shown to regulate flowering and other developmental phenomena such as tuber formation in potato (Solanum tuberosum). FT functions as a component of the florigen activation complex (FAC) with a 14-3-3 scaffold protein and FD, a bZIP transcription factor that activates downstream gene expression. Although 14-3-3 is an important component of FAC, little is known about the function of the 14-3-3 protein itself. Here, we report the results of a high-throughput invitro fluorescence resonance energy transfer (FRET) screening of chemical libraries that enabled us to identify small molecules capable of inhibiting FAC formation. These molecules abrogate the invitro interaction between the 14-3-3 protein and the OsFD1 peptide, a rice (Oryza sativa) FD, by directly binding to the 14-3-3 protein. Treatment with S4, a specific hit molecule, strongly inhibited FAC activity and flowering in duckweed, tuber formation in potato, and branching in rice in a dose-dependent manner. Our results demonstrate that the high-throughput screening approach based on the three-dimensional structure of PPIs is suitable in plants. In this study, we have proposed good candidate compounds for future modification to obtain inhibitors of florigen-dependent processes through inhibition of FAC formation.

OsSPL14 acts upstream of OsPIN1b and PILS6b to modulate axillary bud outgrowth by fine-tuning auxin transport in rice.

As a multigenic trait, rice tillering can optimize plant architecture for the maximum agronomic yield. SQUAMOSA PROMOTER BINDING PROTEIN-LIKE14 (OsSPL14) has been demonstrated to be necessary and sufficient to inhibit rice branching, but the underlying mechanism remains largely unclear. Here, we demonstrated that OsSPL14, which is cleaved by miR529 and miR156, inhibits tillering by fine-tuning auxin transport in rice. RNA interference of OsSPL14 or miR529 and miR156 overexpression significantly increased the tiller number, whereas OsSPL14 overexpression decreased the tiller number. Histological analysis revealed that the OsSPL14-overexpressing line had normal initiation of axillary buds but inhibited outgrowth of tillers. Moreover, OsSPL14 was found to be responsive to indole-acetic acid and 1-naphthylphthalamic acid, and RNA interference of OsSPL14 reduced polar auxin transport and increased 1-naphthylphthalamic acid sensitivity of rice plants. Further analysis revealed that OsSPL14 directly binds to the promoter of PIN-FORMED 1b (OsPIN1b) and PIN-LIKE6b (PILS6b) to regulate their expression positively. OsPIN1b and PILS6b were highly expressed in axillary buds and proved involved in bud outgrowth. Loss of function of OsPIN1b or PILS6b increased the tiller number of rice. Taken together, our findings suggested that OsSPL14 could control axillary bud outgrowth and tiller number by activating the expression of OsPIN1b and PILS6b to fine-tune auxin transport in rice.

Do Kentucky Kami Drink Bourbon? Exploring Parallel Glocalization in Global Shinto Offerings

Scholars of Japanese religion have recently drawn attention to the global repositioning, “greening”, and international popularization of Shinto. However, research on Shinto ritual practice and material religion continues to focus predominantly on cases located within the borders of the Japanese state. This article explores the globalization of Shinto through transnational practitioners’ strategic glocalization of everyday ritual practices outside of Japan. Drawing upon digital ethnographic fieldwork conducted in online Shinto communities, I examine three case studies centering on traditional ritual offerings made at the domestic altar (kamidana): rice, sake, and sakaki branches. I investigate how transnational Shinto communities hold in tension a multiplicity of particularistic understandings of Shinto locality and authenticity when it comes to domestic ritual practice. While relativistic approaches to glocalization locate the sacred and authentic in an archetypical or idealized form of Japanese tradition rooted in its environment, creolization and transformation valorize the particularities of one’s personal surroundings and circumstances. Examining these strategies alongside recent and historical cases in Shinto ritual at shrines within Japan, I propose that attending to processes of “parallel glocalization” helps to illuminate the quasi-fictive notion of the religious “homeland” and close the perceived gap in authenticity between ritual practices at home and abroad.

