Rice CYP734A cytochrome P450s inactivate brassinosteroids in Arabidopsis

Brassinosteroid catabolic enzyme CYP734A129 regulates the morphologies of leaves and floral organs in woodland strawberry

Brassinosteroids (BRs) play critical roles in plant growth and development and regulate many important agronomic traits. However, the functions of BRs in strawberry are unclear. This study identified two mutants, named P6 and R87, in woodland strawberry (Fragaria vesca) from EMS mutagenesis populations that exhibit narrow leaves, petals and sepals. Mapping by sequencing and genetic studies revealed that the F. vesca CYP734A129, encoding a putative BR catabolic enzyme, is the causative gene for both P6 and R87. Overexpression of CYP734A129 in both F. vesca and Arabidopsis causes a severe dwarf phenotype, and the BRI1-EMS-SUPPRESSOR 1 (BES1) protein is less abundant in the CYP734A129-overexpressing Arabidopsis seedlings. This suggests that CYP734A129 is functionally conserved with CYP734A1, as a BR-inactivating enzyme. Transcriptome analysis of young leaves revealed that four BR biosynthetic genes were significantly downregulated in P6 (cyp734a129), and photosynthesis-related genes were highly enriched among the up-regulated genes in P6 compared to the wild type. This further supports that CYP734A129 inactivates BRs in F. vesca. Furthermore, we showed that mutations in CYP734A129 do not affect fruit shape and color during ripening in strawberry. Overall, our results suggest that F. vesca CYP734A129 is a BR catabolic enzyme, and provide insights into the roles of CYP734A129 in strawberry.

Identification of P450 Candidates Associated with the Biosynthesis of Physalin-Class Compounds in Physalis angulata

The Physalis genus has long been used as traditional medicine in the treatment of various diseases. Physalins, the characteristic class of compounds in this genus, are major bioactive constituents. To date, the biogenesis of physalins remains largely unknown, except for the recently established knowledge that 24-methyldesmosterol is a precursor of physalin. To identify the genes encoding P450s that are putatively involved in converting 24-methyldesmosterol to physalins, a total of 306 P450-encoding unigenes were retrieved from our recently constructed P. angulata transcriptome. Extensive phylogenetic analysis proposed 21 P450s that might participate in physalin biosynthesis. To validate the candidates, we developed a virus-induced gene silencing (VIGS) system for P. angulata, and four P450 candidates were selected for the VIGS experiments. The reduction in the transcripts of the four P450 candidates by VIGS all led to decreased levels of physalin-class compounds in the P. angulata leaves. Thus, this study provides a number of P450 candidates that are likely associated with the biosynthesis of physalin-class compounds, forming a strong basis to reveal the unknown physalin biosynthetic pathway in the future.

Genome-Wide Identification and Expression Profiling of Cytochrome P450 Monooxygenase Superfamily in Foxtail Millet

The cytochrome P450 monooxygenases (CYP450) are the largest enzyme family in plant metabolism and widely involved in the biosynthesis of primary and secondary metabolites. Foxtail millet (Setaria italica (L.) P. Beauv) can respond to abiotic stress through a highly complex polygene regulatory network, in which the SiCYP450 family is also involved. Although the CYP450 superfamily has been systematically studied in a few species, the research on the CYP450 superfamily in foxtail millet has not been completed. In this study, three hundred and thirty-one SiCYP450 genes were identified in the foxtail millet genome by bioinformatics methods, which were divided into four groups, including forty-six subgroups. One hundred and sixteen genes were distributed in thirty-three tandem duplicated gene clusters. Chromosome mapping showed that SiCYP450 was distributed on seven chromosomes. In the SiCYP450 family of foxtail millet, 20 conserved motifs were identified. Cis-acting elements in the promoter region of SiCYP450 genes showed that hormone response elements were found in all SiCYP450 genes. Of the three hundred and thirty-one SiCYP450 genes, nine genes were colinear with the Arabidopsis thaliana genes. Two hundred SiCYP450 genes were colinear with the Setaria viridis genes, including two hundred and forty-five gene duplication events. The expression profiles of SiCYP450 genes in different organs and developmental stages showed that SiCYP450 was preferentially expressed in specific tissues, and many tissue-specific genes were identified, such as SiCYP75B6, SiCYP96A7, SiCYP71A55, SiCYP71A61, and SiCYP71A62 in the root, SiCYP78A1 and SiCYP94D9 in leaves, and SiCYP78A6 in the ear. The RT-PCR data showed that SiCYP450 could respond to abiotic stresses, ABA, and herbicides in foxtail millet. Among them, the expression levels of SiCYP709B4, SiCYP71A11, SiCYP71A14, SiCYP78A1, SiCYP94C3, and SiCYP94C4 were significantly increased under the treatment of mesotrione, florasulam, nicosulfuron, fluroxypyr, and sethoxydim, indicating that the same gene might respond to multiple herbicides. The results of this study will help reveal the biological functions of the SiCYP450 family in development regulation and stress response and provide a basis for molecular breeding of foxtail millet.

