BRASSINOSTEROID UPREGULATED1, encoding a helix-loop-helix protein, is a novel gene involved in brassinosteroid signaling and controls bending of the lamina joint in rice

Ectopic expression of the atypical HLH FaPRE1 gene determines changes in cell size and morphology

PACLOBUTRAZOL RESISTANCE (PRE) genes code atypical HLH transcriptional regulators characterized by the absence of a DNA-binding domain but present an HLH dimerization domain. In vegetative tissues, the function of these HLH proteins has been related with cell elongation processes. In strawberry, three FaPRE genes are expressed, two of them (FaPRE2 and FaPRE3) in vegetative tissues while FaPRE1 is fruit receptacle-specific. Ubiquitous FaPRE1 accumulation produced elongated flower receptacles and plants due to the elongation of the main aerial vegetative organs, with the exception of leaves. Histological analysis clearly demonstrated that the observed phenotype was due to significant changes in the parenchymal cell's morphology. In addition, transcriptomic studies of the transgenic elongated flower receptacles allowed to identify a small group of differentially expressed genes that encode cell wall-modifying enzymes. Together, the data seem to indicate that, in the strawberry plant vegetative organs, FaPRE proteins could modulate the expression of genes related with the determination of the size and shape of the parenchymal cells.

The brassinosteroid biosynthesis gene, ZmD11, increases seed size and quality in rice and maize

Brassinosteroids (BRs) are a group of plant steroid hormones that regulate many important agronomic traits. Studies on the functional mechanisms of BR-related genes in crop plants are necessary for the application of BRs in agriculture. In this study, ZmD11, an ortholog of rice DWARF11 (D11), and 42 other BR biosynthesis-related genes were identified in maize (Zea mays). Complementary experiments confirmed that ZmD11 completely rescued the abnormal panicle architecture and plant height of the rice cpb1 mutant. A phylogenetic analysis indicated that ZmD11-like proteins were found in other monocots and dicots, but not in lower plants and that alternative splicing variants of these homologues mainly exist in Triticeae crops. A subcellular localization analysis showed that ZmD11 localized to the endoplasmic reticulum. The ZmD11 gene was predominantly expressed in young ears and seeds from 10 to 16 days after pollination, especially in the scutellar aleurone layer and pericarp. Furthermore, the constitutive expression of the ZmD11 gene significantly increased seed length, seed area, seed weight and both seed starch and protein contents in rice and maize. Our results suggest that ZmD11 is a key gene in the regulation of seed size and quality and that it has a potential application value in the molecular breeding of crops.

Genome-wide transcriptome profiling indicates the putative mechanism underlying enhanced grain size in a wheat mutant

Grain size is an important trait for crops. The endogenous hormones brassinosteroids (BRs) play key roles in grain size and mass. In this study, we identified an ethyl methylsulfonate (EMS) mutant wheat line, SM482gs, with increased grain size, 1000-grain weight, and protein content, but decreased starch content, compared with the levels in the wild type (WT). Comparative transcriptomic analysis of SM482gs and WT at four developmental stages [9, 15, 20, and 25 days post-anthesis (DPA)] revealed a total of 264, 267, 771, and 1038 differentially expressed genes (DEGs) at these stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis showed that some DEGs from the comparison at 15 DPA were involved in the pathway of "brassinosteroid biosynthesis," and eight genes involved in BR biosynthesis and signal transduction were significantly upregulated in SM482gs during at least one stage. This indicated that the enhanced BR signaling in SM482gs might have contributed to its increased grain size via network interactions. The expression of seed storage protein (SSP)-encoding genes in SM482gs was upregulated, mostly at 15 and 20 DPA, while most of the starch synthetase genes showed lower expression in SM482gs at all stages, compared with that in WT. The expression patterns of starch synthase genes and seed storage protein-encoding genes paralleled the decreased level of starch and increased storage protein content of SM482gs, which might be related to the increased seed weight and wrinkled phenotype.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02579-6.

OrMKK3 Influences Morphology and Grain Size in Rice

Although morphology and grain size are important to rice growth and yield, the identity of abundant natural allelic variations that determine agronomically important differences in crops is unknown. Here, we characterized the function of mitogen-activated protein kinase 3 from Oryza officinalis Wall. ex Watt encoded by OrMKK3. Different alternative splicing variants occurred in OrMKK3. Green fluorescent protein (GFP)-OrMKK3 fusion proteins localized to the cell membrane and nuclei of rice protoplasts. Overexpression of OrMKK3 influenced the expression levels of the grain size-related genes SMG1, GW8, GL3, GW2, and DEP3. Phylogenetic analysis showed that OrMKK3 is well conserved in plants while showing large amounts of variation between indica, japonica, and wild rice. In addition, OrMKK3 slightly influenced brassinosteroid (BR) responses and the expression levels of BR-related genes. Our findings thus identify a new gene, OrMKK3, influencing morphology and grain size and that represents a possible link between mitogen-activated protein kinase and BR response pathways in grain growth.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12374-020-09290-2.

Comparative population genomic analysis provides insights into breeding of modern indica rice in China

Comparative genomic analysis within Asian cultivated rice (Oryza sativa L.) populations has greatly enriched our knowledge regarding rice domestication and the divergence of the indica and japonica subspecies, while study on genomic regions associated with improvement within the indica subspecies is still limited. Here, through combined investigation of 2,429 indica cultivar genomes from public sequencing projects, we depict the improvement of modern indica rice in China. We identify three subgroups within indica populations: two geographically distinct, historical subgroups indica I (Ind_I) and indica III (Ind_III) and a modern subgroup indica II (Ind_II). The modern indica subgroup Ind_II shows admixture of the other two subgroups and enrichment of alleles that had been low-frequency in the other two subgroups. The Chinese indica cultivars exhibit a strong subgroup component change from Ind_I to Ind_II in the 1980s. Through haplotype-based comparative analysis, we detect 187 regions associated with separation of Ind_II compared to Ind_I or Ind_III. Within those regions we find strong representation of beneficial agricultural production-related alleles in Ind_II and a positive correlation between grain yield and number of differentiated haplotypes. Phenotypic features of long and slender grain, small tiller angle and decreased flowering time were detected for Ind_II. Through haplotype-based comparative analysis between rice subpopulations and subspecies, we find differentiated haplotypes not only from indica itself but also from japonica and aus, suggesting that introgression from other rice sub-populations has substantially contributed to modern indica rice breeds. These results help clarify the evolutionary landscape of modern indica rice in China and provide useful targets for future improvement.

Enhanced resistance to fungal and bacterial diseases in tomato and Arabidopsis expressing BSR2 from rice

The overexpression of rice BSR2 would offer a simple and effective strategy to protect plants from multiple devastating diseases in tomato and Arabidopsis. Many devastating plant diseases are caused by pathogens possessing a wide host range. Fungal Botrytis cinerea and Rhizoctonia solani, as well as bacterial Pseudomonas syringae and Ralstonia pseudosolanacearum are four such pathogens that infect hundreds of plant species, including agronomically important crops, and cause serious diseases, leading to severe economic losses. However, reports of genes that can confer resistance to broad host-range pathogens via traditional breeding methods are currently limited. We previously reported that Arabidopsis plants overexpressing rice BROAD-SPECTRUM RESISTANCE2 (BSR2/CYP78A15) showed tolerance not only to bacterial P. syringae pv. tomato DC3000 but also to fungal Colletotrichum higginsianum and R. solani. Rice plants overexpressing BSR2 displayed tolerance to two R. solani anastomosis groups. In the present study, first, BSR2-overexpressing (OX) Arabidopsis plants were shown to be additionally tolerant to B. cinerea, R. solani, and R. pseudosolanacearum. Next, tomato 'Micro-Tom' was used as a model to determine whether such tolerance by BSR2 can be introduced into dicot crops to prevent infection from pathogens possessing wide host range. BSR2-OX tomato displayed broad-spectrum disease tolerance to fungal B. cinerea and R. solani, as well as to bacterial P. syringae and R. pseudosolanacearum. Additionally, undesirable traits such as morphological changes were not detected. Thus, BSR2 overexpression can offer a simple and effective strategy to protect crops from multiple destructive diseases.