Identification of a novel mutant allele, fzp‐15, involved in panicle branch pattern of rice (Oryza sativa)

AbstractFRIZZY PANICLE (FZP) is involved in the development of panicle branching in rice. Herein, a novel mutant fzp‐15, demonstrating the sequential rounds of branching and severe defects in SM (spikelet meristem) formation, was identified. Map‐based cloning revealed that the abnormal panicle architecture of fzp‐15 resulted from an amino acid substitution (Glu (E) to Ala (A)) in the N‐terminal ERF domain of rice FZP protein. To generate new advantageous FZP alleles increasing grain numbers, CRISPR/Cas9 multiplex editing system was used to target the 5’ untranslation region (UTR) of FZP in 'Nipponbare' (NIP). The 85‐bp (−156 to ‐72 bp) or 149‐bp (−157 to ‐9 bp) deletion in the upstream region of FZP can significantly increase grain numbers without a decrease in grain size, while the 38‐bp deletion (−44 to −7 bp) in the upstream region of FZP has little effect in changing grain numbers. These results indicated that the 113‐bp fragment (−157 to −45 bp) upstream of FZP is important to its function and deletion of this region can be used to increase grain numbers in rice.

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.

Automated Counting Grains on the Rice Panicle Based on Deep Learning Method.

Grain number per rice panicle, which directly determines grain yield, is an important agronomic trait for rice breeding and yield-related research. However, manually counting grains of rice per panicle is time-consuming, laborious, and error-prone. In this research, a grain detection model was proposed to automatically recognize and count grains on primary branches of a rice panicle. The model used image analysis based on deep learning convolutional neural network (CNN), by integrating the feature pyramid network (FPN) into the faster R-CNN network. The performance of the grain detection model was compared to that of the original faster R-CNN model and the SSD model, and it was found that the grain detection model was more reliable and accurate. The accuracy of the grain detection model was not affected by the lighting condition in which images of rice primary branches were taken. The model worked well for all rice branches with various numbers of grains. Through applying the grain detection model to images of fresh and dry branches, it was found that the model performance was not affected by the grain moisture conditions. The overall accuracy of the grain detection model was 99.4%. Results demonstrated that the model was accurate, reliable, and suitable for detecting grains of rice panicles with various conditions.

Auxin apical dominance governed by the OsAsp1-OsTIF1 complex determines distinctive rice caryopses development on different branches.

In rice (Oryza sativa), caryopses located on proximal secondary branches (CSBs) have smaller grain size and poorer grain filling than those located on apical primary branches (CPBs), greatly limiting grain yield. However, the molecular mechanism responsible for developmental differences between CPBs and CSBs remains elusive. In this transcriptome-wide expression study, we identified the gene Aspartic Protease 1 (OsAsp1), which reaches an earlier and higher transcriptional peak in CPBs than in CSBs after pollination. Disruption of OsAsp1 expression in the heterozygous T-DNA line asp1-1+/-eliminated developmental differences between CPBs and CSBs. OsAsp1 negatively regulated the transcriptional inhibitor of auxin biosynthesis, OsTAA1 transcriptional inhibition factor 1 (OsTIF1), to preserve indole-3-acetic acid (IAA) apical dominance in CPBs and CSBs. IAA also facilitated OsTIF1 translocation from the endoplasmic reticulum (ER) to the nucleus by releasing the interaction of OsTIF1 with OsAsp1 to regulate caryopses IAA levels via a feedback loop. IAA promoted transcription of OsAsp1 through MADS29 to maintain an OsAsp1 differential between CPBs and CSBs during pollination. Together, these findings provide a mechanistic explanation for the distributed auxin differential between CPBs and CSBs to regulate distinct caryopses development in different rice branches and potential targets for engineering yield improvement in crops.

A set of AP2-like genes is associated with inflorescence branching and architecture in domesticated rice.

Rice yield is influenced by inflorescence size and architecture, and inflorescences from domesticated rice accessions produce more branches and grains. Neither the molecular control of branching nor the developmental differences between wild and domesticated rice accessions are fully understood. We surveyed phenotypes related to branching, size, and grain yield across 91 wild and domesticated African and Asian accessions. Characteristics related to axillary meristem identity were the main phenotypic differences between inflorescences from wild and domesticated accessions. We used whole transcriptome sequencing in developing inflorescences to measure gene expression before and after the transition from branching axillary meristems to determinate spikelet meristems. We identified a core set of genes associated with axillary meristem identity in Asian and African rice, and another set associated with phenotypic variability between wild and domesticated accessions. AP2/EREBP-like genes were enriched in both sets, suggesting that they are key factors in inflorescence branching and rice domestication. Our work has identified new candidates in the molecular control of inflorescence development and grain yield, and provides a detailed description of the effects of domestication on phenotype and gene expression.

