Transcriptomic and epigenomic remodeling occurs during vascular cambium periodicity in Populus tomentosa

AbstractTrees in temperate regions exhibit evident seasonal patterns, which play vital roles in their growth and development. The activity of cambial stem cells is the basis for regulating the quantity and quality of wood, which has received considerable attention. However, the underlying mechanisms of these processes have not been fully elucidated. Here we performed a comprehensive analysis of morphological observations, transcriptome profiles, the DNA methylome, and miRNAs of the cambium in Populus tomentosa during the transition from dormancy to activation. Anatomical analysis showed that the active cambial zone exhibited a significant increase in the width and number of cell layers compared with those of the dormant and reactivating cambium. Furthermore, we found that differentially expressed genes associated with vascular development were mainly involved in plant hormone signal transduction, cell division and expansion, and cell wall biosynthesis. In addition, we identified 235 known miRNAs and 125 novel miRNAs. Differentially expressed miRNAs and target genes showed stronger negative correlations than other miRNA/target pairs. Moreover, global methylation and transcription analysis revealed that CG gene body methylation was positively correlated with gene expression, whereas CHG exhibited the opposite trend in the downstream region. Most importantly, we observed that the number of CHH differentially methylated region (DMR) changes was the greatest during cambium periodicity. Intriguingly, the genes with hypomethylated CHH DMRs in the promoter were involved in plant hormone signal transduction, phenylpropanoid biosynthesis, and plant–pathogen interactions during vascular cambium development. These findings improve our systems-level understanding of the epigenomic diversity that exists in the annual growth cycle of trees.

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Genome-Wide Identification of Long Non-coding RNA in Trifoliate Orange (Poncirus trifoliata (L.) Raf) Leaves in Response to Boron Deficiency

International Journal of Molecular Sciences ◽

10.3390/ijms20215419 ◽

2019 ◽

Vol 20 (21) ◽

pp. 5419 ◽

Cited By ~ 4

Author(s):

Gao-Feng Zhou ◽

Li-Ping Zhang ◽

Bi-Xian Li ◽

Ou Sheng ◽

Qing-Jiang Wei ◽

...

Keyword(s):

Signal Transduction ◽

Plant Hormones ◽

Target Genes ◽

Expression Patterns ◽

Poncirus Trifoliata ◽

Differentially Expressed ◽

Boron Deficiency ◽

Trifoliate Orange ◽

Genome Wide ◽

A Genome

Long non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. As a dominant abiotic stress factor in soil, boron (B) deficiency stress has impacted the growth and development of citrus in the red soil region of southern China. In the present work, we performed a genome-wide identification and characterization of lncRNAs in response to B deficiency stress in the leaves of trifoliate orange (Poncirus trifoliata), an important rootstock of citrus. A total of 2101 unique lncRNAs and 24,534 mRNAs were predicted. Quantitative real-time polymerase chain reaction (qRT-PCR) experiments were performed for a total of 16 random mRNAs and lncRNAs to validate their existence and expression patterns. Expression profiling of the leaves of trifoliate orange under B deficiency stress identified 729 up-regulated and 721 down-regulated lncRNAs, and 8419 up-regulated and 8395 down-regulated mRNAs. Further analysis showed that a total of 84 differentially expressed lncRNAs (DELs) were up-regulated and 31 were down-regulated, where the number of up-regulated DELs was 2.71-fold that of down-regulated. A similar trend was also observed in differentially expressed mRNAs (DEMs, 4.21-fold). Functional annotation of these DEMs was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, and the results demonstrated an enrichment of the categories of the biosynthesis of secondary metabolites (including phenylpropanoid biosynthesis/lignin biosynthesis), plant hormone signal transduction and the calcium signaling pathway. LncRNA target gene enrichment identified several target genes that were involved in plant hormones, and the expression of lncRNAs and their target genes was significantly influenced. Therefore, our results suggest that lncRNAs can regulate the metabolism and signal transduction of plant hormones, which play an important role in the responses of citrus plants to B deficiency stress. Co-expression network analysis indicated that 468 significantly differentially expressed genes may be potential targets of 90 lncRNAs, and a total of 838 matched lncRNA-mRNA pairs were identified. In summary, our data provides a rich resource of candidate lncRNAs and mRNAs, as well as their related pathways, thereby improving our understanding of the role of lncRNAs in response to B deficiency stress, and in symptom formation caused by B deficiency in the leaves of trifoliate orange.