Heterologous microProtein expression identifies LITTLE NINJA, a dominant regulator of jasmonic acid signaling

MicroProteins are small, often single-domain proteins that are sequence-related to larger, often multidomain proteins. Here, we used a combination of comparative genomics and heterologous synthetic misexpression to isolate functional cereal microProtein regulators. Our approach identified LITTLE NINJA (LNJ), a microProtein that acts as a modulator of jasmonic acid (JA) signaling. Ectopic expression of LNJ in Arabidopsis resulted in stunted plants that resembled the decuple JAZ (jazD) mutant. In fact, comparing the transcriptomes of transgenic LNJ overexpressor plants and jazD revealed a large overlap of deregulated genes, suggesting that ectopic LNJ expression altered JA signaling. Transgenic Brachypodium plants with elevated LNJ expression levels showed deregulation of JA signaling as well and displayed reduced growth and enhanced production of side shoots (tiller). This tillering effect was transferable between grass species, and overexpression of LNJ in barley and rice caused similar traits. We used a clustered regularly interspaced short palindromic repeats (CRISPR) approach and created a LNJ-like protein in Arabidopsis by deleting parts of the coding sentence of the AFP2 gene that encodes a NINJA-domain protein. These afp2-crispr mutants were also stunted in size and resembled jazD Thus, similar genome-engineering approaches can be exploited as a future tool to create LNJ proteins and produce cereals with altered architectures.

Characterization of the 'Oat-Like Rice' Caused by a Novel Allele OsMADS1Olr Reveals Vital Importance of OsMADS1 in Regulating Grain Shape in Oryza sativa L

BACKGROUND

Grain shape is a critical agronomic trait affecting grain yield and quality. Exploration and functional characterization of grain shape-related genes will facilitate rice breeding for higher quality and yield.

RESULTS

Here, we characterized a recessive mutant named Oat-like rice for its unique grain shape which highly resembles oat grains. The Oat-like rice displayed abnormal floral organs, an open hull formed by remarkably elongated leafy lemmas and paleae, occasionally formed conjugated twin brown rice, an aberrant grain shape and a low seed setting rate. By map-based cloning, we discovered that Oat-like rice harbors a novel allele of OsMADS1 gene (OsMADS1^Olr), which has a spontaneous point mutation that causes the substitution of an amino acid that is highly conserved in the MADS-box domain of the MADS-box family. Further linkage analysis indicated that the point mutation in the OsMADS1^Olr is associated with Oat-like rice phenotype, and expression analysis of the OsMADS1 by qRT-PCR and GUS staining also indicated that it is highly expressed in flower organs as well as in the early stages of grain development. Furthermore, OsMADS1^Olr-overexpressing plants showed similar phenotypes of Oat-like rice in grain shape, possibly due to the dominant negative effect. And OsMADS1-RNAi plants also displayed grain phenotypes like Oat-like rice. These results suggested that OsMADS1^Olr is responsible for the Oat-like rice phenotype including aberrant grain shape. Moreover, the expression levels of representative genes related to grain shape regulation were apparently altered in Oat-like rice, OsMADS1^Olr-overexpressing and OsMADS1-RNAi transgenic plants. Finally, compared with Oat-like rice, OsMADS1^Olr-overexpressing and OsMADS1-RNAi plants, mild phenotype of seed-specific OsMADS1-RNAi transgenic plants indicated that OsMADS1 may has has a direct regulation role in grain development and the grain phenotypes of Oat-like rice, OsMADS1^Olr-overexpressing and OsMADS1-RNAi plants are majorly caused by the abnormal lemma and palea development.

CONCLUSIONS

Altogether, our results showed that grain shape and a low seed setting rate of the notable 'Oat-like rice' are caused by a spontaneous point mutation in the novel allele OsMADS1^Olr. Furthermore, our findings suggested that OsMADS1 mediates grain shape possibly by affecting the expression of representative genes related to grain shape regulation. Thus, this study not only revealed that OsMADS1 plays a vital role in regulating grain shape of rice but also highlighted the importance and value of OsMADS1 to improve the quality and yield of rice by molecular breeding.

The histone deacetylase HDA703 interacts with OsBZR1 to regulate rice brassinosteroid signaling, growth and heading date through repression of Ghd7 expression

The plant steroid hormones brassinosteroids (BRs) play crucial roles in plant growth and development. The BR signal transduction pathway from perception to the key transcription factors has been well understood in Arabidopsis thaliana and in rice (Oryza sativa); however, the mechanisms conferring BR-mediated growth and flowering remain largely unknown, especially in rice. In this study, we show that HDA703 is a histone H4K8 and H4K12 deacetylase in rice. Hda703 mutants display a typical BR loss-of-function phenotype and reduced sensitivity to brassinolide, the most active BR. Rice plants overexpressing HDA703 exhibit some BR gain-of-function phenotypes dependent on BR biosynthesis and signaling. We also show that HDA703 is a direct target of BRASSINAZOLE-RESISTANT1 (OsBZR1), a primary regulator of rice BR signaling, and HDA703 interacts with OsBZR1 in rice. We further show that GRAIN NUMBER, PLANT HEIGHT, and HEADING DATE 7 (Ghd7), a central regulator of growth, development, and the stress response, is a direct target of OsBZR1. HDA703 directly targets Ghd7 and represses its expression through histone H4 deacetylation. HDA703-overexpressing rice plants phenocopy Ghd7-silencing rice plants in both growth and heading date. Together, our study suggests that HDA703, a histone H4 deacetylase, interacts with OsBZR1 to regulate rice BR signaling, growth, and heading date through epigenetic regulation of Ghd7.

SUPER STARCHY1/ONAC025 participates in rice grain filling

NAC transcription factors (TFs) are known for their role in development and stress. This article attempts to functionally validate the role of rice SS1/ ONAC025 (LOC_Os11g31330) during seed development. The gene is seed-specific and its promoter directs reporter expression in the developing endosperm and embryo in rice transgenic plants. Furthermore, rice transgenic plants ectopically expressing SS1/ ONAC025 have a plantlet lethal phenotype with hampered vegetative growth, but increased tillers and an altered shoot apical meristem structure. The vegetative cells of these plantlets are filled with distinct starch granules. RNAseq analysis of two independent plantlets reveals the differential expression of reproductive and photosynthetic genes. A comparison with seed development transcriptome indicates differential regulation of many seed-related genes by SS1/ ONAC025. Genes involved in starch biosynthesis, especially amylopectin and those encoding seed storage proteins, and regulating seed size are also differentially expressed. In conjunction, SS1/ ONAC025 shows highest expression in japonica rice. As a TF, SS1/ ONAC025 is a transcriptional repressor localized to endoplasmic reticulum and nucleus. The article shows that SS1/ ONAC025 is a seed-specific gene promoting grain filling in rice, and negatively affecting vegetative growth.

Spatiotemporal Resolved Leaf Angle Establishment Improves Rice Grain Yield via Controlling Population Density

Leaf angle is mainly determined by the lamina joint (LJ) and contributes to ideal crop architecture for high yield. Here, we dissected five successive stages with distinct cytological features of LJs spanning organogenesis to leaf angle formation and obtained the underlying stage-specific mRNAs and small RNAs, which well explained the cytological dynamics during LJ organogenesis and leaf angle plasticity. Combining the gene coexpression correlation with high-throughput promoter analysis, we identified a set of transcription factors (TFs) determining the stage- and/or cytological structure-specific profiles. The functional studies of these TFs demonstrated that cytological dynamics determined leaf angle and that the knockout rice of these TFs with erect leaves significantly enhanced yield by maintaining the proper tiller number under dense planting. This work revealed the high-resolution mechanisms of how the cytological dynamics of LJ determined leaf erectness and served as a valuable resource to remodel rice architecture for high yield by controlling population density.

Obtusifoliol 14α-demethylase OsCYP51G1 is involved in phytosterol synthesis and affects pollen and seed development

As structural components of biological membranes, phytosterols are essential not only for a variety of cellular functions but are also precursors for brassinosteroid (BR) biosynthesis. Plant CYP51 is the oldest and most conserved obtusifoliol 14α-demethylase in eukaryotes and is an essential component of the sterol biosynthesis pathway. However, little is known about rice (Oryza sativa L.) CYP51G1. In this study, we showed that rice OsCYP51G1 shared high homology with obtusifoliol 14α-demethylase and OsCYP51G1 was strongly expressed in most of rice organs. Subcellular localization analysis indicated that OsCYP51G1 was localized to the endoplasmic reticulum. Knockdown and knockout of OsCYP51G1 resulted in delayed flowering, impaired membrane integrity, abnormal pollen, and reduced grain yield, whereas OsCYP51G1 overexpression led to increased grain yield. Knockdown of OsCYP51G1 also reduced the levels of end-products (sitosterol and stigmasterol) and increased those of upstream intermediates (24-methylene-cycloartenol and cycloeucalenol) of the OsCYP51G1-mediated sterol biosynthesis step. In contrast, overexpression of OsCYP51G1 increased the sitosterol and stigmasterol content and reduced that of cycloeucalenol. However, knockdown of OsCYP51G1 by RNAi did not elicit these BR deficiency-related phenotypes, such as dwarfism, erect leaves and small seeds, nor was the leaf lamina angle sensitive to brassinolide treatment. These results revealed that rice OsCYP15G1 encodes an obtusifoliol 14α-demethylase for the phytosterols biosynthesis and possible without affecting the biosynthesis of downstream BRs, which was different from its homolog, OsCYP51G3.