Transcriptome analysis revealed the interaction among strigolactones, auxin, and cytokinin in controlling the shoot branching of rice

Strigolactones inhibit bud growth by negatively regulating the auxin transport without changing the auxin biosynthesis and suppressing the expression of A-ARR in buds. Strigolactones (SLs) are important phytohormones associated with regulation of shoot branching in rice. Rice shoot branching is persuasively mediated by plant hormones like auxin, cytokinins (CKs) and SLs. The interactions among these hormones were diversely investigated by many researchers but remained a subject of debate. In the present study, the removal of panicle and application of subsequent synthetic SLs were used to regulate rice bud growth on node 2 (the second node from panicle) at full heading stage. The bud growth was significantly induced after panicle removal but GR24 (synthetic SLs) application inhibited it, along with variations in endogenous hormone contents in bud. RNA samples from buds were subjected to RNA sequencing through Illumina HiSeq 2000 (RNA-seq). Comparison of transcript expression levels among three treatments, viz. (1) intact (Co), (2) removed panicle (RP) and (3) RP combined with synthetic SL GR24 (GR) revealed the involvement of numerous genes associated with hormone signal transduction. GR24 supply minimized the RP-induced enhancement of auxin early response genes, independent of ARF. CK signal transduction was also induced by RP, but type-A ARR were the only genes responding to GR without any other CK signal associated genes. Additionally, RP and GR can also modulate auxin transport and CK degradation by regulating the genes' expression involved in the biosynthesis of flavonoid, phenylpropanoid and benzoxazinoid. Contemplating the results obtained so far, it is possible to open new vistas of research to reveal the interactions among SLs, auxin and CK in controlling the shoot branching of rice.

Two Splicing Variants of OsNPF7.7 Regulate Shoot Branching and Nitrogen Utilization Efficiency in Rice.

Rice includes 93 nitrate and peptide transporters family (NPF) members that facilitate the soil uptake and internal reallocation of nitrogen for growth and development. This study demonstrated that OsNPF7.7 had two splicing variants, and altered expression of each variant could regulate shoot branching and nitrogen utilization efficiency (NUtE) in rice. The expression of both variants was down-regulated in the buds by increased nitrogen level in the Japonica rice variety ZH11. The expression level of long-variant OsNPF7.7-1 was higher in panicles at reproductive stage, however, the expression level of short-variant OsNPF7.7-2 was higher in buds and leaves at vegetative stage compared to each other in ZH11. OsNPF7.7-1 was localized in the plasma membrane, whereas OsNPF7.7-2 was localized in the vacuole membrane. Furthermore, the results indicated that the expression level of each variant for OsNPF7.7 determined axillary bud outgrowth, and then influenced the rice tiller number. Overexpression of OsNPF7.7-1 could promote nitrate influx and concentration in root, whereas overexpression of OsNPF7.7-2 could improve ammonium influx and concentration in root. RNAi and osnpf7.7 lines of OsNPF7.7 showed an increased amount of amino acids in leaf sheaths, but a decreased amount in leaf blades, which affected nitrogen allocation and plant growth. The elevated expression of each variant for OsNPF7.7 in ZH11 enhanced NUtE using certain fertilization regimes under paddy field conditions. Moreover, overexpression of each variant for OsNPF7.7 in KY131 increased significantly the filled grain number per plant. Thus, increased each variant of OsNPF7.7 has the potential to improve grain yield and NUtE in rice.

The COMPASS-Like Complex Promotes Flowering and Panicle Branching in Rice.

