Panicle Architecture In Rice Research Articles

Competitive binding of small antagonistic peptides to the OsER1 receptor optimizes rice panicle architecture.

Rice panicle architecture is a pivotal trait that strongly contributes to grain yield. Small peptide ligands from the OsEPF/EPFL family synergistically control panicle architecture by recognition of the OsER1 receptor and subsequent activation of the OsMKKK10-OsMKK4-OsMPK6 cascade, indicating that specific ligand-receptor pairs orchestrate rice panicle development. However, how small homologous peptides fine-tune organ morphogenesis by targeting a common receptor remains elusive. Here, we report that the small peptide OsEPFL5 acts as a ligand of the OsER1 receptor that inactivates the OsMKKK10-OsMKK4-OsMPK6 cascade, suggesting that OsEPFL5 plays the opposite role to that of the OsEPFL6/7/8/9 subfamily in regulating spikelet number per panicle and grain size. Notably, OsEPFL5 competitively replaces the OsEPFL6, OsEPFL7, OsEPFL8, or OsEPFL9 binding to the OsER1 receptor, exposing antagonistic competition between small homologous peptides. Specifically enhancing expression of OsEPFL5 significantly improves grain yield by suppressing functions of the ligand-receptor pairs of OsEPFL6-OsER1, OsEPFL7-OsER1, OsEPFL8-OsER1, and OsEPFL9-OsER1, suggesting that competitive binding to the OsER1 receptor by small antagonistic peptides can optimize rice panicle architecture. Our findings elucidate how a receptor agonist and antagonist define inductive and inhibitory cues to shape rice panicle architecture, thus providing a new method of rationally breaking yield trait coupling by manipulating small antagonistic peptides.

Identification of genomic regions controlling spikelet degeneration under FRIZZLE PANICLE (FZP) defect genetic background in rice

The FZP gene plays a critical role in the formation of lateral branches and spikelets in rice panicle architecture. This study investigates the qSBN7 allele, a hypomorphic variant of FZP, and its influence on panicle architectures in different genetic backgrounds. We evaluated two backcross inbred lines (BILs), BC5_TCS10sbn and BC3_TCS10sbn, each possessing the homozygous qSBN7 allele but demonstrating differing degrees of spikelet degeneration. Our analysis revealed that BC5_TCS10sbn had markedly low FZP expression, which corresponded with an increase in axillary branches and severe spikelet degeneration. Conversely, BC3_TCS10sbn exhibited significantly elevated FZP expression, leading to fewer secondary and tertiary branches, and consequently decreased spikelet degeneration. Compared to BC5_TCS10sbn, BC3_TCS10sbn carries three additional chromosomal substitution segments from its donor parent, IR65598-112-2. All three segments significantly enhance the expression of FZP and reduce the occurrence of tertiary branch and spikelet degeneration. These findings enhance our understanding of the mechanisms regulating FZP and aid rice breeding efforts.

A 48-bp deletion upstream of LIGULELESS 1 alters rice panicle architecture

Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop improvement. To investigate its molecular mechanisms in rice, we performed map-based cloning and characterization of OPEN PANICLE 1 (OP1), a gain-of-function allele of LIGULELESS 1 (LG1), controlling the spread-panicle phenotype. This allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary branch. Increased OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1 (sp1). Knocking out BRASSINOSTEROID UPREGULATED1 (BU1) gene in the background of OP1 complementary plants resulted in compact panicles, suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling pathway. We regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture.

Panicle Architecture in Enhancing Grain Yield in Rice (Oryza sativa L.)

The architecture of the rice panicle is a crucial focus in breeding for both high yield and quality. It stands as a significant agronomic trait that influences the number of grains per panicle, playing a direct role in contributing to the overall yield of rice grains. Unravelling the genetic basis of panicle architecture is crucial for improving the grain yield in rice. In this study, the panicle architecture traits were meticulously dissected into five distinct components viz., number of primary rachis, number of secondary rachis, grain number on primary rachis, grain number on secondary rachis and total grain number. These components were systematically phenotyped in F2 and F3 population derived from a cross between DRR Dhan 48 and Maudamani. ‘DRR Dhan 48’ is a biofortified elite fine grain medium slender grain type cultivar with high zinc (22 ppm in polished rice) and low glycemic index (51.1). It has resistance to bacterial blight with the incorporation of xa5, xa13 and Xa21 in the background of Improved Samba Mahsuri. ‘Maudamani’ is a high yielding cultivar with high grain number and short bold grain type. Analysis of variance, histograms and boxplots revealed highly significant variation for the studied traits. Grain number in F2 population ranged from 29 to 333 grain with a mean of 162.72 whereas in F3, its varied from 49 to 368 with a mean of 184.17. Correlation analysis revealed significant correlation among the studied traits. The continuous variation observed in the population for panicle traits indicates that genetic control is governed by multiple minor loci. The presence of superior transgressive segregants highlights a complementary gene action influencing panicle architecture traits. The present investigation on panicle architecture offers scope for improving rice varieties and creating new germplasm resources and provides valuable information for further unravelling the genetic basis determining rice panicle architecture.

Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks

Panicle architecture is a key determinant of rice grain yield and is mainly determined at the 1-2 mm young panicle stage. Here, we investigated the transcriptome of the 1-2 mm young panicles from 275 rice varieties and identified thousands of genes whose expression levels were associated with panicle traits. Multimodel association studies suggested that many small-effect genetic loci determine spikelet per panicle (SPP) by regulating the expression of genes associated with panicle traits. We found that alleles at cis-expression quantitative trait loci of SPP-associated genes underwent positive selection, with a strong preference for alleles increasing SPP. We further developed a method that integrates the associations of cis- and trans-expression components of genes with traits to identify causal genes at even small-effect loci and construct regulatory networks. We identified 36 putative causal genes of SPP, including SDT (MIR156j) and OsMADS17, and inferred that OsMADS17 regulates SDT expression, which was experimentally validated. Our study reveals the impact of regulatory variants on rice panicle architecture and provides new insights into the gene regulatory networks of panicle traits.

The OsNLP3/4-OsRFL module regulates nitrogen-promoted panicle architecture in rice.

Rice panicles, a major component of yield, are regulated by phytohormones and nutrients. How mineral nutrients promote panicle architecture remains largely unknown. Here, we report that NIN-LIKE PROTEIN3 and 4 (OsNLP3/4) are crucial positive regulators of rice panicle architecture in response to nitrogen (N). Loss-of-function mutants of either OsNLP3 or OsNLP4 produced smaller panicles with reduced primary and secondary branches and fewer grains than wild-type, whereas their overexpression plants showed the opposite phenotypes. The OsNLP3/4-regulated panicle architecture was positively correlated with N availability. OsNLP3/4 directly bind to the promoter of OsRFL and activate its expression to promote inflorescence meristem development. Furthermore, OsRFL activates OsMOC1 expression by binding to its promoter. Our findings reveal the novel N-responsive OsNLP3/4-OsRFL-OsMOC1 module that integrates N availability to regulate panicle architecture, shedding light on how N nutrient signals regulate panicle architecture and providing candidate targets for the improvement of crop yield.

Three QTL from Oryza meridionalis Could Improve Panicle Architecture in Asian Cultivated Rice

Rice panicle architecture is directly associated with grain yield and is also the key target in high-yield rice breeding program. In this study, three BC6F2 segregation populations derived from the crosses between two accessions of Oryza meridionalis and a O. sativa spp. japonica cultivar Dianjingyou 1, were employed to map QTL for panicle architecture. Three QTL, EP4.2, DEP7 and DEP8 were identified and validated using substitution mapping strategy on chromosome 4, 9 and 8, respectively. The three QTL showed pleiotropic phenotype on panicle length (PL), grain number per panicle (GNPP), number of primary branches (NPB), number of secondary branches (NSB), and grain width. DEP7 and DEP8 showed yield-enhancing potential by increasing GNPP, NPB and NSB, while EP4.2 exhibited wide grain, short stalk and panicle which can improve plant and panicle architecture, too. Moreover, epistatic interaction for PL was detected between EP4.2 and DEP7, and epistatic analysis between DEP7 and DEP8 for GNPP and NPB also revealed significant two QTL interactions. The result would help us understand the molecular basis of panicle architecture and lay the foundation for using these three QTL in rice breeding.