Synergistic Interaction of Phytohormones in Determining Leaf Angle in Crops

Leaf angle (LA), defined as the angle between the plant stem and leaf adaxial side of the blade, generally shapes the plant architecture into a loosen or dense structure, and thus influences the light interception and competition between neighboring plants in natural settings, ultimately contributing to the crop yield and productivity. It has been elucidated that brassinosteroid (BR) plays a dominant role in determining LA, and other phytohormones also positively or negatively participate in regulating LA. Accumulating evidences have revealed that these phytohormones interact with each other in modulating various biological processes. However, the comprehensive discussion of how the phytohormones and their interaction involved in shaping LA is relatively lack. Here, we intend to summarize the advances in the LA regulation mediated by the phytohormones and their crosstalk in different plant species, mainly in rice and maize, hopefully providing further insights into the genetic manipulation of LA trait in crop breeding and improvement in regarding to overcoming the challenge from the continuous demands for food under limited arable land area.

Knock-Down the Expression of Brassinosteroid Receptor TaBRI1 Reduces Photosynthesis, Tolerance to High Light and High Temperature Stresses and Grain Yield in Wheat

Brassinosteroid (BR)-deficient or -insensitive mutants exhibited altered plant architecture with the potential to impact yield, the underlying physiological and molecular mechanisms are still to be explored. In this study, we cloned three BR receptor homologous genes TaBRI1-A1, -B1 and -D1 from hexaploid wheat (Triticum estivum L.) and further isolated the TaBRI1-A1, TaBRI1-D1 deletion mutants from the ion beam-induced mutants of variety Xiaoyan81, TaBRI1-A1 and TaBRI1-D1 in which the expression of total receptor TaBRI1 was significantly decreased. The TaBRI1 knock-down mutants exhibited relatively erect leaves and a significant decrease in the 1000-grain weight. Further studies showed that TaBRI1 knock-down mutants showed a significant reduction in photosynthetic rate during the whole grain-filling stage. TaBRI1 knock-down plants generated by TaBRI1-A1, TaBRI1-D1 deletion or using virus-induced gene silencing exhibited the reduction in the efficiency of photosystem II (PSII) (Fv/Fm, Φ_PSII and electron transport rate, ETR) especially under high light and high temperature stresses. The 24-epibrassinolide (EBR) treatment increased CO₂ assimilation rate in the wild type under both normal and high light and high temperature stresses conditions, but this increasing effect was not observed in the TaBRI1 knock-down mutants. Meanwhile, the expression levels of BR biosynthetic genes including TaDWARF4, TaCPD1 and TaCPD90C1 is not decreased or decreased to a lesser extent in the TaBRI1 knock-down mutants after EBR treatment. These results suggested that TaBRI1 is required for maintaining photosynthesis and tolerance to high light and high temperature stresses both of which are important for grain yield and will be a possible engineered target to control plant photosynthesis and yields in wheat.

The rice PLATZ protein SHORT GRAIN6 determines grain size by regulating spikelet hull cell division

Grain size is a major determinant of cereal grain yields; however, the relevant regulatory mechanisms controlling this trait have not been fully elucidated. The rice (Oryza sativa) mutant short grain6 (sg6) was identified based on its reduced grain length and weight. Here, we functionally characterized the role of SG6 in determining grain size through the regulation of spikelet hull cell division. SG6 encodes a previously uncharacterized plant AT-rich sequence and zinc-binding (PLATZ) protein that is ubiquitously localized throughout the cell and is preferentially expressed in the early developing panicles but not in the endosperm. The overexpression of SG6 resulted in significantly larger and heavier grains, as well as increased plant heights, which is consistent with its elevated spikelet hull cell division rate. Yeast two-hybrid analyses revealed that SG6 interacts with the core cell cycle machinery DP protein and several other putative cell division regulators, consistent with our transcriptomic analysis, which showed that SG6 activates the expression of many DNA replication and cell-cycle-related genes. These results confirm the crucial role of SG6 in determining grain size by regulating spikelet hull cell division and provide clues for understanding the functions of PLATZ family proteins and the network regulating cereal grain size.

Oryza sativa mediator subunit OsMED25 interacts with OsBZR1 to regulate brassinosteroid signaling and plant architecture in rice

Brassinosteroids (BRs) are plant-specific steroid hormones which regulate plant growth, development, and adaptation. Transcriptional regulation plays key roles in plant hormone signaling. A mediator can serve as a bridge between gene-specific transcription factors and the RNA polymerase machinery, functioning as an essential component in regulating the transcriptional process. However, whether a mediator is involved in BR signaling is unknown. Here, we discovered that Oryza sativa mediator subunit 25 (OsMED25) is an important regulator of rice BR signaling. Phenotypic analyses showed that the OsMED25-RNAi and osmed25 mutant presented erect leaves, as observed in BR-deficient mutants. In addition, the OsMED25-RNAi and osmed25 mutant exhibited decreased BR sensitivity. Genetic analysis indicated that OsMED25-RNAi could suppress the enhanced BR signaling phenotype of Osbzr1-D. Further biochemical analysis showed that OsMED25 interacts with OsBZR1 in vivo, and OsMED25 is enriched on the promoter of OsBZR1 target genes. RNA sequencing analysis indicated that OsMED25 affects the expression of approximately 45% of OsBZR1-regulated genes and mainly functions as a corepressor of OsBZR1. Together, these findings revealed that OsMED25 regulates rice BR signaling by interacting with OsBZR1 and modulating the expression of OsBZR1 target genes, thus expanding our understanding of the roles of mediators in plant hormone signaling.

The basic helix-loop-helix transcription factor OsBLR1 regulates leaf angle in rice via brassinosteroid signalling

Leaf angle is a key factor in plant architecture and crop yield. Brassinosteroids (BRs) regulate many developmental processes, especially the leaf angle in monocots. However, the BR signalling pathway is complex and includes many unknown members. Here, we propose that Oryza sativa BRASSINOSTEROID-RESPONSIVE LEAF ANGLE REGULATOR 1 (OsBLR1) encodes a bHLH transcription factor, and positively regulates BR signalling to increase the leaf angle and grain length in rice (Oryza sativa L.). Lines overexpressing OsBLR1 (blr1-D and BLR1-OE-1/2/3) had similar traits, with increased leaf angle and grain length. Conversely, OsBLR1-knockout mutants (blr1-1/2/3) had erect leaves and shorter grains. Lamina joint inclination, coleoptile elongation, and root elongation assay results indicated that these overexpression lines were more sensitive to BR, while the knockout mutants were less sensitive. There was no significant difference in the endogenous BR contents of blr1-1/2 and wild-type plants. These results suggest that OsBLR1 is involved in BR signal transduction. The blr1-D mutant, with increased cell growth in the lamina joint and smaller leaf midrib, showed significant changes in gene expression related to the cell wall and leaf development compared with wild-type plants; furthermore, the cellulose and protopectin contents in blr1-D were reduced, which resulted in the increased leaf angle and bent leaves. As the potential downstream target gene of OsBLR1, the REGULATOR OF LEAF INCLINATION1 (OsRLI1) gene expression was up-regulated in OsBLR1-overexpression lines and down-regulated in OsBLR1-knockout mutants. Moreover, we screened OsRACK1A as an interaction protein of OsBLR1 using a yeast two-hybrid assay and glutathione-S-transferase pull-down.