Transcriptomic analysis of Chinese yam (Dioscorea polystachya Turcz.) variants indicates brassinosteroid involvement in tuber development

Dioscorea is an important but underutilized genus of flowering plants that grows predominantly in tropical and subtropical regions. Several species, known as yam, develop large underground tubers and aerial bulbils that are used as food. The Chinese yam (D. polystachya Turcz.) is one of the few Dioscorea species that grows well in temperate regions and has been proposed as a climate-resilient crop to enhance food security in Europe. However, the fragile, club-like tubers are unsuitable for mechanical harvesting, which is facilitated by shorter and thicker storage organs. Brassinosteroids (BRs) play a key role in plant cell division, cell elongation and proliferation, as well as in the gravitropic response. We collected RNA-Seq data from the head, middle and tip of two tuber shape variants: F60 (long, thin) and F2000 (short, thick). Comparative transcriptome analysis of F60 vs. F2000 revealed 30,229 differentially expressed genes (DEGs), 1,393 of which were differentially expressed in the growing tip. Several DEGs are involved in steroid/BR biosynthesis or signaling, or may be regulated by BRs. The quantification of endogenous BRs revealed higher levels of castasterone (CS), 28-norCS, 28-homoCS and brassinolide in F2000 compared to F60 tubers. The highest BR levels were detected in the growing tip, and CS was the most abundant (439.6 ± 196.41 pmol/g in F2000 and 365.6 ± 112.78 pmol/g in F60). Exogenous 24-epi-brassinolide (epi-BL) treatment (20 nM) in an aeroponic system significantly increased the width-to-length ratio (0.045 ± 0.002) compared to the mock-treated plants (0.03 ± 0.002) after 7 weeks, indicating that exogenous epi-BL produces shorter and thicker tubers. In this study we demonstrate the role of BRs in D. polystachya tuber shape, providing insight into the role of plant hormones in yam storage organ development. We found that BRs can influence tuber shape in Chinese yam by regulating the expression of genes involved cell expansion. Our data can help to improve the efficiency of Chinese yam cultivation, which could provide an alternative food source and thus contribute to future food security in Europe.

The fine mapping of dwarf gene Rht5 in bread wheat and its effects on plant height and main agronomic traits

Rht5 was narrowed to an approximately 1 Mb interval and had pleiotropic effects on plant height, spike length and grain size. TraesCS3B02G025600 was predicted as the possible candidate gene. Plant height is an important component related to plant architecture, lodging resistance, and yield performance. The utilization of dwarf genes has made great contributions to wheat breeding and production. In this study, two F₂ populations derived from the crosses of Jinmai47 and Ningchun45 with Marfed M were employed to identify the genetic region of reduce plant height 5 (Rht5), and their derived lines were used to evaluate its effects on plant height and main agronomic traits. Rht5 was fine-mapped between markers Kasp-25 and Kasp-23, in approximately 1 Mb region on chromosome 3BS, which harbored 17 high-confidence annotated genes based on the reference genome of Chinese Spring (IWGSC RefSeq v1.1). TraesCS3B02G025600 were predicted as the possible candidate gene based on its differential expression and sequence variation between dwarf and tall lines and parents. The results of phenotypic evaluation showed that Rht5 had pleiotropic effects on plant height, spike length, culm diameter, grain size and grain yield. The plant height of Rht5 dwarf lines was reduced by an average of 32.67% (32.53 cm) and 27.84% (33.62 cm) in the Jinmai47 and Ningchun45 population, respectively. While Rht5 showed significant and negative pleiotropic effects on culm diameter, aboveground biomass, grain yield, spike length, spikelet number, grain number per spike, grain size, grain weight and filling degree of basal second internode. The culm lodging resistance index (CLRI) of dwarf lines was significantly higher than that of tall lines in the two population. In conclusion, these results lay a foundation for understanding the dwarfing mechanism of Rht5.