Optimization of rice panicle architecture by specifically suppressing ligand–receptor pairs

Rice panicle architecture determines the grain number per panicle and therefore impacts grain yield. The OsER1–OsMKKK10–OsMKK4–OsMPK6 pathway shapes panicle architecture by regulating cytokinin metabolism. However, the specific upstream ligands perceived by the OsER1 receptor are unknown. Here, we report that the EPIDERMAL PATTERNING FACTOR (EPF)/EPF-LIKE (EPFL) small secreted peptide family members OsEPFL6, OsEPFL7, OsEPFL8, and OsEPFL9 synergistically contribute to rice panicle morphogenesis by recognizing the OsER1 receptor and activating the mitogen-activated protein kinase cascade. Notably, OsEPFL6, OsEPFL7, OsEPFL8, and OsEPFL9 negatively regulate spikelet number per panicle, but OsEPFL8 also controls rice spikelet fertility. A osepfl6 osepfl7 osepfl9 triple mutant had significantly enhanced grain yield without affecting spikelet fertility, suggesting that specifically suppressing the OsEPFL6–OsER1, OsEPFL7–OsER1, and OsEPFL9–OsER1 ligand–receptor pairs can optimize rice panicle architecture. These findings provide a framework for fundamental understanding of the role of ligand–receptor signaling in rice panicle development and demonstrate a potential method to overcome the trade-off between spikelet number and fertility.

Independent control of organ number and distribution pattern in rice panicle.

As the determinants of yield products, rice panicle traits are important targets for breeding. Despite their importance in grain filling and subsequent yield productivity, knowledge on the organ distribution pattern in rice panicles is limited owing to the lack of objective evaluation methods. In this study, we developed a method for quantifying rice panicle organ distribution patterns. To validate our method for practical application in biology, we integrated this method into a quantitative trait locus (QTL) analysis and identified QTLs for panicle organ distribution patterns in rice. Interestingly, Grain number 1 (Gn1), a major QTL of organ number, was not identified as a QTL for distribution pattern, indicating that the number and distribution of panicle organs are independently controlled. This study provides insight into rice panicle organ distribution patterns that will help improve breeding targeting rice panicle architecture.

Designing rice panicle architecture via developmental regulatory genes.

Rice panicle architecture displays remarkable diversity in branch number, branch length, and grain arrangement; however, much remains unknown about how such diversity in patterns is generated. Although several genes related to panicle branch number and panicle length have been identified, how panicle branch number and panicle length are coordinately regulated is unclear. Here, we show that panicle length and panicle branch number are independently regulated by the genes Prl5/OsGA20ox4, Pbl6/APO1, and Gn1a/OsCKX2. We produced near-isogenic lines (NILs) in the Koshihikari genetic background harboring the elite alleles for Prl5, regulating panicle rachis length; Pbl6, regulating primary branch length; and Gn1a, regulating panicle branching in various combinations. A pyramiding line carrying Prl5, Pbl6, and Gn1a showed increased panicle length and branching without any trade-off relationship between branch length or number. We successfully produced various arrangement patterns of grains by changing the combination of alleles at these three loci. Improvement of panicle architecture raised yield without associated negative effects on yield-related traits except for panicle number. Three-dimensional (3D) analyses by X-ray computed tomography (CT) of panicles revealed that differences in panicle architecture affect grain filling. Importantly, we determined that Prl5 improves grain filling without affecting grain number.

Analyzing rice (Oryza sativa L.) panicle structure of 122 RILs using P-TRAP software for spikelet related traits

Panicle architecture is shown to have a direct impact on rice grain yield, making it an important characteristic for rice varietal improvement. In this study, we focus on the Panicle Trait Phenotyping Tool (P-TRAP), freely accessible, platform-independent software for analyzing rice panicle architecture, as one of the ways for generating comprehensive and reproducible panicle structure data and identifying superior breeding lines. In this analysis, the rice panicle structures of 122 RILs along with their parents were analyzed using P-TRAP software. P-TRAP assesses nine spikelet characteristics and its impact on grain yield. All traits had positive and significant associations and have a direct influence on grain yield. The findings indicate that most characteristics’ coefficients of variation had lower values, with the exception of the characteristics spikelet number, spikelet area and grain yield. In comparison to other traits, the standard error for the traits spikelet number and grain yield had a larger value. To better understand their genetic basis, these quantitative traits can be exploited in genome-wide association analyses. Hence, analyzing these traits is crucial. The P-TRAP tool is preferred because it reduces human effort and provides data in a shorter time span when compared to the traditional method. Keywords: Rice, spikelet, p-trap, grain yield