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Integrated mRNA and small RNA sequencing reveals microRNA regulatory network associated with internode elongation in sugarcane (Saccharum officinarum L.)

BMC Genomics ◽

10.1186/s12864-019-6201-4 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Lihang Qiu ◽

Rongfa Chen ◽

Yegeng Fan ◽

Xing Huang ◽

Hanmin Luo ◽

...

Keyword(s):

Signal Transduction ◽

Nitrogen Metabolism ◽

Differentially Expressed Genes ◽

Small Rna ◽

Plant Hormone ◽

Expression Profiles ◽

Differentially Expressed ◽

Small Rna Sequencing ◽

Internode Elongation ◽

Mirna Regulation

Abstract Background Internode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internode elongation would help develop molecular improvement strategies but they are not yet well-investigated. To identify genes and miRNAs involved in internode elongation, the cDNA and small RNA libraries from the pre-elongation stage (EI), early elongation stage (EII) and rapid elongation stage (EIII) were sequenced and their expression were studied. Results Based on the sequencing results, 499,495,518 reads and 80,745 unigenes were identified from stem internodes of sugarcane. The comparisons of EI vs. EII, EI vs. EIII, and EII vs. EIII identified 493, 5035 and 3041 differentially expressed genes, respectively. Further analysis revealed that the differentially expressed genes were enriched in the GO terms oxidoreductase activity and tetrapyrrole binding. KEGG pathway annotation showed significant enrichment in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction”, which might be participating in internode elongation. miRNA identification showed 241 known miRNAs and 245 novel candidate miRNAs. By pairwise comparison, 11, 42 and 26 differentially expressed miRNAs were identified from EI and EII, EI and EIII, and EII and EIII comparisons, respectively. The target prediction revealed that the genes involved in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction” pathways are targets of the miRNAs. We found that the known miRNAs miR2592-y, miR1520-x, miR390-x, miR5658-x, miR6169-x and miR8154-x were likely regulators of genes with internode elongation in sugarcane. Conclusions The results of this study provided a global view of mRNA and miRNA regulation during sugarcane internode elongation. A genetic network of miRNA-mRNA was identified with miRNA-mediated gene expression as a mechanism in sugarcane internode elongation. Such evidence will be valuable for further investigations of the molecular regulatory mechanisms underpinning sugarcane growth and development.

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Integrated Analysis of Transcriptomic and Proteomics Data Reveals the Induction Effects of Rotenoid Biosynthesis of Mirabilis himalaica Caused by UV-B Radiation

International Journal of Molecular Sciences ◽

10.3390/ijms19113324 ◽

2018 ◽

Vol 19 (11) ◽

pp. 3324 ◽

Cited By ~ 1

Author(s):

Li Gu ◽

Weilie Zheng ◽

Mingjie Li ◽

Hong Quan ◽

Jianming Wang ◽

...

Keyword(s):

Signal Transduction ◽

Plant Hormone ◽

Absolute Quantification ◽

Differentially Expressed ◽

Integrated Analysis ◽

Signaling System ◽

Proteomics Data ◽

Adaptation Mechanism ◽

Molecular Events ◽

Isobaric Tags

Mirabilis himalaica (Edgew.) Heimerl is one of the most important genuine medicinal plants in Tibet, in which the special plateau habitat has been associated with its excellent medicinal quality and efficacy. However, the mechanisms by which environmental factors affect biosynthesis of secondary metabolic components remain unclear in this species. In this study, RNA sequencing and iTRAQ (isobaric Tags for Relative and Absolute Quantification) techniques were used to investigate the critical molecular “events” of rotenoid biosynthesis responding to UV-B radiation, a typical plateau ecological factor presented in native environment-grown M. himalaica plants. A total of 3641 differentially expressed genes (DEGs) and 106 differentially expressed proteins (DEPs) were identified in M. himalaica between UV-B treatment and control check (CK). Comprehensive analysis of protein and transcript data sets resulted in 14 and 7 DEGs from the plant hormone signal transduction and phosphatidylinositol signaling system pathways, respectively, being significantly enriched. The result showed that the plant hormone signal transduction and phosphatidylinositol signaling system might be the key metabolic strategy of UV-B radiation to improve the biosynthesis of rotenoid in M. himalaica. At same time, most of the DEGs were associated with auxin and calcium signaling, inferring that they might drive the downstream transmission of these signal transduction pathways. Regarding those pathways, two chalcone synthase enzymes, which play key roles in the biosynthesis of rotenoid that were thought as the representative medicinal component of M. himalaica, were significantly upregulated in UV-B radiation. This study provides a theoretical basis for further exploration of the adaptation mechanism of M. himalaica to UV-B radiation, and references for cultivation standardization.