Cytochrome P450 Superfamily: Evolutionary and Functional Divergence in Sorghum (Sorghum bicolor) Stress Resistance

Cytochrome P450 (CYP) genes encode enzymes that catalyze various growth-, development-, and stress-related reactions. Sorghum (Sorghum bicolor) is a type of C4 plant and an important cash crop. However, systematic identification and analysis of functional differentiation and evolution of CYP genes have not been carried out in this species. In the present study, we revealed that the sorghum genome contains 351 CYP genes, which can be divided into nine classes. These genes are from ancestors and repeated segments, rather than tandem repeats. Based on collinearity results, a large number of CYPs were extended before cotyledon differentiation, during the emergence of Gramineae, suggesting that genomewide duplication events and stress adaptation processes were important for the expansion of CYP genes. Their gene structure and motifs contain conserved regions and include various changes and loci. The expression characteristics and functional annotation of CYP genes indicated tissue specificity and selective expression. Overall, we identified all CYP genes in the sorghum genome and preliminarily explored their naming, structure, evolution, expression, and functional differentiation. The results advanced our understanding of plant gene family evolution and functional differentiation.

Two ATAF transcription factors ANAC102 and ATAF1 contribute to the suppression of cytochrome P450-mediated brassinosteroid catabolism in Arabidopsis

PHYB ACTIVATION TAGGED SUPPRESSOR 1 (BAS1) and SUPPRESSOR OF PHYB-4 7 (SOB7) are two cytochrome P450 enzymes that inactivate brassinosteroids (BRs) in Arabidopsis. The NAC transcription factor (TF) ATAF2 (ANAC081) and the core circadian clock regulator CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) both suppress the expression of BAS1 and SOB7 via direct promoter binding. Additionally, BRs cause feedback suppression on ATAF2 expression. Here, we report that two ATAF-subgroup TFs, ANAC102 and ATAF1 (ANAC002), also contribute to the transcriptional suppression of BAS1 and SOB7. ANAC102 and ATAF1 gene-knockout mutants exhibit elevated expression of both BAS1 and SOB7, expanded tissue-level accumulation of their protein products and reduced hypocotyl growth in response to exogenous BR treatments. Similar to ATAF2, both ANAC102 and ATAF1 are transcriptionally suppressed by BRs and white light. Neither BAS1 nor SOB7 expression is further elevated in ATAF double or triple mutants, suggesting that the suppression effect of these three ATAFs is not additive. In addition, ATAF single, double, and triple mutants have similar levels of BR responsiveness with regard to hypocotyl elongation. ATAF2, ANAC102, ATAF1, and CCA1 physically interact with itself and each other, suggesting that they may coordinately suppress BAS1 and SOB7 expression via protein-protein interactions. Despite the absence of CCA1-binding elements in their promoters, ANAC102 and ATAF1 have similar transcript circadian oscillation patterns as that of CCA1, suggesting that these two ATAF genes may be indirectly regulated by the circadian clock.