The Elite Alleles of OsSPL4 Regulate Grain Size and Increase Grain Yield in Rice

Grain weight and grain number, the two important yield traits, are mainly determined by grain size and panicle architecture in rice. Herein, we report the identification and functional analysis of OsSPL4 in panicle and grain development of rice. Using CRISPR/Cas9 system, two elite alleles of OsSPL4 were obtained, which exhibited an increasing number of grains per panicle and grain size, resulting in increase of rice yield. Cytological analysis showed that OsSPL4 could regulate spikelet development by promoting cell division. The results of RNA-seq and qRT-PCR validations also demonstrated that several MADS-box and cell-cycle genes were up-regulated in the mutation lines. Co-expression network revealed that many yield-related genes were involved in the regulation network of OsSPL4. In addition, OsSPL4 could be cleaved by the osa-miR156 in vivo, and the OsmiR156-OsSPL4 module might regulate the grain size in rice. Further analysis indicated that the large-grain allele of OsSPL4 in indica rice might introgress from aus varieties under artificial selection. Taken together, our findings suggested that OsSPL4 could be as a key regulator of grain size by acting on cell division control and provided a strategy for panicle architecture and grain size modification for yield improvement in rice.

Dissection of the Genetic Basis of Rice Panicle Architecture Using a Genome-wide Association Study

Panicle architecture is one of the major factors influencing productivity of rice crops. The regulatory mechanisms underlying this complex trait are still unclear and genetic resources for rice breeders to improve panicle architecture are limited. Here, we have performed a genome-wide association study (GWAS) to analyze and identify genetic determinants underlying three panicle architecture traits. A population of 340 rice accessions from the 3000 Rice Genomes Project was phenotyped for panicle length, primary panicle number and secondary branch number over two years; GWAS was performed across the whole panel, and also across the japonica and indica sub-panels. A total of 153 quantitative trait loci (QTLs) were detected, of which 5 were associated with multiple traits, 8 were unique to either indica or japonica sub-panels, while 37 QTLs were stable across both years. Using haplotype and expression analysis, we reveal that genetic variations in the OsSPL18 promoter significantly affect gene expression and correlate with panicle length phenotypes. Three new candidate genes with putative roles in determining panicle length were also identified. Haplotype analysis of OsGRRP and LOC_Os03g03480 revealed high association with panicle length variation. Gene expression of DSM2, involved in abscisic acid biosynthesis, was up-regulated in long panicle accessions. Our results provide valuable information and resources for further unravelling the genetic basis determining rice panicle architecture. Identified candidate genes and molecular markers can be used in marker-assisted selection to improve rice panicle architecture through molecular breeding.

VPB1 Encoding BELL-like Homeodomain Protein Is Involved in Rice Panicle Architecture.

Inflorescence architecture in rice (Oryza sativa) is mainly determined by spikelets and the branch arrangement. Primary branches initiate from inflorescence meristem in a spiral phyllotaxic manner, and further develop into the panicle branches. The branching patterns contribute largely to rice production. In this study, we characterized a rice verticillate primary branch 1(vpb1) mutant, which exhibited a clustered primary branches phenotype. Gene isolation revealed that VPB1 was a allele of RI, that it encoded a BELL-like homeodomain (BLH) protein. VPB1 gene preferentially expressed in the inflorescence and branch meristems. The arrangement of primary branch meristems was disturbed in the vpb1 mutant. Transcriptome analysis further revealed that VPB1 affected the expression of some genes involved in inflorescence meristem identity and hormone signaling pathways. In addition, the differentially expressed gene (DEG) promoter analysis showed that OsBOPs involved in boundary organ initiation were potential target genes of VPB1 protein. Electrophoretic mobility shift assay (EMSA) and dual-luciferase reporter system further verified that VPB1 protein bound to the promoter of OsBOP1 gene. Overall, our findings demonstrate that VPB1 controls inflorescence architecture by regulating the expression of genes involved in meristem maintenance and hormone pathways and by interacting with OsBOP genes.

Genetic control of panicle architecture in rice

Rice panicle architecture affects grain number per panicle and thereby grain yield. Many genes involved in control of panicle architecture have been identified in the past decades. According to their effect on phenotype, these genes are divided into three categories: panicle branch and lateral spikelets, multifloret spikelets, and panicle type. We review these genes, describe their genetic regulatory network, and propose a strategy for using them in rice breeding. These findings on rice panicle architecture may facilitate related studies in other crops.

