Gene Set Subtraction Reveals 633 Candidate Genes for Bamboo Culm Wall Thickening

Hu, Yaping; Zhou, Jie; Yu, Zhaoyan; Li, Jiajia; Cai, Jinfeng; Wang, Guibin; Guo, Qirong

doi:10.3390/f11121331

Cited by 3 publications

(4 citation statements)

References 41 publications

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“…Combined analysis of transcriptome and metabolome can be applied to reveal internal relationship between the regulation mechanism and biomolecular function systematically (Jewett et . Nitrogen metabolism pathway and tyrosine metabolism metabolic pathways and their uniquely expressed genes were related to culm wall thickness in Phyllostachys edulis 'Pachyloen' (variant of moso bamboo) (Hu et al 2020a(Hu et al , 2020b. These studies provide a reference for detecting core genes related to bamboo morphology and anatomical characteristics, and exploring the gene regulation mechanism in the malformation of bamboo stem.…”

Section: Introductionmentioning

confidence: 78%

“…The application of a multi-omics approach can be applied for investigating the molecular biological mechanism systematically and comprehensively (Hori et al 2020). By considering the most effective method, analyses of phenotypic characters combined with transcriptome and metabolome has been extensively validated (Kasirajan et al 2018;Hu et al 2020aHu et al , 2020b. A transcriptome represents the intermediate state of gene expression and offered a relatively holistic approach to interpreting molecular mechanism of plant development (Shi, 2011;Wang et al 2009).…”

Section: Introductionmentioning

confidence: 99%

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Multi-omic analysis reveals formation mechanism of square stems of Chimonobambusa utilis Keng f.

Jiang

Gao

Zhang

et al. 2022

Preprint

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Different from the normal circular-stem plants, the Chimonobambusa utilis presents an unusual square-like culm. Bamboo culms can alter its shape by adjusting the expression patterns of genes for appealing different living conditions. However, underling mechanism for biomolecular function and regulation patterns of square-like culm is still absurd. Multi-omics analysis can be applied for revealing its molecular biological mechanism. In our study, phenotypic analysis suggested that change of stem wall thickness (STW) showed a trend of corner region (CR) > side region (SR), and fibre wall thickness (WT) showed a trend of SR > CR. It has been showed that there is an intrinsic correlation between Lignin content and cell wall thickness. Based on the anatomical features, FTIR spectroscopy analysis suggested that the relative lignin content at SR was higher than CR. It suggested that the deposition of lignin at CR and SR was different with each other. Therefore, the phenotypic analysis combined with transcriptome and metabolome were performed for identifying differential expressed genes and the relative metabolic pathways. Transcriptome results suggested that lignin biosynthesis related genes were up-regulated at SR. Metabolome results suggested that lignin precursors at SR accumulated more that CR and significantly enriched in phenylpropanoid biosynthesis KEGG pathway. These findings indicate that lignin accumulation that has a great possibility for change, leading to change of lignin content at different circumferential positions accordingly. It is suggested a coherence in phenotypic, chemical components, transcriptome, metabolome analysis. It is concluded that lignin biosynthesis related genes were up-regulated at SR which caused lignin biosynthesis precursors accumulated more at SR, leading to lignin content at SR was higher than at CR. After that, in position of the SR, cells have been enlarged. For those, the stem changed from its morphology from circle to square. The findings manifest the regulation mechanism of lignin related genes on the square-like stem. The analysis method provides an innovative means for revealing the molecular biological mechanism involved in the formation of non-circular plant.

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Section: Introductionmentioning

confidence: 78%

Section: Introductionmentioning

confidence: 99%

Multi-omic analysis reveals formation mechanism of square stems of Chimonobambusa utilis Keng f.

Jiang

Gao

Zhang

et al. 2022

Preprint

View full text Add to dashboard Cite

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“…edulis “Pachyloen” and Ph. heteroclada f. solida (Wei et al, 2017 ; Yue et al, 2017 ; Hu et al, 2020 ). In addition, comprehensive study on the anatomical characteristics and variation mechanism of culm variation of these valuable bamboo variants was still limited.…”

Section: Discussionmentioning

confidence: 99%

“…However, a number of obstacles, such as the complex genomic background of bamboo plants and the long and uncertain sexual reproductive cycle (Peng et al, 2013b ; Guo et al, 2019 ; Zheng et al, 2020 , 2022 ), makes it difficult to deepen the relevant research. Fortunately, several bamboo variants have attracted people's attention in the recent years (Wei et al, 2017 , 2018 ; Wang et al, 2018 ; Hu et al, 2020 ). Systematic analysis of the phenotypes of these bamboo variants, combined with comparative transcriptome analysis and other biological study methods, people can further investigate the genes responsible for regulating key traits, and also provides a new avenue to further explore the molecular basis and regulatory mechanism associated with bamboo morphogenesis.…”

Section: Introductionmentioning

confidence: 99%

Anatomical Characteristics and Variation Mechanisms on the Thick-Walled and Dwarfed Culm of Shidu Bamboo (Phyllostachys nidularia f. farcta)

Wang

Qiao

et al. 2022

Front. Plant Sci.