Self-transcriptional repression of the Arabidopsis NAC transcription factor ATAF2 and its genetic interaction with phytochrome A in modulating seedling photomorphogenesis

The NAC transcription factor ATAF2 suppresses its own transcription via self-promoter binding. ATAF2 genetically interacts with the circadian regulator CCA1 and phytochrome A to modulate seedling photomorphogenesis in Arabidopsis thaliana. ATAF2 (ANAC081) is a NAC (NAM, ATAF and CUC) transcription factor (TF) that participates in the regulation of disease resistance, stress tolerance and hormone metabolism in Arabidopsis thaliana. We previously reported that ATAF2 promotes Arabidopsis hypocotyl growth in a light-dependent manner via transcriptionally suppressing the brassinosteroid (BR)-inactivating cytochrome P450 genes BAS1 (CYP734A1, formerly CYP72B1) and SOB7 (CYP72C1). Assays using low light intensities suggest that the photoreceptor phytochrome A (PHYA) may play a more critical role in ATAF2-regulated photomorphogenesis than phytochrome B (PHYB) and cryptochrome 1 (CRY1). In addition, ATAF2 is also regulated by the circadian clock. The core circadian TF CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) physically interacts with ATAF2 at the DNA-protein and protein-protein levels, and both differentially suppress BAS1- and SOB7-mediated BR catabolism. In this research, we show that ATAF2 can bind its own promoter as a transcriptional self-repressor. This self-feedback-suppression loop is a typical feature of multiple circadian-regulated genes. Additionally, ATAF2 and CCA1 synergistically suppress seedling photomorphogenesis as reflected by the light-dependent hypocotyl growth analysis of their single and double gene knock-out mutants. Similar fluence-rate response assays using ATAF2 and photoreceptor (PHYB, CRY1 and PHYA) knock-out mutants demonstrate that PHYA is required for ATAF2-regulated photomorphogenesis in a wide range of light intensities. Furthermore, disruption of PHYA can suppress the BR-insensitive hypocotyl-growth phenotype of ATAF2 loss-of-function seedlings in the light, but not in darkness. Collectively, our results provide a genetic interaction synopsis of the circadian-clock-photomorphogenesis-BR integration node involving ATAF2, CCA1 and PHYA.

Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize

BACKGROUND

The cytochrome P450s (CYP450s) as the largest enzyme family of plant metabolism participate in various physiological processes, whereas no study has demonstrated interest in comprehensive comparison of the genes in wheat and maize. Genome-wide survey, characterization and comparison of wheat and maize CYP450 gene superfamily are useful for genetic manipulation of the Gramineae crops.

RESULTS

In total, 1285 and 263 full-length CYP450s were identified in wheat and maize, respectively. According to standard nomenclature, wheat CYP450s (TaCYP450s) were categorized into 45 families, while maize CYP450s (ZmCYP450s) into 43 families. A comprehensive analysis of wheat and maize CYP450s, involved in functional domains, conserved motifs, phylogeny, gene structures, chromosome locations and duplicated events was performed. The result showed that each family/subfamily in both species exhibited characteristic features, suggesting their phylogenetic relationship and the potential divergence in their functions. Functional divergence analysis at the amino acid level of representative clans CYP51, CYP74 and CYP97 in wheat, maize and rice identified some critical amino acid sites that are responsible for functional divergence of a gene family. Expression profiles of Ta-, ZmCYP450s were investigated using RNA-seq data, which contribute to infer the potential functions of the genes during development and stress responses. We found in both species CYP450s had preferential expression in specific tissues, and many tissue-specific genes were identified. Under water-deficit condition, 82 and 39 significantly differentially expressed CYP450s were respectively detected in wheat and maize. These genes may have some roles in protecting plants against drought damage. Thereinto, fourteen CYP450s were selected to validate their expression level through qRT-PCR. To further elucidating molecular mechanisms of CYP450 action, gene co-expression network was constructed. In total, 477 TaCYP450s were distributed in 22 co-expression modules, and some co-expressed genes that likely take part in the same biochemical pathway were identified. For instance, the expression of TaCYP74A98_4D was highly correlated with TaLOX9, TaLOX36, TaLOX39, TaLOX44 and TaOPR8, and all of them may be involved in jasmonate (JA) biosynthesis. TaCYP73A201_3A showed coexpression with TaPAL1.25, TaCCoAOMT1.2, TaCOMT.1, TaCCR1.6 and TaLAC5, which probably act in the wheat stem and/or root lignin synthesis pathway.