Genome-wide association study to identify chromosomal regions related to panicle architecture in rice (Oryza sativa)

Panicle architecture directly affects the grain yield of rice; meanwhile, crop domestication has increased the complexity of rice panicle size and branching pattern. Genome-wide association study (GWAS) was performed to investigate the genetic basis underlying panicle architecture using 183 rice accessions from around the world and a 7 K SNP array. Phenotyping was conducted at Texas A&M AgriLife Research Center in Beaumont, TX. GWAS was performed using MLM (Q + K) model using GAPIT software. At p-value < 0.001, a total of 49 GWAS QTLs controlling various panicle architecture traits were mapped. Considering the recurring and linked SNPs across the panicle architecture traits, 42 independent QTL regions were identified. Among these, 27 QTL regions co-localized with known genes or previously reported QTLs or significant SNP markers, while 15 were potentially novel QTL regions. The results of our study offer useful information on genetic bases controlling panicle architecture in rice, which could be further validated and utilized for designing markers for use in markers assisted selection (MAS) in rice breeding programs.

Uncovering the genetic mechanisms regulating panicle architecture in rice with GPWAS and GWAS

BackgroundThe number of panicles per plant, number of grains per panicle, and 1000-grain weight are important factors contributing to the grain yield per plant in rice. The Rice Diversity Panel 1 (RDP1) contains a total of 421 purified, homozygous rice accessions representing diverse genetic variations within O. sativa. The release of High-Density Rice Array (HDRA, 700 k SNPs) dataset provides a new opportunity to discover the genetic variants of panicle architectures in rice.ResultsIn this report, a new method genome-phenome wide association study (GPWAS) was performed with 391 individuals and 27 traits derived from RDP1 to scan the relationship between the genes and multi-traits. A total of 1985 gene models were linked to phenomic variation with a p-value cutoff of 4.49E-18. Besides, 406 accessions derived from RDP1 with 411,066 SNPs were used to identify QTLs associated with the total spikelets number per panicle (TSNP), grain number per panicle (GNP), empty grain number per panicle (EGNP), primary branch number (PBN), panicle length (PL), and panicle number per plant (PN) by GLM, MLM, FarmCPU, and BLINK models for genome-wide association study (GWAS) analyses. A total of 18, 21, 18, 17, 15, and 17 QTLs were identified tightly linked with TSNP, GNP, EGNP, PBN, PL, and PN, respectively. Then, a total of 23 candidate genes were mapped simultaneously using both GWAS and GPWAS methods, composed of 6, 4, 5, 4, and 4 for TSNP, GNP, EGNP, PBN, and PL. Notably, one overlapped gene (Os01g0140100) were further investigated based on the haplotype and gene expression profile, indicating this gene might regulate the TSNP or panicle architecture in rice.ConclusionsNearly 30 % (30/106) QTLs co-located with the previous published genes or QTLs, indicating the power of GWAS. Besides, GPWAS is a new method to discover the relationship between genes and traits, especially the pleiotropy genes. Through comparing the results from GWAS and GPWAS, we identified 23 candidate genes related to panicle architectures in rice. This comprehensive study provides new insights into the genetic basis controlling panicle architectures in rice, which lays a foundation in rice improvement.

Heterosis analysis and underlying molecular regulatory mechanism in a wide-compatible neo-tetraploid rice line with long panicles

BackgroundNeo-tetraploid rice, which is a new germplasm developed from autotetraploid rice, has a powerful biological and yield potential and could be used for commercial utilization. The length of panicle, as a part of rice panicle architecture, contributes greatly to high yield. However, little information about long panicle associated with heterosis or hybrid vigor is available in neo-tetraploid rice.ResultsIn the present study, we developed a neo-tetraploid rice line, Huaduo 8 (H8), with long panicles and harboring wide-compatibility genes for pollen and embryo sac fertility. All the hybrids generated by H8 produced significant high-parent yield heterosis and displayed long panicles similar to H8. RNA-seq analysis detected a total of 4013, 7050, 6787 and 6195 differentially expressed genes uniquely belonging to F1 and specifically (DEGFu-sp) associated with leaf, sheath, main panicle axis and spikelet in the two hybrids, respectively. Of these DEGFu-sp, 279 and 89 genes were involved in kinase and synthase, and 714 cloned genes, such as GW8, OsGA20ox1, Ghd8, GW6a, and LP1, were identified and validated by qRT-PCR. A total of 2925 known QTLs intervals, with an average of 1~100 genes per interval, were detected in both hybrids. Of these, 109 yield-related QTLs were associated with seven important traits in rice. Moreover, 1393 non-additive DEGs, including 766 up-regulated and 627 down-regulated, were detected in both hybrids. Importantly, eight up-regulated genes associated with panicle were detected in young panicles of the two hybrids compared to their parents by qRT-PCR. Re-sequencing analysis depicted that LP (a gene controlling long panicle) sequence of H8 was different from many other neo-tetraploid rice and most of the diploid and autotetraploid lines. The qRT-PCR results showed that LP was up-regulated in the hybrid compared to its parents at very young stage of panicle development.ConclusionsThese results suggested that H8 could overcome the intersubspecific autotetraploid hybrid rice sterility caused by embryo sac and pollen sterility loci. Notably, long panicles of H8 showed dominance phenomenon and played an important role in yield heterosis, which is a complex molecular mechanism. The neo-tetraploid rice is a useful germplasm to attain high yield of polyploid rice.