Flowering time (heading date) and panicle branch number are important agronomic traits that determine yield in rice (Oryza sativa). The activation of flowering requires histone methylation, but the roles of trimethylation of Lys 4 of histone 3 (H3K4me3) in modulating heading date and panicle development are unclear. Here, we showed that the COMPASS-like complex promotes flowering and panicle branching. The rice (Oryza sativa) WD40 protein OsWDR5a interacts with the TRITHORAX-like protein OsTrx1/SET domain group protein 723 (SDG723) to form the core components of the COMPASS-like complex. Plants in which OsWDR5a or OsTrx1 expression was decreased by RNA interference produced fewer secondary branches and less grain and exhibited a delayed heading date under long-day and short-day conditions, whereas loss of OsWDR5a function resulted in embryo lethality. OsWDR5a binds to Early heading date 1 to regulate its H3K4me3 and expression levels. Together, our results show that the COMPASS-like complex promotes flowering and panicle development and suggest that modulation of H3K4me3 levels by the COMPASS-like complex is critical for rice development.

Design, fabrication, and comparative evaluation of plant power shredder

Fresh organic materials have to be shredded into smaller sizes to increase their decomposition rate. Hence, a plant shredder is necessary. This study illustrates the importance of traditional or local knowledge to agriculture and natural resource management by providing households with adaptive strategies. A plant shredding machine known as “Plant Power Shredder (PPS)” suitable for village-scale use was developed following the design criteria such as: portability, affordability, efficiency and versatility. The machine is 1.5mL×1.05m W×1.10m H, weighs 150kg and costs PHP75,000 (including 7hp Diesel engine). It is mounted in an angular bar framing fitted with 2 free-wheeling wheels to be pulled by a hand tractor. The prototype used combination of shear and impact forces through the combination of radially mounted blades and hammer-members. Comparative evaluation of PPS was done with the RUMVD35000-16 and RUMVD35000-14 in terms of capacity, efficiency, fuel consumption, power-output ratio, sizes of shredded materials, percent decomposition of shredded output and break-even cost of each machine. Shredding was done on rice straw (RC 216), kakawate leaves and branches and dried coconut husk at three replications. Results showed that PPS has the highest efficiency of 95.71%, lowest fuel cost of PHP57.17 per hour and PHP0.15 per kg, highest power to output ratio of 0.014hp per kg and lowest break even cost of PHP0.68 per kg. RU 14 has the highest capacity of 471.90kg per hour and has the greatest percentage of short-size shredded material of 70.94 %.

Fine mapping of LOW TILLER 1, a gene controlling tillering and panicle branching in rice

Tillering and panicle branching are important agronomic traits that affect rice grain yield. In this study, we characterized the low tiller 1 (lt1) mutant, which was isolated from an ethyl methanesulfonate-treated population of the indica cultivar Shuhui 527. The lt1 mutant had fewer tillers, thicker culms, fewer panicle branches, abnormal spikelets and larger grains. The transcript levels of cell proliferation and expansion-associated genes were altered in the lt1 plant, implying that LT1 affected grain size by regulating cell proliferation and expansion. Genetic analysis showed that the lt1 mutant phenotype was a single, recessive mutation. Using SSR and SNP markers, the LT1 gene was narrowed to a 63 kb distance between the markers ID6 and S12 on the chromosome 6. DNA sequencing revealed no mutations in this region. Despite this, two candidate genes, LOC_Os06g40780/MOC1 and LOC_Os06g40840, exhibited lower expression levels in both tiller buds and young panicles in lt1 compared to wild type. Thus, LOC_Os06g40780/MOC1 or LOC_Os06g40840 may be responsible for the lt1 mutant phenotypes, but more work will be needed for the cloning and functional analysis of LT1. This work lays the foundation for elucidation of the molecular mechanism for tillering and panicle branching, and provides new opportunities for improving rice grain yield.