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Serum microRNA Expression Profiling in Malaria Patients and Bioinformatic Analysis of Hsa-miR-106b-5p

10.21203/rs.3.rs-680474/v1 ◽

2021 ◽

Author(s):

Jiacong Peng ◽

Xiaohong Peng ◽

Ying Wang ◽

Liping Jiang ◽

Dayu Li ◽

...

Keyword(s):

Signal Transduction ◽

Mirna Expression ◽

Expression Profiling ◽

Target Genes ◽

Small Gtpase ◽

Differentially Expressed ◽

Ppi Network ◽

Kegg Analysis ◽

Significant Difference ◽

Mirna Expression Profiling

Abstract BackgroundMalaria, caused by Plasmodium, is one of the three major infectious diseases that seriously endangers public health. Resistance to anti-malarial drugs and insecticides has made the prevention and control of malaria shown little improvement in the last four years. This study aimed to explore the changes in microRNA (miRNA) expression profiling of malaria patient and predict malaria-related miRNA by bioinformatics methods to provide theoretical basis for further verification of the correlation between specific miRNAs and immune regulation of malaria.MethodsSerum of patients infected by Plasmodium falciparum and healthy people from Myanmar border area was collected. miRNA expression profiling was obtained by RT-qPCR. Then the differentially expressed miRNA was screened and target genes were predicted by four miRNA databases (TargetScan, DIANA-microT, miRDB, and miRTarbase) and an intersection of target genes was obtained by Venn analysis. GO and KEGG analysis were performed for the overlapping target genes via Metascape. The results were further visualized by Cytoscape. Finally, Protein-protein interaction (PPI) network of predicted overlapping target genes was built by STRING.ResultsAmong the 341 tested serum miRNAs, 64 were differentially expressed in malaria patients (P<0.05), 27 miRNAs were up-regulated and 37 miRNAs were down-regulated. The miRNA with the most significant difference was hsa-miR-106b-5p (FC=14.871, adjusted.P.value<0.01); GO and KEGG analysis found that its overlapping predicted target gene set was remarkably enriched in biological functions such as GO:0007264~small GTPase mediated signal transduction, GO:0051056~regulation of small GTPase mediated signal transduction, GO:0051020~GTPase binding, GO:0048514~blood vessel morphogenesis(P<0.01) and signal pathway such as hsa04144: Endocytosis, hsa01521:EGFR tyrosine kinase inhibitor resistance, hsa05212:Pancreatic cancer (P<0.01); Besides, a PPI network containing 39 predicted target genes of hsa-miR-106b-5p was constructed, and 5 hub genes VEGFA, STAT3, RACGAP1, OCRL, and RBBP7 have been selected.ConclusionThe bioinformatics analysis results indicated that hsa-miR-106b-5p has a great relationship with malaria, it plays a part in inhibiting the emergence of ARTs resistance in Plasmodium and tumor progression, which may be achieved by regulating vascular morphogenesis, endocytosis, and VEGFA. The underlying mechanism needs to be further elucidated. We believe that this finding will facilitate an in-depth research on the association between malaria and miRNA.

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MAPK Signal Transduction Pathway Regulation: A Novel Mechanism of Rat HSC-T6 Cell Apoptosis Induced by FUZHENGHUAYU Tablet

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2013/368103 ◽

2013 ◽

Vol 2013 ◽

pp. 1-13 ◽

Cited By ~ 3

Author(s):

Qi Wang ◽

Hongbo Du ◽

Min Li ◽

Yue Li ◽

Shunai Liu ◽

...