MiR156f integrates panicle architecture through genetic modulation of branch number and pedicel length pathways

BackgroundRice (Oryza sativa) panicle architecture is the major determinant of the ideal plant architecture that directly influence yield potential. Many genes influencing development of primary branches, secondary branches, spikelet and pedicel would also influence panicle architecture, which is thus a complex trait regulated by genes from various aspects. miR156, an extensively studied miRNA, has recently emerged as promising target for crop improvement because of its role in plant architecture regulation, such as the number of tillers, plant height and the panicle architecture. Increasing evidence suggests that miR156 might play an important role in panicle architecture regulation.Main bodyTo study the detailed function of miR156 in rice panicle architecture regulation, we examined the genetic interaction or transcriptional regulation of miR156/OsSPL to other panicle regulating genes. Our results revealed that expression of many panicle related genes were influenced by miR156. Through biochemical analysis, we further proved that miR156 directly regulated the axillary meristem regulating gene, LAX1, at the transcription level. And the intimate relations between miR156 and LAX1, and miR156 and LAX2 were also uncovered by genetic analysis. On the other hand, a tight genetic linkage between miR156 and RCN2, the panicle branch promoting gene, was also detected, which suggested a buffering mechanism for the miR156 mediated panicle architecture regulation. Furthermore, genetic analysis also demonstrated that miR156 functioned in the same pathway with OsRA2 to regulate pedicel length.Short conclusionAltogether, miR156 integrates several genetic pathways mediated by genes such as LAX1, LAX2, RCN2 and OsRA2, and comprehensively regulates panicle development in rice. Based on these analysis, we concluded that miR156 acts as an important regulator for panicle architecture through influencing various aspects of panicle development.

Panicle Morphology Mutant 1 (PMM1) determines the inflorescence architecture of rice by controlling brassinosteroid biosynthesis

BackgroundPanicle architecture is one of the main important agronomical traits that determine branch number and grain number in rice. Although a large number of genes involved in panicle development have been identified in recent years, the complex processes of inflorescence patterning need to be further characterized in rice. Brassinosteroids (BRs) are a class of steroid phytohormones. A great understanding of how BRs contribute to plant height and leaf erectness have been reported, however, the molecular and genetic mechanisms of panicle architecture influenced by BRs remain unclear.ResultsHere, we identified PMM1, encoding a cytochrome P450 protein involved in BRs biosynthesis, and characterized its role in panicle architecture in rice. Three alleles of pmm1 were identified from our T-DNA insertional mutant library. Map-based cloning revealed that a large fragment deletion from the 2nd to 9th exons of PMM1 was responsible for the clustered primary branch morphology in pmm1–1. PMM1 is a new allele of DWARF11 (D11) PMM1 transcripts are preferentially expressed in young panicles, particularly expressed in the primordia of branches and spikelets during inflorescence development. Furthermore, overexpression of OsDWARF4 (D4), another gene encoding cytochrome P450, completely rescued the abnormal panicle phenotype of pmm1–1. Overall, it can be concluded that PMM1 is an important gene involved in BRs biosynthesis and affecting the differentiation of spikelet primordia and patterns of panicle branches in rice.ConclusionsPMM1 is a new allele of D11, which encodes a cytochrome P450 protein involved in BRs biosynthesis pathway. Overexpression of D4 could successfully rescue the abnormal panicle architecture of pmm1 plants, indicating that PMM1/D11 and D4 function redundantly in BRs biosynthesis. Thus, our results demonstrated that PMM1 determines the inflorescence architecture by controlling brassinosteroid biosynthesis in rice.