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Stable culm variants are valuable and important material for the study of culm development in bamboo plants. However, to date, there are few reports on the mechanism of variation of these bamboo variants. Phyllostachys nidularia f. farcta (Shidu bamboo) is a bamboo variant with stable phenotypes such as a dwarf culm with a thickened wall. In this study, we systematically investigated the cytological characteristics and underlying mechanism of morphological variation in culms of this variant using anatomical, mathematical statistical, physiological, and genomic methods. The anatomical observation and statistical results showed that the lateral increase of ground tissue in the inner layer of culm wall and the enlargement of vascular bundles are the anatomical essence of the wall thickening of Shidu bamboo; the limited elongation of fiber cells and the decrease in the number of parenchyma cells longitudinally are probably the main causes of the shortening of its internodes. A number of genes involved in the gibberellin synthesis pathway and in the synthesis of cell wall components are differentially expressed between the variant and its prototype, Ph. nidularia, and may play an important role in determining the phenotype of internode shortening in Shidu bamboo. The decrease in gibberellin content and the content of the major chemical components of the cell wall of Shidu bamboo confirmed the results of the above transcriptome. In addition, the variation in culm morphology in Shidu bamboo had little effect on the volume of the culm wall of individual internodes, suggesting that the decrease in the total number of internodes and the decrease in dry matter content (lignin, cellulose, etc.) may be the main factor for the sharp decline in culm biomass of Shidu bamboo.

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Transcriptome and miRNAome reveal components regulating primary thickening of bamboo shoots

Liu

Zhang²,

Lou

et al. 2021

Preprint

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Primary thickening determines bamboo yield and wood property. However, little is known about the regulatory networks involved in this process. The present study identified a total of 58,652 genes and 521 miRNAs via transcriptome and small RNA sequencing using the underground thickening shoot samples of wild type (WT) Moso bamboo (Phyllostachys edulis) and a thick wall (TW) variant (P. edulis cv. Pachyloen) at five developmental stages (WTS1/TWS1-WTS5/TWS5). A total of 11,636 (54.05%) differentially expressed genes (DEGs) and 515 (98.85%) differentially expressed miRNAs (DEmiRs) were identified from the WT, TW, and WTTW groups. The first two groups were composed of four pairwise combinations each between two successive stages (WTS2/TWS2_vs_WTS1/TWS1, WTS3/TWS3_vs_WTS2/TWS2, WTS4/TWS4_vs_WTS3/TWS3 and WTS5/TWS5_vs_WTS4/TWS4), and the WTTW group was composed of five between two relative stages (TWS1-5_vs_WTS1-5). Additionally, among the phytohormones, zeatin (ZT) showed more remarkable changes in concentrations than indole-3-acetic acid (IAA), gibberellic acid (GA3), and abscisic acid (ABA) throughout the five stages in the WT and the TW groups. Moreover, 118 sites were identified for 590 miRNA-mRNA pairs via degradome sequencing. The dual-luciferase reporter assay confirmed that 14 miRNAs bound to 12 targets. Fluorescence in situ hybridization (FISH) localized miR166 and miR160 in the shoot apical meristem (SAM) and the procambium of Moso bamboo shoots at the S1 stage. Thus, primary thickening is a complex process regulated by miRNA-gene-phytohormone networks, and the miRNAome and transcriptome dynamics regulate phenotypic plasticity. These findings provide insights into the molecular mechanisms underlying wood formation and properties and propose targets for bamboo breeding.

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Gene Set Subtraction Reveals 633 Candidate Genes for Bamboo Culm Wall Thickening

Cited by 3 publications

References 41 publications

Multi-omic analysis reveals formation mechanism of square stems of Chimonobambusa utilis Keng f.

Multi-omic analysis reveals formation mechanism of square stems of Chimonobambusa utilis Keng f.

Anatomical Characteristics and Variation Mechanisms on the Thick-Walled and Dwarfed Culm of Shidu Bamboo (Phyllostachys nidularia f. farcta)

Transcriptome and miRNAome reveal components regulating primary thickening of bamboo shoots

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