Keyword(s):

Signal Transduction ◽

Target Genes ◽

Stellate Cell ◽

Signal Transduction Pathway ◽

Differentially Expressed ◽

Mrna Levels ◽

Protein Levels ◽

Control Serum ◽

Pathway Regulation ◽

Induced Apoptosis

FUZHENGHUAYU Tablets have been widely used in the treatment of liver fibrosis in China. Here, we investigate the apoptotic effect of FUZHENGHUAYU Tablet in rat liver stellate cell line HSC-T6. HSC-T6 cells were incubated with control serum or drug serum from rats fed with 0.9% NaCl or FUZHENGHUAYU Tablet, respectively. Cells exposed to drug serum showed higher proportions of early and late apoptotic cells than controls. The mRNA levels of collagens I and III, TGF-β1 andα-SMA were reduced by drug serum compared to control serum. Differentially expressed mRNAs and miRNAs were analyzed by microarray and sequencing, respectively. We identified 334 differentially expressed mRNAs and also 60 GOs and two pathways related to the mRNAs. Seventy-five differentially expressed miRNAs were down-regulated by drug serum and 1963 target genes were predicted. 134 GOs up-regulated in drug serum group were linked to miRNA targets, and drug serum also regulated 43 miRNA signal transduction pathways. Protein levels were evaluated by Western blot. Drug serum down-regulated (phospho-SAPK/JNK)/(SAPK/JNK) and up-regulated phospho-p38/p38 ratios. The study showed that FUZHENGHUAYU Tablet induced apoptosis in rat HSC-T6 cells possibly in part by activating p38 and inhibiting SAPK/JNK.

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RNA-Seq And WGCNA Analysis Identifies Salt-Responsive Genes In Pear (Pyrus Ussuriensis Maxim)

10.21203/rs.3.rs-847089/v1 ◽

2021 ◽

Author(s):

Qiming Chen ◽

Huizhen Dong ◽

Zhihua Xie ◽

Kaijie Qi ◽

Xiaosan Huang ◽

...

Keyword(s):

Signal Transduction ◽

Salt Stress ◽

Salt Tolerance ◽

Plant Hormone ◽

Enrichment Analysis ◽

Salt Resistance ◽

Mapk Signaling ◽

Differentially Expressed ◽

Signal Transduction Pathways ◽

Rna Seq

Abstract Background: Pear is one of the most abundant fruit crops and has been cultivated world-wide. However, the salt injury events caused by increased salinity limited the distribution and sustainable production of pear crops. Therefore, it is needed to take further efforts to understand the genetics and mechanisms of salt tolerance to improved salt resistance and productivity.Results: In this work, we analyzed the dynamic transcriptome of pear (Pyrus ussuriensis Maxim) under salt stress by using RNA-Seq and WGCNA. A total of 3540, 3831, 8374, 6267 and 5381 genes were identified that were differentially expressed after exposure to 200mM NaCl for 4, 6, 12, 24 and 48 hours, respectively, and 1163 genes were shared among the five comparisons. KEGG enrichment analysis of these DEGs (differentially expressed genes) revealed that “MAPK signaling” and “Plant hormone signal transduction” pathways were highly enriched. Meanwhile, 622 DEGs identified from WGCNA were highly correlated with these pathways, and some of them were able to indicate the salt tolerance of pear varieties. In addition, we provide a network to demonstrate the time-sequence of these co-expressed MAPK and hormone related genes.Conclusion: A comprehensive analysis about salt-responsive pear transcriptome were performed by using RNA-Seq and WGCNA. We demonstrated that “MAPK signaling” and “Plant hormone signal transduction” pathways were highly recruited during salt stress, and provided new insights into the metabolism of plant hormones related signaling at transcriptome level underlying salt resistance in pear. The dynamic transcriptome data obtained from this study and these salt-sensitive DEGs may provide potential genes as suitable targets for further biotechnological manipulation to improve pear salt tolerance.

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Integrative analysis of transcriptome and proteome revealed nectary and nectar traits in the plant-pollinator interaction of Nitraria tangutorum Bobrov

BMC Plant Biology ◽

10.1186/s12870-021-03002-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Tingting Chen ◽

Yanwei Zhou ◽

Jingbo Zhang ◽

Ye Peng ◽

Xiuyan Yang ◽

...