The Rice Basic Helix-Loop-Helix 79 (OsbHLH079) Determines Leaf Angle and Grain Shape

Changes in plant architecture, such as leaf size, leaf shape, leaf angle, plant height, and floral organs, have been major factors in improving the yield of cereal crops. Moreover, changes in grain size and weight can also increase yield. Therefore, screens for additional factors affecting plant architecture and grain morphology may enable additional improvements in yield. Among the basic Helix-Loop-Helix (bHLH) transcription factors in rice (Oryza sativa), we found an enhancer-trap T-DNA insertion mutant of OsbHLH079 (termed osbhlh079-D). The osbhlh079-D mutant showed a wide leaf angle phenotype and produced long grains, similar to the phenotypes of mutants with increased brassinosteroid (BR) levels or enhanced BR signaling. Reverse transcription-quantitative PCR analysis showed that BR signaling-associated genes are largely upregulated in osbhlh079-D, but BR biosynthesis-associated genes are not upregulated, compared with its parental japonica cultivar ‘Dongjin’. Consistent with this, osbhlh079-D was hypersensitive to BR treatment. Scanning electron microscopy revealed that the expansion of cell size in the adaxial side of the lamina joint was responsible for the increase in leaf angle in osbhlh079-D. The expression of cell-elongation-associated genes encoding expansins and xyloglucan endotransglycosylases/hydrolases increased in the lamina joints of leaves in osbhlh079-D. The regulatory function of OsbHLH079 was further confirmed by analyzing 35S::OsbHLH079 overexpression and 35S::RNAi-OsbHLH079 gene silencing lines. The 35S::OsbHLH079 plants showed similar phenotypes to osbhlh079-D, and the 35S::RNAi-OsbHLH079 plants displayed opposite phenotypes to osbhlh079-D. Taking these observations together, we propose that OsbHLH079 functions as a positive regulator of BR signaling in rice.

Promotion of BR Biosynthesis by miR444 Is Required for Ammonium-Triggered Inhibition of Root Growth

Rice (Oryza sativa), the staple food for almost half of the world's population, prefers ammonium (NH₄ ⁺) as the major nitrogen resource, and while NH₄ ⁺ has profound effects on rice growth and yields, the underlying regulatory mechanisms remain largely unknown. Brassinosteroids (BRs) are a class of steroidal hormones playing key roles in plant growth and development. In this study, we show that NH₄ ⁺ promotes BR biosynthesis through miR444 to regulate rice root growth. miR444 targeted five homologous MADS-box transcription repressors potentially forming homologous or heterogeneous complexes in rice. miR444 positively regulated BR biosynthesis through its MADS-box targets, which directly repress the transcription of BR-deficient dwarf 1 (OsBRD1), a key BR biosynthetic gene. NH₄ ⁺ induced the miR444-OsBRD1 signaling cascade in roots, thereby increasing the amount of BRs, whose biosynthesis and signaling were required for NH₄ ⁺ -dependent root elongation inhibition. Consistently, miR444-overexpressing rice roots were hypersensitive to NH₄ ⁺ depending on BR biosynthesis, and overexpression of miR444's target, OsMADS57, resulted in rice hyposensitivity to NH₄ ⁺ in root elongation, which was associated with a reduction of BR content. In summary, our findings reveal a cross talk mechanism between NH₄ ⁺ and BR in which NH₄ ⁺ activates miR444-OsBRD1, an undescribed BR biosynthesis-promoting signaling cascade, to increase BR content, inhibiting root elongation in rice.

The Role of Brassinosteroids in Controlling Plant Height in Poaceae: A Genetic Perspective

The most consistent phenotype of the brassinosteroid (BR)-related mutants is the dwarf habit. This observation has been reported in every species in which BR action has been studied through a mutational approach. On this basis, a significant role has been attributed to BRs in promoting plant growth. In this review, we summarize the work conducted in rice, maize, and barley for the genetic dissection of the pathway and the functional analysis of the genes involved. Similarities and differences detected in these species for the BR role in plant development are presented. BR promotes plant cell elongation through a complex signalling cascade that modulates the activities of growth-related genes and through the interaction with gibberellins (GAs), another class of important growth-promoting hormones. Evidence of BR–GA cross-talk in controlling plant height has been collected, and mechanisms of interaction have been studied in detail in Arabidopsis thaliana and in rice (Oryza sativa). The complex picture emerging from the studies has highlighted points of interaction involving both metabolic and signalling pathways. Variations in plant stature influence plant performance in terms of stability and yield. The comprehension of BR’s functional mechanisms will therefore be fundamental for future applications in plant-breeding programs.

Brassinosteroids: Multidimensional Regulators of Plant Growth, Development, and Stress Responses

Brassinosteroids (BRs) are a group of polyhydroxylated plant steroid hormones that are crucial for many aspects of a plant's life. BRs were originally characterized for their function in cell elongation, but it is becoming clear that they play major roles in plant growth, development, and responses to several stresses such as extreme temperatures and drought. A BR signaling pathway from cell surface receptors to central transcription factors has been well characterized. Here, we summarize recent progress toward understanding the BR pathway, including BR perception and the molecular mechanisms of BR signaling. Next, we discuss the roles of BRs in development and stress responses. Finally, we show how knowledge of the BR pathway is being applied to manipulate the growth and stress responses of crops. These studies highlight the complex regulation of BR signaling, multiple points of crosstalk between BRs and other hormones or stress responses, and the finely tuned spatiotemporal regulation of BR signaling.

MINI SEED 2 (MIS2) Encodes a Receptor-like Kinase that Controls Grain Size and Shape in Rice

BACKGROUND

Grain size is a key agronomic trait that is directly associated with grain yield in rice. Although several genes related to grain size in rice have been identified, our understanding of the mechanism of grain development is still limited.

RESULTS

In this study, we reported the characterization of a novel seed size mutant mini seed 2 (mis2), in which the grain showed reduced length, width and thickness along with wrinkled surface. Microscopic analysis revealed that the spikelet epidermal cell size was reduced but the cell number was increased in the mis2 mutant, suggesting that MIS2 controls grain size by coordinately regulating epidermal cell size and cell number. Map-based cloning revealed that MIS2 encodes a receptor-like kinase CRINKLY4 (CR4) which showed the highest expression in developing panicles. The MIS2 protein is localized primarily on the plasma membrane along with the endosome. However, the Arg258Gln mutation located in extracellular domain in the mis2 mutant disturbed its subcellular localization. Additionally, three major haplotypes of MIS2 were identified in the japonica, indica and aus rice cultivars. The 18-bp InDel (insertion and deletion) in the 5'-UTR (untranslated region) caused different expression level of MIS2 in haplotypes.

CONCLUSIONS

We reported a key role of OsCR4 in controlling grain size and shape by coordinately regulating epidermal cell size and cell number. The Arg258 in the extracellular seven-repeat domain is essential for the correct subcellular behavior and function of the OsCR4 protein.

Exploring the Brassinosteroid Signaling in Monocots Reveals Novel Components of the Pathway and Implications for Plant Breeding

Brassinosteroids (BRs) are a class of steroidal phytohormones which are key regulators of diverse processes during whole life cycle of plants. Studies conducted in the dicot model species Arabidopsis thaliana have allowed identification and characterization of various components of the BR signaling. It is currently known that the BR signaling is interconnected at various stages with other phytohormonal and stress signaling pathways. It enables a rapid and efficient adaptation of plant metabolism to constantly changing environmental conditions. However, our knowledge about mechanism of the BR signaling in the monocot species is rather limited. Thus, identification of new components of the BR signaling in monocots, including cereals, is an ongoing process and has already led to identification of some monocot-specific components of the BR signaling. It is of great importance as disturbances in the BR signaling influence architecture of mutant plants, and as a consequence, the reaction to environmental conditions. Currently, the modulation of the BR signaling is considered as a target to enhance yield and stress tolerance in cereals, which is of particular importance in the face of global climate change.

Designed Manipulation of the Brassinosteroid Signal to Enhance Crop Yield

Brassinosteroid (BR), a plant steroid hormone, plays crucial role in modulating plant growth and development, which affect crop architecture and yield. However, BR application cannot highly benefit to agricultural production as expectation, because it regulates multiple processes in different tissues and leads to side effect. In addition, accurately modifying BR signal at transcriptional level is difficult. Effective manipulation of the BR signal and avoidance of side effects are required to enhance yield in different crops. Application of BR by spraying at specific developmental stages can enhance crop yield, but this method is impractical for use on a large scale. The accurate molecular design of crops would be much more helpful to manipulate the BR signal in specific organs and/or at particular developmental stages to enhance crop yield. This minireview summarizes the BR regulation of yield in different crops, especially horticultural crops, and the strategies used to regulate the BR signal to enhance crop yield. One popular strategy is to directly modulate the BR signal through modifying the functions of important components in the BR signal transduction pathway. Another strategy is to identify and modulate regulators downstream of, or in crosstalk with, the BR signal to manipulate its role in specific processes and increase crop yield. Efforts to accurately design a BR manipulation strategy will ultimately lead to effective control of the BR signal to avoid side effects and enhance crop yield.