CONCLUSION

Our study first established systematic information about evolutionary relationship, expression pattern and function characterization of CYP450s in wheat and maize.

CIRCADIAN CLOCK ASSOCIATED 1 and ATAF2 differentially suppress cytochrome P450-mediated brassinosteroid inactivation

Brassinosteroids (BRs) are a group of steroid hormones regulating plant growth and development. Since BRs do not undergo transport among plant tissues, their metabolism is tightly regulated by transcription factors (TFs) and feedback loops. BAS1 (CYP734A1, formerly CYP72B1) and SOB7 (CYP72C1) are two BR-inactivating cytochrome P450s identified in Arabidopsis thaliana. We previously found that a TF ATAF2 (ANAC081) suppresses BAS1 and SOB7 expression by binding to the Evening Element (EE) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1)-binding site (CBS) on their promoters. Both the EE and CBS are known binding targets of the circadian regulatory protein CCA1. Here, we confirm that CCA1 binds the EE and CBS motifs on BAS1 and SOB7 promoters, respectively. Elevated accumulations of BAS1 and SOB7 transcripts in the CCA1 null mutant cca1-1 indicate that CCA1 is a repressor of their expression. When compared with either cca1-1 or the ATAF2 null mutant ataf2-2, the cca1-1 ataf2-2 double mutant shows higher SOB7 transcript accumulations and a stronger BR-insensitive phenotype of hypocotyl elongation in white light. CCA1 interacts with ATAF2 at both DNA-protein and protein-protein levels. ATAF2, BAS1, and SOB7 are all circadian regulated with distinct expression patterns. These results demonstrate that CCA1 and ATAF2 differentially suppress BAS1- and SOB7-mediated BR inactivation.

Regulation of Brassinosteroid Homeostasis in Higher Plants

Brassinosteroids (BRs) are known as one of the major classes of phytohormones essential for various processes during normal plant growth, development, and adaptations to biotic and abiotic stresses. Significant progress has been achieved on revealing mechanisms regulating BR biosynthesis, catabolism, and signaling in many crops and in model plant Arabidopsis. It is known that BRs control plant growth and development in a dosage-dependent manner. Maintenance of BR homeostasis is therefore critical for optimal functions of BRs. In this review, updated discoveries on mechanisms controlling BR homeostasis in higher plants in response to internal and external cues are discussed.

Global transcriptome and gene co-expression network analyses on the development of distyly in Primula oreodoxa

Distyly is a genetically controlled flower polymorphism that has intrigued both botanists and evolutionary biologists ever since Darwin's time. Despite extensive reports on the pollination and evolution of distylous systems, the genetic basis and mechanism of molecular regulation remain unclear. In the present study, comparative transcriptome profiling was conducted in primrose (Primula oreodoxa), the prime research model for heterostyly. Thirty-six transcriptomes were sequenced for styles at different stages and corolla tube in the three morphs of P. oreodoxa. Large numbers of differentially expressed genes (DEGs) were detected in the transcriptomes of styles across different morphs. Several transcription factors (TFs) and phytohormone metabolism-related genes were highlighted in S-morphs. A growing number of genes showed differential expression patterns along with the development of styles, suggesting that the genetic control of distyly may be more complicated than ever expected. Analysis of co-expression networks and module-trait relationships identified modules significantly associated with style development. CYP734A50, a key S-locus gene whose products degrade brassinosteroids, was co-expressed with many genes in the module and showed significant negative association with style length. In addition, crucial TFs involved in phytohormone signaling pathways were found to be connected with CYP734A50 in the co-expression module. Our global transcriptomic analysis has identified DEGs that are potentially involved in regulation of style length in P. oreodoxa, and may shed light on the evolution and broad biological processes of heterostyly.