Keyword(s):

Signal Transduction ◽

Differentially Expressed Genes ◽

Plant Pathogen ◽

Plant Hormone ◽

Flavonoid Biosynthesis ◽

Epidermal Cells ◽

Differentially Expressed ◽

Ascorbate Oxidase ◽

Nitraria Tangutorum ◽

Plant Pathogen Interaction

Abstract Background Nitraria tangutorum is an important desert shrub that shows resistance to drought, salt and wind erosion stresses. It is a central ecological species in its area. Here, we have studied how N. tangutorum has adapted to achieve a successful reproduction strategy. Results We found that N. tangutorum is mainly pollinated by insects of the Hymenoptera, Diptera and Coleoptera orders. Nitraria tangutorum has very small flowers, with the nectary composed of secretive epidermal cells from which nectar is secreted, located within the inner petals. In addition, analyzing the transcriptome of four successive flower developmental stages revealed that mainly differentially expressed genes associated with flower and nectary development, nectar biosynthesis and secretion, flavonoid biosynthesis, plant hormone signal transduction and plant-pathogen interaction show dynamic expression. From the nectar, we could identify seven important proteins, of which the L-ascorbate oxidase protein was first found in plant nectar. Based on the physiological functions of these proteins, we predict that floral nectar proteins of N. tangutorum play an important role in defending against microbial infestation and scavenging active oxygen. Conclusions This study revealed that N. tangutorum is an insect-pollinated plant and its nectary is composed of secretive epidermal cells that specialized into secretive trichomes. We identified a large number of differentially expressed genes controlling flower and nectary development, nectar biosynthesis and secretion, flavonoid biosynthesis, plant hormone signal transduction and plant-pathogen interaction. We suggest that proteins present in N. tangutorum nectar may have both an antibacterial and oxygen scavenging effect. These results provide a scientific basis for exploring how the reproductive system of N. tangutorum and other arid-desert plants functions.

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Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of AtENO2 Regulating Seed Germination

International Journal of Molecular Sciences ◽

10.3390/ijms22105088 ◽

2021 ◽

Vol 22 (10) ◽

pp. 5088

Author(s):

Yu Wu ◽

Lamei Zheng ◽

Jie Bing ◽

Huimin Liu ◽

Genfa Zhang

Keyword(s):

Signal Transduction ◽

Seed Germination ◽

Deep Sequencing ◽

Small Rna ◽

Stress Responses ◽

Target Genes ◽

Differentially Expressed ◽

Signal Transduction Pathways ◽

Go Annotation ◽

Differentially Expressed Mirnas

Seed germination is a key step in the new life cycle of plants. In agriculture, we regard the rapid and consistent process of seed germination as one of the necessary conditions to measure the high quality and yield of crops. ENO2 is a key enzyme in glycolysis, which also plays an important role in plant growth and abiotic stress responses. In our study, we found that the time of seed germination in AtENO2 mutation (eno2−) was earlier than that of wild type (WT) in Arabidopsis thaliana. Previous studies have shown that microRNAs (miRNAs) were vital in seed germination. After deep sequencing of small RNA, we found 590 differentially expressed miRNAs in total, of which 87 were significantly differentially expressed miRNAs. By predicting the target genes of miRNAs and analyzing the GO annotation, we have counted 18 genes related to seed germination, including ARF family, TIR1, INVC, RR19, TUDOR2, GA3OX2, PXMT1, and TGA1. MiR9736-z, miR5059-z, ath-miR167a-5p, ath-miR167b, ath-miR5665, ath-miR866-3p, miR10186-z, miR8165-z, ath-miR857, ath-miR399b, ath-miR399c-3p, miR399-y, miR163-z, ath-miR393a-5p, and ath-miR393b-5p are the key miRNAs regulating seed germination-related genes. Through KEGG enrichment analysis, we found that phytohormone signal transduction pathways were significantly enriched, and these miRNAs mentioned above also participate in the regulation of the genes in plant hormone signal transduction pathways, thus affecting the synthesis of plant hormones and further affecting the process of seed germination. This study laid the foundation for further exploration of the AtENO2 regulation for seed germination.