Genome-Wide Transcriptome Analysis of Rice Seedlings after Seed Dressing with Paenibacillus yonginensis DCY84T and Silicon

Plant-growth-promoting bacteria (PGPB) are beneficial microorganisms that can also protect against disease and environmental stress. Silicon (Si) is the second most abundant element in soil, and is known to increase plant growth, grain yield, resistance to biotic stress, and tolerance to abiotic stress. Combined treatment of PGPB and Si has been shown to further enhance plant growth and crop yield. To determine the global effects of the PGPB and Si on rice growth, we compared rice plants treated with Paenibacillus yonginensis DCY84^T (DCY84^T) and Si with untreated rice. To identify the genes that respond to DCY84^T+Si treatment in rice, we performed an RNA-Seq transcriptome analysis by sampling treated and untreated roots on a weekly basis for three weeks. Overall, 576 genes were upregulated, and 394 genes were downregulated in treated roots, using threshold fold-changes of at least 2 (log₂) and p-values < 0.05. Gene ontology analysis showed that phenylpropanoids and the L-phenylalanine metabolic process were prominent in the upregulated genes. In a metabolic overview analysis using the MapMan toolkit, pathways involving phenylpropanoids and ethylene were strongly associated with upregulated genes. The functions of seven upregulated genes were identified as being associated with drought stress through a literature search, and a stress experiment confirmed that plants treated with DCY84^T+Si exhibited greater drought tolerance than the untreated control plants. Furthermore, the predicted protein–protein interaction network analysis associated with DCY84^T+ Si suggests mechanisms underlying growth promotion and stress tolerance.

Wheat TaSPL8 Modulates Leaf Angle Through Auxin and Brassinosteroid Signaling

In grass crops, leaf angle is determined by development of the lamina joint, the tissue connecting the leaf blade and sheath, and is closely related to crop architecture and yield. In this study, we identified a mutant generated by fast neutron radiation that exhibited an erect leaf phenotype caused by defects in lamina joint development. Map-based cloning revealed that the gene TaSPL8, encoding a SQUAMOSA PROMOTER BINDING-LIKE (SPL) protein, is deleted in this mutant. TaSPL8 knock-out mutants exhibit erect leaves due to loss of the lamina joint, compact architecture, and increased spike number especially in high planting density, suggesting similarity with its LIGULESS1 homologs in maize (Zea mays) and rice (Oryza sativa). Hence, LG1 could be a robust target for plant architecture improvement in grass species. Common wheat (Triticum aestivum, 2n = 6× = 42; BBAADD) is an allohexaploid containing A, B, and D subgenomes and the homeologous gene of TaSPL8 from the D subgenome contributes to the length of the lamina joint to a greater extent than that from the A and B subgenomes. Comparison of the transcriptome between the Taspl8 mutant and the wild type revealed that TaSPL8 is involved in the activation of genes related to auxin and brassinosteroid pathways and cell elongation. TaSPL8 binds to the promoters of the AUXIN RESPONSE FACTOR gene and of the brassinosteroid biogenesis gene CYP90D2 and activates their expression. These results indicate that TaSPL8 might regulate lamina joint development through auxin signaling and the brassinosteroid biosynthesis pathway.

Brassinosteroid Regulates Root Development with Highly Redundant Genes in Hexaploid Wheat

Brassinosteroid (BR) plays an important role in plant development and biotic and abiotic stress tolerance, but its specific function remains largely unknown in wheat (Triticum aestivum L.), preventing its utilization in this important crop. In this study, the function of BR and its underlying cytological role in wheat root development were comprehensively investigated. Our findings demonstrated that BR has a conserved function in regulating root length in wheat, and novel roles in regulating lateral root emergence and root diameter were uncovered. Analyses of BR homologous gene composition and evolutionary divergence demonstrated that the genetic framework of the wheat BR pathway was close to that of rice, but contained highly redundant homologous copies of genes from the subgenome A, B and D. These homologous copies showed active expression and shared a conserved BR response. The expression of wheat DWF4 and glycogen synthase kinase (GSK) genes in Arabidopsis confirmed that multiple homologous copies maintained their conserved function in regulating root development, highlighting their redundant status and indicating that a special challenge exists in wheat gene modification to deal with this high redundancy. However, our results suggested that the hypermorphic effect of T. aestivum GSK (TaGSK) genes with point mutations may be an effective approach to overcome this redundancy in the manipulation of BR signaling in wheat. Our study provides fundamental data uncovering the function of BR in wheat root development, the underlying genetic basis and a possible strategy to manipulate BR signaling in hexaploid wheat.

Molecular insights into the regulation of rice kernel elongation

A large number of rice agronomic traits are complex, multi factorial and polygenic. As the mechanisms and genes determining grain size and yield are largely unknown, the identification of regulatory genes related to grain development remains a preeminent approach in rice genetic studies and breeding programs. Genes regulating cell proliferation and expansion in spikelet hulls and participating in endosperm development are the main controllers of rice kernel elongation and grain size. We review here and discuss recent findings on genes controlling rice grain size and the mechanisms, epialleles, epigenomic variation, and assessment of controlling genes using genome-editing tools relating to kernel elongation.

Effective Modulating Brassinosteroids Signal to Study Their Specific Regulation of Reproductive Development and Enhance Yield

Brassinosteroid (BR) is a family of bioactive steroid hormones that plays vital roles in plant growth and development. The BR-mediated regulation of plant growth and architecture has been well studied. However, relatively few studies have investigated the BR-related regulation of reproductive development because of the difficulties in excluding non-specific regulation and secondary responses from severe vegetative phenotypes and poor nutritional status. Furthermore, differentially regulating the BR signal in vegetative and reproductive organs is problematic. Thus, establishing a method for modulating the BR signal only in reproductive organs or during reproductive developmental stages will be beneficial. Additionally, the utility of BR applications for crop production is limited because of deleterious side-effects, including the associated decrease in the planting density and lodging resistance. Moreover, enhancing the BR signal may lead to feedback inhibition. In this study, we developed a transformation system for modulating the BR signal differentially during reproductive and vegetative developmental stages. This system involves transformations with different combinations of a reproductive tissue-specific promoter, coding sequences that increase or decrease the BR signal, and various genotypic backgrounds with enhanced or decreased BR signals. The enhanced BR signal generated in transformants was targeted to reproductive organs without affecting vegetative organs. This system may be useful for studying the BR-specific regulation of plant reproductive development and shows promise for optimizing seed yield.

Comparative functional genomics analysis of bHLH gene family in rice, maize and wheat

BACKGROUND

The basic helix-loop-helix transcription factors play important roles in diverse cellular and molecular processes. Comparative functional genomics can provide powerful approaches to draw inferences about gene function and evolution among species. The comprehensive comparison of bHLH gene family in different gramineous plants has not yet been reported.

RESULTS

In this study, a total of 183, 231 and 571 bHLHs were identified in rice, maize and wheat genomes respectively, and 1154 bHLH genes from the three species and Arabidopsis were classified into 36 subfamilies. Of the identified genes, 110 OsbHLHs, 188 ZmbHLHs and 209 TabHLHs with relatively high mRNA abundances were detected in one or more tissues during development, and some of them exhibited tissue-specific expression such as TabHLH454-459, ZmbHLH099-101 and OsbHLH037 in root, TabHLH559-562, - 046, - 047 and ZmbHLH010, - 072, - 226 in leaf, TabHLH216-221, - 333, - 335, - 340 and OsbHLH005, - 141 in inflorescence, TabHLH081, ZmbHLH139 and OsbHLH144 in seed. Forty five, twenty nine and thirty one differentially expressed bHLHs were respectively detected in wheat, maize and rice under drought stresses using RNA-seq technology. Among them, the expressions of TabHLH046, - 047, ZmbHLH097, - 098, OsbHLH006 and - 185 were strongly induced, whereas TabHLH303, - 562, ZmbHLH155, - 154, OsbHLH152 and - 113 showed significant down-regulation. Twenty two TabHLHs were induced after stripe rust infection at 24 h and nine of them were suppressed at 72 hpi, whereas 28 and 6 TabHLHs exhibited obviously down- and up-regulation after powdery mildew attack respectively. Forty one ZmbHLHs were differentially expressed in response to F. verticillioides infection. Twenty two co-expression modules were identified by the WGCNA, some of which were associated with particular tissue types. And GO enrichment analysis for the modules showed that some TabHLHs were involved in the control of several biological processes, such as tapetal PCD, lipid metabolism, iron absorption, stress responses and signal regulation.

CONCLUSION

The present study identifies the bHLH family in rice, maize and wheat genomes, and detailedly discusses the evolutionary relationships, expression and function of bHLHs. This study provides some novel and detail information about bHLHs, and may facilitate understanding the molecular basis of the plant growth, development and stress physiology.