Comparative Analysis of Transcriptomes to Identify Genes Associated with Fruit Size in the Early Stage of Fruit Development in Pyrus pyrifolia

Pear (Pyrus L.) is an important commercial fruit in the world. The fruit size is one of the important characters in fruit quality. The previous research reported that the fruit size of pear was mainly caused by the number of cell in about 40 days after blossom (DAB) in nature. However, studies about the mechanisms underlying cell division in young fruit development are very limited in pear. Two pear accessions codenamed ‘GH59B’ with big fruit and ‘GH81S’ with small fruit in three stages were sampled and the RNA-seq high-throughput sequencing was used to evaluate changes of gene transcription levels in the early stage of fruit development. The difference of cell size among two samples was little in 40 DAB, implying that the difference of the fruit size was caused by the number of the cell. More than 274,517,982 high quality reads from six libraries of fruit development were sequenced. A total of 797 differentially expressed genes (DEGs) were identified. Three cytokinin dehydrogenase genes and two gibberellin 2-beta-dioxygenase gene were identified in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to zeatin and gibberellin. Their expression was upregulated at 20 DAB in ‘GH81S’ and at 30 DAB in ‘GH59B’, suggesting that the small fruit size might be related to the early degradation of cytokinin and gibberellin inducing a short period of cell division. A total of 38 DEGs of transcription factors were found and 23 DEGs including NAC, ERF and bHLH transcription factors were highly related with cytokinin dehydrogenase and gibberellin dioxygenase genes. Altogether, the results of the present study provide information from a comprehensive gene expression analysis and insight into the molecular mechanism underlying the difference of fruit size in Pyrus pyrifolia.

A short story gets longer: recent insights into the molecular basis of heterostyly

Heterostyly is a fascinating adaptation to promote outbreeding and a classical paradigm of botany. In the most common type of heterostyly, plants either form flowers with long styles and short stamens, or short styles and long stamens. This reciprocal organ positioning reduces pollen wastage and promotes cross-pollination, thus increasing male fitness. In addition, in many heterostylous species selfing and the generation of unfit progeny due to inbreeding depression is limited by a self-incompatibility system, thus promoting female fitness. The two floral forms are genetically determined by the S locus as a complex supergene, namely a chromosomal region containing several individual genes that control the different traits, such as style or stamen length, and are held together by very tight linkage due to suppressed recombination. Recent molecular-genetic studies in several systems, including Turnera, Fagopyrum, Linum, and Primula have begun to identify and characterize the causal heterostyly genes residing at the S locus. An emerging theme from several families is that the dominant S haplotype represents a hemizygous region not present on the recessive s haplotype. This provides an explanation for the suppressed recombination and suggests a scenario for the chromosomal evolution of the S locus. In this review, we discuss the results from recent molecular-genetic analyses in light of the classical models on the genetics and evolution of heterostyly.

Transcriptional Regulation of Brassinosteroid Accumulation during Carrot Development and the Potential Role of Brassinosteroids in Petiole Elongation

It is widely known that brassinosteroids (BRs) are involved in various physiological processes during plant growth and development. Roles of BRs have been reported in many plants. However, relevant report is yet not found in carrot. Carrot is a nutrient-rich vegetable from the Apiaceae family. Here, we measured the bioactive contents of BRs at five successive stages and analyzed the expression profiles of genes involved in BR biosynthesis, signaling pathway and catabolism. We found that most biosynthesis regulated genes had higher expression level at the first development stage of carrot and the catabolism gene BAS1/CYP734A1 had significantly high expression level at the first stage in carrot roots and petioles. In addition, we treated carrot plants with exogenous 24-epibrassinolide (24-EBL) and examined the morphological changes after treating. Compared with control plants, carrot plants treated with 24-EBL had higher plant height, more number of petioles and heavier aboveground weight. The expression levels of DcBRI1, DcBZR1, and DcBSU1 in the petioles were significantly up-regulated by treating with exogenous 24-EBL. The expression profiles of DcCYP734A1 were all significantly up-regulated in the three organs when treated with 0.5 mg/L 24-EBL. The elongation of carrot petioles can be promoted by treating with exogenous 24-EBL. These results indicate that BRs playing potential roles during the growth and development of carrot.