Origin of Chain Length Specificites of Starch Branching Enzyme

Starch Branching enzyme (BE) is one of the three enzymes involved in starch biosynthesis. It is responsible for synthesizing the alpha-1,6-glucan branches, remodeling the linear alpha-1,4-glucan polymer to produce amylopectin. There are at least two isoforms of the enzyme in most plants, with each having distinct reactivities and product chain-length specificities. Though the chemistry of the active site of branching enzyme is relatively well studied, the origin of the chain length specificity is yet to be understood. Using protein crystallography and biochemical studies on rice branching enzyme, we aim to understand the factors controlling the chain-length specificity of branching enzymes. The mechanism of branching enzyme involves two steps: (1) An oligosaccharide (donor chain) binds to the enzyme and is cleaved by the action of a nucleophilic aspartate residue to form a covalently-linked enzyme-glucan intermediate. (2) A second oligosaccharide (acceptor chain) then reacts, by nucleophilic attack of one of its alpha-1,6-hydroxyl groups, to form a new alpha-1,6-branch. We have focused on discovering the surface glucan binding sites in branching enzyme because they are likely essential to understanding the specificity of the enzyme. To this end we have obtained a crystal structure of an oligosaccharide (M12)-bound rice branching enzyme, which reveals oligosaccharide binding from the outer surface of the enzyme almost to the active site. Mutations of the residues interacting with the M12 can substantially compromise the enzyme's activity, though none have affected the branch chain specificity. On the other hand, comparison of an isoamylase maltoheptaose (M7)-bound structure with rice branching enzyme suggested another potential glucan surface binding site. Interestingly, mutations in this new site did effect the chain-length specificity of the enzyme. These results suggest that the bound M12 is part of the acceptor chain and the newly identified binding site hosts the donor chain. Together, the data allow us to, for the first time propose a detailed mechanism for the enzyme, explaining how disparate surface glucan binding sites far from the active site create the enzyme's activity and specificity against its polymeric substrate.

Highly branched dextrin prepared from high-amylose maize starch using waxy rice branching enzyme (WRBE)

Branching enzyme (BE, EC 2.4.1.18) was isolated from the developing waxy rice endosperm and used to prepare a highly branched dextrin based on high-amylose maize starch (HAMS) as a substrate. The molecular mass of the starch initially degraded quickly from 2.5×107 to 4.1×105Da, and then stabilized, with a minimal increase during the BE treatment. The resultant branched dextrin had a narrow size distribution, with a mean molecular weight of 5.1×105Da and a polydispersity index (PI) of 1.567. The results of high-performance anion exchange chromatography indicated that the degree of polymerization (DP) of the branched chains ranged from 3 to 27; approximately 75.26% of these chains were short (DP<10). These findings suggest that the isolated BE can cleave long chains into oligosaccharides, subsequently transferring oligosaccharides into highly branched dextrins with a narrow size distribution and short side chains.

Regulatory role of FZP in the determination of panicle branching and spikelet formation in rice

FRIZZLE PANICLE (FZP) and RFL/ABERRANT PANICLE ORGANIZATION 2 (APO2) play important roles in regulating the ABCDE floral organ identity genes. However, the relationships among FZP and these floral identity genes in the regulation of panicle formation remain unclear. Here, we used the novel mutant fzp-11, wild-type and FZP-overexpressing plants to compare the expression of these genes during panicle development by real-time PCR and in situ hybridization. The results indicate that FZP is a major negative regulator of RFL/APO2 and determines the transition from panicle branching to spikelet formation. Moreover, overexpression of FZP severely represses axillary meristem formation in both the vegetative and reproductive phases and the outgrowth of secondary branches in panicle. FZP overexpression positively regulates the expression of a subset of the class B genes, AGL6 genes (OsMADS6 and OsMADS17) as well as class E genes (OsMADS1, OsMADS7 and OsMADS8) in floral meristem (FM). Thus, it suggested that FZP could specify floral organ identity by regulating the related OsMADS-box genes.

Coordinated regulation of vegetative and reproductive branching in rice

Grasses produce tiller and panicle branching at vegetative and reproductive stages; the branching patterns largely define the diversity of grasses and constitute a major determinant for grain yield of many cereals. Here we show that a spatiotemporally coordinated gene network consisting of the MicroRNA 156 (miR156/)miR529/SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) and miR172/APETALA2 (AP2) pathways regulates tiller and panicle branching in rice. SPL genes negatively control tillering, but positively regulate inflorescence meristem and spikelet transition. Underproduction or overproduction of SPLs reduces panicle branching, but by distinct mechanisms: miR156 and miR529 fine-tune the SPL levels for optimal panicle size. miR172 regulates spikelet transition by targeting AP2-like genes, which does not affect tillering, and the AP2-like proteins play the roles by interacting with TOPLESS-related proteins (TPRs). SPLs modulate panicle branching by directly regulating the miR172/AP2 and PANICLE PHYTOMER2 (PAP2)/Rice TFL1/CEN homolog 1 (RCN1) pathways and also by integrating other regulators, most of which are not involved in tillering regulation. These findings may also have significant implications for understanding branching regulation of other grasses and for application in rice genetic improvement.