Functional Specificities of Brassinosteroid and Potential Utilization for Crop Improvement

Brassinosteroid (BR) regulates many important agronomic traits and thus has great potential in agriculture. However, BR application is limited due to its complex effects on plants. The identification of specific downstream BR components and pathways in the crop plant rice (Oryza sativa) further demonstrates the feasibility of modulating BR responses to obtain desirable traits for breeding. Here, we review advances on how BR regulates various biological processes or agronomic traits such as plant architecture and grain yield in rice. We discuss how these functional specificities of BR can and could be utilized to enhance plant performance and productivity. We propose that unraveling the mechanisms underlying the diverse BR functions will favor BR application in molecular design for crop improvement.

A brassinosteroid responsive miRNA-target module regulates gibberellin biosynthesis and plant development

Plant growth and development are highly coordinated by hormones, including brassinosteroid (BR) and gibberellin (GA). Although much progress has been made in understanding the fundamental signaling transduction in BR and GA, their relationship remains elusive in rice. Here, we show that BR suppresses the level of OsmiR159d, which cleaves the target OsGAMYBL2 gene. The OsmiR159d-OsGAMYBL2 pair functions as an early BR-responsive module regulating the expression of BU1, a BR-regulated gene involved in BR signaling, and CPS1 and GA3ox2, two genes in GA biosynthesis, by binding to the promoters of these genes. Furthermore, OsGSK2, a key negative player in BR signaling, interacts with OsGAMYBL2 and prevents it from being degraded under 24-epibrassinolide treatment, whereas SLR1, a rice DELLA protein negatively regulating GA signaling, interacts with OsGAMYBL2 and prevents OsGAMYBL2 from binding to the target gene promoter. GA signaling induces degradation of OsGAMYBL2 and, consequently, enhances BR signaling. These results demonstrate that a BR-responsive module acts as a common component functioning in both BR and GA pathways, which connects BR signaling and GA biosynthesis, and thus coordinates the regulation of BR and GA in plant growth and development.

Crosstalk of the Brassinosteroid Signalosome with Phytohormonal and Stress Signaling Components Maintains a Balance between the Processes of Growth and Stress Tolerance

Brassinosteroids (BRs) are a class of phytohormones, which regulate various processes during plant life cycle. Intensive studies conducted with genetic, physiological and molecular approaches allowed identification of various components participating in the BR signaling—from the ligand perception, through cytoplasmic signal transduction, up to the BR-dependent gene expression, which is regulated by transcription factors and chromatin modifying enzymes. The identification of new components of the BR signaling is an ongoing process, however an emerging view of the BR signalosome indicates that this process is interconnected at various stages with other metabolic pathways. The signaling crosstalk is mediated by the BR signaling proteins, which function as components of the transmembrane BR receptor, by a cytoplasmic kinase playing a role of the major negative regulator of the BR signaling, and by the transcription factors, which regulate the BR-dependent gene expression and form a complicated regulatory system. This molecular network of interdependencies allows a balance in homeostasis of various phytohormones to be maintained. Moreover, the components of the BR signalosome interact with factors regulating plant reactions to environmental cues and stress conditions. This intricate network of interactions enables a rapid adaptation of plant metabolism to constantly changing environmental conditions.

Control of grain size in rice

Summary of rice grain size. Rice is one of the most important crops in the world. Increasing rice yield has been an urgent need to support the rapid growth of global population. The size of grains is one of major components determining rice yield; thus, grain size has been an essential target during rice breeding. Understanding the genetic and molecular mechanisms of grain size control can provide new strategies for yield improvement in rice. In general, the final size of rice grains is coordinately controlled by cell proliferation and cell expansion in the spikelet hull, which sets the storage capacity of the grain and limits grain filling. Recent studies have identified several quantitative trait loci and a number of genes as key grain size regulators. These regulators are involved in G protein signaling, the mitogen-activated protein kinase signaling pathway, the ubiquitin-proteasome pathway, phytohormone signalings, or transcriptional regulation. In this review, we summarize current knowledge on grain size control in rice and discuss the genetic and molecular mechanisms of these grain size regulators.

LTBSG1, a New Allele of BRD2, Regulates Panicle and Grain Development in Rice by Brassinosteroid Biosynthetic Pathway

Panicle architecture and grain size are two important agronomic traits which determine grain yield directly in rice. In the present study, a mutant named ltbsg1 (longer top branch and shorter grain 1) was isolated from the cultivar “Zhenong 34” (Oryza sativa L. ssp. indica) by ethyl methane sulfonate (EMS) mutagenesis. The target gene was studied through phenotype observation, genetic analysis, map-based cloning and functional analysis. The histocytological analysis indicated that the elongated top branch and shorter grain of mutant ltbsg1 were caused from the defects of cell elongation. The ltbsg1 gene in mutant revealed a single nucleotide substitution (G-A) in the exon 2 of LOC_Os10g25780, causing an amino acid variation (Glycine-Arginine) in the FAD (Flavin-adenine dinucleotide)-binding domain of delta (24)-sterol reductase, which was involved in the brassinosteroid (BR) biosynthesis. LTBSG1 was constitutively expressed and the protein was widely localized in chloroplast, nucleus and cytomembrane. The ltbsg1 seedlings had a lower endogenous BR level and could be restored to the phenotype of wild type by exogenous BR. The LTBSG1 knock-out lines showed similar phenotype defects as mutant ltbsg1, which confirmed that LTBSG1 was responsible for top branch elongation and grain size reduction. Furthermore, LTBSG1 along with other BR-related genes were feedback-regulated due to their obvious altered expression in mutant ltbsg1. This study demonstrated that LTBSG1 could play a new role in regulating panicle and grain development by BR biosynthetic pathway.

A Novel QTL qTGW3 Encodes the GSK3/SHAGGY-Like Kinase OsGSK5/OsSK41 that Interacts with OsARF4 to Negatively Regulate Grain Size and Weight in Rice

Grain size and shape are important determinants of grain weight and yield in rice. Here, we report a new major quantitative trait locus (QTL), qTGW3, that controls grain size and weight in rice. This locus, qTGW3, encodes OsSK41 (also known as OsGSK5), a member of the GLYCOGEN SYNTHASE KINASE 3/SHAGGY-like family. Rice near-isogenic lines carrying the loss-of-function allele of OsSK41 have increased grain length and weight. We demonstrate that OsSK41 interacts with and phosphorylates AUXIN RESPONSE FACTOR 4 (OsARF4). Co-expression of OsSK41 with OsARF4 increases the accumulation of OsARF4 in rice protoplasts. Loss of function of OsARF4 results in larger rice grains. RNA-sequencing analysis suggests that OsARF4 and OsSK41 repress the expression of a common set of downstream genes, including some auxin-responsive genes, during rice grain development. The loss-of-function form of OsSK41 at qTGW3 represents a rare allele that has not been extensively utilized in rice breeding. Suppression of OsSK41 function by either targeted gene editing or QTL pyramiding enhances rice grain size and weight. Thus, our study reveals the important role of OsSK41 in rice grain development and provides new candidate genes for genetic improvement of grain yield in rice and perhaps in other cereal crops.

An SPX-RLI1 Module Regulates Leaf Inclination in Response to Phosphate Availability in Rice

Leaf erectness is one of the key traits of plant architecture; in grains, plants with upright leaves can be planted close together, thus benefiting yield/unit area. Many factors, such as hormones, affect leaf inclination; however, how nutrition status, in particular phosphate (Pi) availability, affects leaf inclination remains largely unexplained. Here, we show that in rice (Oryza sativa), Pi deficiency stress inhibits lamina joint cell elongation, thus restricting lamina joint size and inducing leaf erectness in rice. The Pi starvation-induced proteins SPX1 (for Syg1/Pho81/XPR1) and SPX2 play a negative role in the regulation of leaf inclination. We further identified an SPX1-interacting protein, REGULATOR OF LEAF INCLINATION1 (RLI1), which positively regulates leaf inclination by affecting lamina joint cell elongation in rice. The rli1 mutants showed reduced leaf inclination and the RLI1 overexpressors showed increased leaf inclination. RLI1 directly activates the downstream genes BRASSINOSTEROID UPREGULATED1 (BU1) and BU1-LIKE 1 COMPLEX1 to control elongation of the lamina joint cells, therefore enhancing leaf inclination. We also found that Pi deficiency repressed the expression of RLI1 SPX1 protein interacts directly with RLI1, which could prevent RLI1 binding to the promoters of downstream genes. Therefore, SPX and RLI1 form a module to regulate leaf inclination in response to external Pi availability in rice.