Novel rice mutants overexpressing the brassinosteroid catabolic gene CYP734A4

Moderate overexpression of CYP734A4 improves grain number per main panicle and seed setting rate. Brassinosteroid (BR) homeostasis and signaling are crucial for plant growth and development. CYP734A genes encode cytochrome P450 monooxygenases that control the level of bioactive BRs by degrading BRs. However, fertile plants overexpressing CYP734As have not been reported in rice. Here, we isolated a novel semi-dominant mutant brd3-D, in which T-DNA was inserted approximately 4 kb upstream of the CYP734A4 gene (GenBank Accession AB488667), causing its overexpression. The mutant is characterized by dwarfism, small grains, and erect leaves and is less sensitive to brassinolide-induced lamina joint inclination and primary root elongation. However, increased grain number per main panicle and improved seed setting rate were also found in heterozygous brd3-D. To our knowledge, these traits have not been reported in other BR deficient mutants. Quantitative real-time PCR analysis indicated that phenotypic severity of the brd3-D mutant is positively correlated with the CYP734A4 transcription level. In accordance with the increased expression of CYP734A4, a lower castasterone (a rice BR) content was detected in the brd3-D mutants. Knockout of brd3-D by using the CRISPR/Cas9 system rescued the mutation. In addition, transgenic plants overexpressing CYP734A4 with the 35S enhancer mimicked the brd3-D phenotypes, confirming that moderate overexpression of the CYP734A4 gene can improve grain number per main panicle and the seed setting rate in rice. Further studies showed that overexpression of CYP734A4 influences the expressions of multiple genes involved in the BR pathway, and the expression of CYP734A4 is induced by exogenous brassinolide, confirming the negative regulatory role of CYP734A4 in the BR pathway. CYP734A4 might provide a useful gene resource for developing new high-yielding rice varieties.

Presence versus absence of CYP734A50 underlies the style-length dimorphism in primroses

Heterostyly is a wide-spread floral adaptation to promote outbreeding, yet its genetic basis and evolutionary origin remain poorly understood. In Primula (primroses), heterostyly is controlled by the S-locus supergene that determines the reciprocal arrangement of reproductive organs and incompatibility between the two morphs. However, the identities of the component genes remain unknown. Here, we identify the Primula CYP734A50 gene, encoding a putative brassinosteroid-degrading enzyme, as the G locus that determines the style-length dimorphism. CYP734A50 is only present on the short-styled S-morph haplotype, it is specifically expressed in S-morph styles, and its loss or inactivation leads to long styles. The gene arose by a duplication specific to the Primulaceae lineage and shows an accelerated rate of molecular evolution. Thus, our results provide a mechanistic explanation for the Primula style-length dimorphism and begin to shed light on the evolution of the S-locus as a prime model for a complex plant supergene.

DOI:http://dx.doi.org/10.7554/eLife.17956.001

Flowers are highly specialized structures that many plants use to reproduce. Male organs called stamens on the flowers make pollen that can be transferred – usually by insect carriers or the wind – to a female structure called the stigma on another plant. However, since many flowers contain both male and female organs, it is also possible for the pollen to land on the stigma of the same flower, leading to a process called “self-fertilization”.

Many plants have developed mechanisms that prevent self-fertilization. For example, primroses produce two different types of flowers that arrange their stamens and stigmas differently. The stigma sits on the top of a stalk known as the style. Some primroses produce flowers with short stamens and a long style, resulting in the stigma being located high up in the flower (“pin” flowers), while others produce flowers with a short style and long stamens (“thrum” flowers). Primrose pollen is carried by insects and the different lengths of the styles and stamens make it more likely that pollen from a pin flower will land on the stigma of a thrum flower instead of a pin flower (and vice versa).

Although primrose flowers have fascinated botanists for centuries, the genes responsible for making the two types of flower had not been identified. Genetic studies indicated that different genes control the length of the stamens and style. However, these genes appear to be very close to each other on primrose DNA, which made it difficult to study them individually.