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Revealing the Specific Regulations of Brassinolide on Tomato Fruit Chilling Injury by Integrated Multi-Omics

Frontiers in Nutrition ◽

10.3389/fnut.2021.769715 ◽

2021 ◽

Vol 8 ◽

Author(s):

Chunmei Bai ◽

Yanyan Zheng ◽

Christopher B. Watkins ◽

Anzhen Fu ◽

Lili Ma ◽

...

Keyword(s):

Signal Transduction ◽

Transcription Factors ◽

Stress Response ◽

Cold Stress ◽

Plant Hormone ◽

Tomato Fruit ◽

Chilling Injury ◽

Differentially Expressed ◽

Regulation Mechanism ◽

Fruit Texture

Tomato fruit is susceptible to chilling injury (CI) when stored at low temperatures, limiting its storage potential, and resulting in economic loss if inappropriate temperatures are used. Brassinolide (BR) is a plant growth regulator that is known to decrease the susceptibility of fruit to CI. In this study, transcriptome, metabolome, and proteome analysis revealed the regulation mechanism of BR treatment in alleviating tomato fruit CI. The results showed that the differentially expressed metabolites mainly included amino acids, organic acids, carbohydrates, and lipids. Differentially expressed genes (DEGs) were involved in plant cold stress response (HSFA3, SHSP, and TPR), fruit redox process (POD, PAL, and LOX), related to the fruit texture (CESA, β-Gal, and PAE), plant hormone signal transduction (ACS3, ARF, and ERF,), transcription factors (TCP, bHLH, GATA). Moreover, differentially expressed proteins were associated with fruit texture (CESA, PE, PL, and CHI), plant oxidation processes (LOX, GPX, CAT, and POD), plant cold stress response (HSF, HSP20, HSP70, and HSP90B), plant hormone signal transduction (BSK1 and JAR1) and transcription factors (WRKY and MYB). Our study showed that BR alleviates CI symptoms of tomato fruit by regulating LOX in the α-linolenic acid metabolism pathway, enhancing jasmonic acid-CoA (JA-CoA) synthesis, inhibiting cell wall and membrane lipid damage. The results provided a theoretical basis for further study on the CI mechanism of tomato fruit.

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Transcriptome Analysis of a Multiple-Branches Mutant Terminal Buds in Betula platyphylla × B. pendula

Forests ◽

10.3390/f10050374 ◽

2019 ◽

Vol 10 (5) ◽

pp. 374 ◽

Cited By ~ 1

Author(s):

Rui Han ◽

Shuo Wang ◽

Chaoyi Liu ◽

Wendi Xu ◽

Xiuyan Bian ◽

...

Keyword(s):

Signal Transduction ◽

Cell Division ◽

Plant Architecture ◽

Plant Hormone ◽

Differentially Expressed ◽

Apical Buds ◽

Genome Wide ◽

Hormone Biosynthesis ◽

Terminal Buds ◽

Lateral Branches

To investigate the molecular mechanism of the mutation of a multiple-branches birch mutant (br), we explored genes that were genome-wide differentially expressed in the main and lateral branches’ apical buds of br. The plant architecture not only has effects on the process of plant growth and development, but also affects the agronomic characters. In woody plants, branches determine the application value of timber. Therefore, analyzing genes that were differentially expressed in br apical buds will bring new insights to understand the molecular basis of plant architecture alteration. Wild type (WT) birch, Cinnamoyl-CoA reductase 1 (CCR1)-overexpressed transgenic birch (OE2) and the mutant br were used as materials to observe phenotype differences between br and the control lines (WT and OE2). The transcriptome sequencing of the main and lateral branches’ apical buds of br and controls were further performed to explore genes that were genome-wide differentially expressed in br. Compared to the control lines, br exhibited a multiple-branches and dwarf phenotype. In addition, biomass, rooting number, leaf area, internal diameter, and external diameter of stomata, and the size of terminal buds of br were less than that of WT and OE2. Transcriptome analysis results indicated that gene expression profiles of br were different from the control lines. The genes that were differentially expressed in br apical buds were involved in multiple pathways, including organogenesis, fertility regulation, cell division and differentiation, plant hormone biosynthesis, and signal transduction. The multiple-branches, dwarf, and small leaves and buds of br might be due to the differentially expressed genes (DEGs) involved in organogenesis, cell division and differentiation, plant hormone biosynthesis and signal transduction.

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