Genome-wide association studies reveal that members of bHLH subfamily 16 share a conserved function in regulating flag leaf angle in rice (Oryza sativa)

As a major component of ideal plant architecture, leaf angle especially flag leaf angle (FLA) makes a large contribution to grain yield in rice. We utilized a worldwide germplasm collection to elucidate the genetic basis of FLA that would be helpful for molecular design breeding in rice. Genome-wide association studies (GWAS) identified a total of 40 and 32 QTLs for FLA in Wuhan and Hainan, respectively. Eight QTLs were commonly detected in both conditions. Of these, 2 and 3 QTLs were identified in the indica and japonica subpopulations, respectively. In addition, the candidates of 5 FLA QTLs were verified by haplotype-level association analysis. These results indicate diverse genetic bases for FLA between the indica and japonica subpopulations. Three candidates, OsbHLH153, OsbHLH173 and OsbHLH174, quickly responded to BR and IAA involved in plant architecture except for OsbHLH173, whose expression level was too low to be detected; their overexpression in plants increased rice leaf angle. Together with previous studies, it was concluded that all 6 members in bHLH subfamily 16 had the conserved function in regulating FLA in rice. A comparison with our previous GWAS for tiller angle (TA) showed only one QTL had pleiotropic effects on FLA and TA, which explained low similarity of the genetic basis between FLA and TA. An ideal plant architecture is expected to be efficiently developed by combining favorable alleles for FLA from indica with favorable alleles for TA from japonica by inter-subspecies hybridization.

OsmiR396d Affects Gibberellin and Brassinosteroid Signaling to Regulate Plant Architecture in Rice

Genetic improvement of plant architecture is one of the strategies for increasing the yield potential of rice (Oryza sativa). Although great progress has been made in the understanding of plant architecture regulation, the precise mechanism is still an urgent need to be revealed. Here, we report that over-expression of OsMIR396d in rice results in semidwarf and increased leaf angle, a typical phenotype of brassinosteroid (BR) enhanced mutant. OsmiR396d is involved in the interaction network of BR and gibberellin (GA) signaling. In OsMIR396d over-expression plants, BR signaling was enhanced. In contrast, both the signaling and biosynthesis of GA were impaired. BRASSINAZOLE-RESISTANT1, a core transcription activator of BR signaling, directly promoted the accumulation of OsmiR396d, which controlled BR response and GA biosynthesis by regulating the expression of different target genes respectively. GROWTH REGULATING FACTOR 6, one of OsmiR396d targets, participated in GA biosynthesis and signal transduction but was not directly involved in BR signaling. This study provides a new insight into the understanding of interaction between BR and GA from multiple levels on controlling plant architecture.

The genetic and molecular basis of crop height based on a rice model

This review presents genetic and molecular basis of crop height using a rice crop model. Height is controlled by multiple genes with potential to be manipulated through breeding strategies to improve productivity. Height is an important factor affecting crop architecture, apical dominance, biomass, resistance to lodging, tolerance to crowding and mechanical harvesting. The impressive increase in wheat and rice yield during the 'green revolution' benefited from a combination of breeding for high-yielding dwarf varieties together with advances in agricultural mechanization, irrigation and agrochemical/fertilizer use. To maximize yield under irrigation and high fertilizer use, semi-dwarfing is optimal, whereas extreme dwarfing leads to decreased yield. Rice plant height is controlled by genes that lie in a complex regulatory network, mainly involved in the biosynthesis or signal transduction of phytohormones such as gibberellins, brassinosteroids and strigolactones. Additional dwarfing genes have been discovered that are involved in other pathways, some of which are uncharacterized. This review discusses our current understanding of the regulation of plant height using rice as a well-characterized model and highlights some of the most promising research that could lead to the development of new, high-yielding varieties. This knowledge underpins future work towards the genetic improvement of plant height in rice and other crops.

Differential manipulation of leaf angle throughout the canopy: current status and prospects

Leaf angle is defined as the inclination between the midrib of the leaf blade and the vertical stem of a plant. This trait has been identified as a key component in the development of high-yielding varieties of cereal species, particularly maize, rice, wheat, and sorghum. The effect of leaf angle on light interception efficiency, photosynthetic rate, and yield has been investigated since the 1960s, yet, significant knowledge gaps remain in understanding the genetic control of this complex trait. Recent advances in physiology and modeling have proposed a plant ideotype with varying leaf angles throughout the canopy. In this context, we present historical and recent evidence of: (i) the effect of leaf angle on photosynthetic efficiency and yield; (ii) the hormonal regulation of this trait; (iii) the current knowledge on its quantitative genetic control; and (iv) the opportunity to utilize high-throughput phenotyping methods to characterize leaf angle at multiple canopy levels. We focus on research conducted on grass species of economic importance, with similar plant architecture and growth patterns. Finally, we present the challenges and strategies plant breeders will need to embrace in order to manipulate leaf angle differentially throughout the canopy and develop superior crops for food, feed, and fuel production.

Rice ERECT LEAF 1 acts in an alternative brassinosteroid signaling pathway independent of the receptor kinase OsBRI1

ERECT LEAF 1 (ELF1) was previously identified as a component of brassinosteroid signaling in rice. A double mutant obtained by crossing elf1-1 (a null mutant of ELF1) with d61-1 (a leaky mutant of OsBRI1) showed a more severe phenotype than did the elf1-1 single mutant, resembling that of a severe brassinosteroid-deficient mutant. Microarray analysis showed that the gene expression profile of elf1-1 was distinct from that of d61-12 (a leaky mutant of OsBRI1 with a phenotype similar to that of elf1-1), and fewer than half of genes differentially expressed between the wild-type and elf1-1 showed similar differences in d61-12 relative to the wild-type. These results indicate that less than half of ELF1-regulated genes in rice seedlings are affected by OsBRI1, and suggest that ELF1 acts in a rice brassinosteroid signaling pathway different from that initiated by OsBRI1. Gene expression analysis showed that some stress response-related genes were induced in elf1-1 but not in d61-12, and 8 of 9 genes oppositely regulated in elf1-1 and d61-12 were significantly up- or down-regulated in both elf1-1 and jasmonic acid-treated wild-type. These results imply that ELF1 suppresses stress-induced signalling, and that jasmonic acid signaling is stimulated in elf1-1; therefore, ELF1 may be involved in the brassinosteroid-mediated suppression of jasmonic acid response in rice.

08SG2/OsBAK1 regulates grain size and number, and functions differently in Indica and Japonica backgrounds in rice

BACKGROUND

Both grain size and grain number are significant for rice yield. In the past decade, a number of genes related to grain size and grain number have been documented, however, the regulatory mechanisms underlying them remains ambiguous.

RESULTS

We identified a rice small grain (sg2) mutant in an EMS mutant library generated from an indica variety, Shuhui498. Using the MutMap gene mapping strategy, we identified two linkage regions on chromosome 7 and 8, respectively, consistent with the segregation ratios in the F₂ population. We focused on the linkage region on chromosome 8, and named this locus as 08sg2. One of three SNPs identified in the linkage region was located in an exon of OsBAK1, leading to a nonsynonymous mutation in the kinase domain. The plant harboring the mutant version 08sg2 locus exhibited a decreased grain size, grain number and plant height. Cytological analysis indicated that 08SG2 regulated spikelet hull development by affecting cell proliferation. The grain size and number of knockout mutants of OsBAK1 in the japonica background were significantly decreased, but less so than in 08sg2, supporting the idea that the SNP in OsBAK1 was responsible for the 08sg2 phenotype, but that 08SG2/OsBAK1 function differently in indica and japonica backgrounds. 08sg2 was insensitive to 24-epiBL, and the expression of BR-related genes was obviously altered in 08sg2. The proportionally decreased grain length when 08sg2 and GS3 were combined indicate that 08SG2 and GS3 regulate grain length independently.

CONCLUSIONS

Our work shows that 08SG2/OsBAK1 is important for rice yield in both indica and japonica backgrounds, by regulating grain size and grain number, and the function of 08SG2/OsBAK1 is obviously affected by genetic background. The amino acid substituted in 08sg2 is highly conserved among different species, supporting the idea that it is important for the molecular function of 08SG2/OsBAK1. Together, our work is helpful for fully understanding the function of 08SG2/OsBAK1.