Huu et al. identified a gene called CYP734A50 that is responsible for the difference in style length in the flowers of a primrose called Primula veris. The gene is only present in the plants that have thrum flowers across a wide range of primrose species and genetic mutations that inactivate the gene in these plants result in flowers with longer styles. CYP734A50 encodes an enzyme that breaks down plant hormones called brassinosteroids, which normally promote growth. Treating thrum flowers with brassinosteroids increased the length of the styles. Future challenges are to identify the other genes that are responsible for producing pin and thrum flowers and to understand how this group of genes evolved.

DOI:http://dx.doi.org/10.7554/eLife.17956.002

Overexpression of OsDof12 affects plant architecture in rice (Oryza sativa L.)

Dof (DNA binding with one finger) proteins, a class of plant-specific transcription factors, are involved in plant growth and developmental processes and stress responses. However, their biological functions remain to be elucidated, especially in rice (Oryza sativa L.). Previously, we have reported that OsDof12 can promote rice flowering under long-day conditions. Here, we further investigated the other important agronomical traits of the transgenic plants overexpressing OsDof12 and found that overexpressing OsDof12 could lead to reduced plant height, erected leaf, shortened leaf blade, and smaller panicle resulted from decreased primary and secondary branches number. These results implied that OsDof12 is involved in rice plant architecture formation. Furthermore, we performed a series of Brassinosteroid (BR)-responsive tests and found that overexpression of OsDof12 could also result in BR hyposensitivity. Of note, in WT plants the expression of OsDof12 was found up-regulated by BR treatment while in OsDof12 overexpression plants two positive BR signaling regulators, OsBRI1 and OsBZR1, were significantly down-regulated, indicating that OsDof12 may act as a negative BR regulator in rice. Taken together, our results suggested that overexpression of OsDof12 could lead to altered plant architecture by suppressing BR signaling. Thus, OsDof12 might be used as a new potential genetic regulator for future rice molecular breeding.

PAG1, a cotton brassinosteroid catabolism gene, modulates fiber elongation

Cotton (Gossypium hirsutum) is the major source of natural textile fibers. Brassinosteroids (BRs) play crucial roles in regulating fiber development. The molecular mechanisms of BRs in regulating fiber elongation, however, are poorly understood. pagoda1 (pag1) was identified via an activation tagging genetic screen and characterized by genome walking and brassinolide (BL) supplementation. RNA-Seq analysis was employed to elucidate the mechanisms of PAG1 in regulating fiber development. pag1 exhibited dwarfism and reduced fiber length due to significant inhibition of cell elongation and expansion. BL treatment rescued its growth and fiber elongation. PAG1 encodes a homolog of Arabidopsis CYP734A1 that inactivates BRs via C-26 hydroxylation. RNA-Seq analyses showed that the constitutive expression of PAG1 downregulated the expression of genes involved in very-long-chain fatty acids (VLCFA) biosynthesis, ethylene-mediated signaling, response to cadmium, cell wall development, cytoskeleton organization and cell growth. Our results demonstrate that PAG1 plays crucial roles in regulating fiber development via controlling the level of endogenous bioactive BRs, which may affect ethylene signaling cascade by mediating VLCFA. Therefore, BR may be a critical regulator of fiber elongation, a role which may in turn be linked to effects on VLCFA biosynthesis, ethylene and cadmium signaling, cell wall- and cytoskeleton-related gene expression.

Regulation of brassinosteroid biosynthesis and inactivation

Brassinosteroids (BRs) are a group of naturally-occurring steroidal phytohormones playing fundamental roles during normal plant growth and development. Using a combination of experimental approaches, including analytical chemistry, genetics, and biochemistry, the major BR biosynthetic pathway has been largely elucidated. The least-understood knowledge in the BR research field is probably the molecular mechanisms controlling the bioactive levels of BRs in response to various developmental and environmental cues. In this review, we focus our discussion on a recently-proposed, 8-step predominant BR biosynthetic pathway, several newly-identified transcription factors regulating the expression of key enzymes that catalyze BR biosynthesis, and up-to-date information about the mechanisms that plants use to inactivate unnecessary BRs.