Top Bending Panicle1 is involved in brassinosteroid signaling and regulates the plant architecture in rice

Brassinosteroids (BRs) regulate several aspects of plant growth and development. Although extensive studies have shown that BR signaling is conservative in higher plants, the molecular mechanism of regulating plant architecture in rice still remains to be explored. Here, we characterized a rice mutant named top bending panicle1 (tbp1). Compared to wild type, tbp1 mutant plants displayed semi-dwarf stature, erect leaves, small and round grains, as well as more tillers. Remarkably, the panicles of tbp1 plants were shorter and denser, and the tops of the panicles were curved by rolling of the base of flag leaves, which was later verified as due to reduced bulliform cell numbers. Map-based cloning, together with transgenic complementation and RNA-interference tests, revealed that TBP1 is a member of the somatic embryogenesis receptor kinases (SERKs) family involved in BR signaling. Furthermore, bimolecular fluorescence complementation and co-immunoprecipitation analysis demonstrated that a substitution at 61st amino acid (^His61^Leu) in the tbp1 mutant may result in a reduction of the interaction between TBP1 and OsBRI1 (BR receptor in rice). Taken together, our results demonstrate that TBP1 plays a significant role in regulating plant architecture via the brassinosteroid signaling pathway.

Transcription Factor OsWRKY53 Positively Regulates Brassinosteroid Signaling and Plant Architecture

Brassinosteroids (BRs) are a class of steroid hormones regulating multiple aspects of plant growth, development, and adaptation. Compared with extensive studies in Arabidopsis (Arabidopsis thaliana), the mechanism of BR signaling in rice (Oryza sativa) is less understood. Here, we identified OsWRKY53, a transcription factor involved in defense responses, as an important regulator of rice BR signaling. Phenotypic analyses showed that OsWRKY53 overexpression led to enlarged leaf angles and increased grain size, in contrast to the erect leaves and smaller seeds in oswrky53 mutant. In addition, the oswrky53 exhibited decreased BR sensitivity, whereas OsWRKY53 overexpression plants were hypersensitive to BR, suggesting that OsWRKY53 positively regulates rice BR signaling. Moreover, we show that OsWRKY53 can interact with and be phosphorylated by the OsMAPKK4-OsMAPK6 cascade, and the phosphorylation is required for the biological function of OsWRKY53 in regulating BR responses. Furthermore, we found that BR promotes OsWRKY53 protein accumulation but represses OsWRKY53 transcript level. Taken together, this study revealed the novel role of OsWRKY53 as a regulator of rice BR signaling and also suggested a potential role of OsWRKY53 in mediating the cross talk between the hormone and other signaling pathways.

Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon

BACKGROUND

As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae.

RESULTS

A total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies. BdbHLHs in the same subfamily share similar protein motifs and gene structures. Gene duplication events showed a close relationship to rice, maize and sorghum, and segment duplications might play a key role in the expansion of this gene family. The amino acid sequence of the bHLH domains were quite conservative, especially Leu-27 and Leu-54. Based on the predicted binding activities, the BdbHLHs were divided into DNA binding and non-DNA binding types. According to the gene ontology (GO) analysis, BdbHLHs were speculated to function in homodimer or heterodimer manner. By integrating the available high throughput data in public database and results of quantitative RT-PCR, we found the expression profiles of BdbHLHs were different, implying their differentiated functions.

CONCLUSION

One hundred fourty-six BdbHLHs were identified and their conserved domains, sequence features, phylogenetic relationship, chromosomal distribution, GO annotations, gene structures, gene duplication and expression profiles were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of BdbHLH genes.

Overexpression of SlPRE2, an atypical bHLH transcription factor, affects plant morphology and fruit pigment accumulation in tomato

The basic helix-loop-helix (bHLH) proteins are a large family of transcription factors that control various developmental processes in eukaryotes, but the biological roles of most bHLH proteins are not very clear, especially in tomato. In this study, a PRE-like atypical bHLH gene was isolated and designated as SlPRE2 in tomato. SlPRE2 was highly expressed in immature-green fruits, moderately in young leaves, flowers, and mature-green fruits. To further research the function of SlPRE2, a 35 S:PRE2 binary vector was constructed and transformed into wild type tomato. The transgenic plants showed increased leaf angle and stem internode length, rolling leaves with decreased chlorophyll content. The water loss rate of detached leaves was increased in young transgenic lines but depressed in mature leaves. Besides, overexpression of SlPRE2 promoted morphogenesis in seedling development, producing light-green unripening fruits and yellowing ripen fruits with reduced chlorophyll and carotenoid accumulation in pericarps, respectively. Quantitative RT-PCR analysis showed that expression of the chlorophyll related genes, such as GOLDEN 2-LIKE and RbcS, were decreased in unripening 35  S:PRE2 fruit, and carotenoid biosynthesis-related genes PHYTOENE SYNTHASE1A and ζ-CAROTENE DESATURASE in ripening fruit were also down-regulated. These results suggest that SlPRE2 affects plant morphology and is a negative regulator of fruit pigment accumulation.

Dynamic Cytology and Transcriptional Regulation of Rice Lamina Joint Development

Rice (Oryza sativa) leaf angle is determined by lamina joint and is an important agricultural trait determining leaf erectness and, hence, the photosynthesis efficiency and grain yield. Genetic studies reveal a complex regulatory network of lamina joint development; however, the morphological changes, cytological transitions, and underlying transcriptional programming remain to be elucidated. A systemic morphological and cytological study reveals a dynamic developmental process and suggests a common but distinct regulation of the lamina joint. Successive and sequential cell division and expansion, cell wall thickening, and programmed cell death at the adaxial or abaxial sides form the cytological basis of the lamina joint, and the increased leaf angle results from the asymmetric cell proliferation and elongation. Analysis of the gene expression profiles at four distinct developmental stages ranging from initiation to senescence showed that genes related to cell division and growth, hormone synthesis and signaling, transcription (transcription factors), and protein phosphorylation (protein kinases) exhibit distinct spatiotemporal patterns during lamina joint development. Phytohormones play crucial roles by promoting cell differentiation and growth at early stages or regulating the maturation and senescence at later stages, which is consistent with the quantitative analysis of hormones at different stages. Further comparison with the gene expression profile of leaf inclination1, a mutant with decreased auxin and increased leaf angle, indicates the coordinated effects of hormones in regulating lamina joint. These results reveal a dynamic cytology of rice lamina joint that is fine-regulated by multiple factors, providing informative clues for illustrating the regulatory mechanisms of leaf angle and plant architecture.

The RLA1/SMOS1 Transcription Factor Functions with OsBZR1 to Regulate Brassinosteroid Signaling and Rice Architecture

Brassinosteroids (BRs) are plant-specific steroid hormones that control plant growth and development. Recent studies have identified key components of the BR signaling pathway in Arabidopsis thaliana and in rice (Oryza sativa); however, the mechanism of BR signaling in rice, especially downstream of GSK3/SHAGGY-like kinase (GSK2), remains unclear. Here, we identified a BR-insensitive rice mutant, reduced leaf angle1 (rla1), and cloned the corresponding gene. RLA1 was identical to the previously reported SMALL ORGAN SIZE1 (SMOS1), which was cloned from another allele. RLA1/SMOS1 encodes a transcription factor with an APETALA2 DNA binding domain. Genetic analysis indicated that RLA1/SMOS1 functions as a positive regulator in the BR signaling pathway and is required for the function of BRASSINAZOLE-RESISTANT1 (OsBZR1). In addition, RLA1/SMOS1 can interact with OsBZR1 to enhance its transcriptional activity. GSK2 can interact with and phosphorylate RLA1/SMOS1 to reduce its stability. These results demonstrate that RLA1/SMOS1 acts as an integrator of the transcriptional complex directly downstream of GSK2 and plays an essential role in BR signaling and plant development in rice.

A novel trimeric complex in plant cells that contributes to the lamina inclination of rice

The architecture determining grain production in rice is mainly affected by factors such as lamina angle, tillering, plant height and panicle morphology. In particular, leaf angle, the degree of bending between the leaf blade and leaf sheath directly affects crop architecture and grain yields. Balancing activities between the 2 antagonistic groups of proteins, atypical helix-loop-helix (HLH) and basic HLH (bHLH) proteins have been regarded as one of the major molecular machineries regulating lamina angles through the control of cell elongation in the lamina joint of rice. Recently, formation of a complex consisting of atypical HLH protein, OsBUL1, a KxDL motif-containing protein, LO9-177 and a bHLH protein, OsBC1 has been reported to play a positive role in lamina inclination of rice unraveling a novel layer of cell elongation control in rice lamina joint. Here, we demonstrate a trimeric complex formation in rice cells by a combination of BiFC and FRET-FLIM assays.