Genome-wide identification, characterization and expression profiling of gibberellin metabolism genes in jute

Honi, Ummay; Amin, Md. Ruhul; Kabir, Shah Md. Tamim; Bashar, Kazi Khayrul; Moniruzzaman, Md.; Jahan, Rownak; Jahan, Sharmin; Haque, Masudul; Islam, Serajul

doi:10.1186/s12870-020-02512-2

Cited by 17 publications

(8 citation statements)

References 64 publications

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“…A total of 7728 internodes of 124 individuals of P. edulis were measured in the present study. Our results showed that the internode numbers of P. edulis were not significantly increased under exogenous GA treatment compared with the CTRL, consistent with Honi et al [98], who found no significant change in the internode numbers of jute under GA treatment. There are few studies concerning internode numbers, and almost all such studies investigated crops.…”

Section: Effects Of the Exogenous Treatments On The Internode Numberssupporting

confidence: 92%

Plasticity in the Morphology of Growing Bamboo: A Bayesian Analysis of Exogenous Treatment Effects on Plant Height, Internode Length, and Internode Numbers

Bai

Cao³

et al. 2023

Plants

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Sucrose (Suc) and gibberellin (GA) can promote the elongation of certain internodes in bamboo. However, there is a lack of field studies to support these findings and no evidence concerning how Suc and GA promote the plant height of bamboo by regulating the internode elongation and number. We investigated the plant height, the length of each internode, and the total number of internodes of Moso bamboo (Phyllostachys edulis) under exogenous Suc, GA, and control group (CTRL) treatments in the field and analyzed how Suc and GA affected the height of Moso bamboo by promoting the internode length and number. The lengths of the 10th–50th internodes were significantly increased under the exogenous Suc and GA treatments, and the number of internodes was significantly increased by the exogenous Suc treatment. The increased effect of Suc and GA exogenous treatment on the proportion of longer internodes showed a weakening trend near the plant height of 15–16 m compared with the CTRL, suggesting that these exogenous treatments may be more effective in regions where bamboo growth is suboptimal. This study demonstrated that both the exogenous Suc and GA treatments could promote internode elongation of Moso bamboo in the field. The exogenous GA treatment had a stronger effect on internode elongation, and the exogenous Suc treatment had a stronger effect on increasing the internode numbers. The increase in plant height by the exogenous Suc and GA treatments was promoted by the co-elongation of most internodes or the increase in the proportion of longer internodes.

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Section: Effects Of the Exogenous Treatments On The Internode Numberssupporting

confidence: 92%

Plasticity in the Morphology of Growing Bamboo: A Bayesian Analysis of Exogenous Treatment Effects on Plant Height, Internode Length, and Internode Numbers

Bai

Cao³

et al. 2023

Plants

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“…The role of these phytohormone auxins in developmental regulation is important against the cold condition in plants [ 123 ]. GC motif (enhancer-like element involved in anoxic-specific inducibility) [ 124 , 125 ], GARE motif, P box, and TATC box are a type of gibberellin- (GA-) responsive element that are the important phytohormones responsible for various plant growth and development such as seed germination, shoot elongation, leaf expansion, flower development, and fruit senescence [ 126 ].…”

Section: Resultsmentioning

confidence: 99%

Comprehensive In Silico Analysis of RNA Silencing‐Related Genes and Their Regulatory Elements in Wheat (Triticum aestivum L.)

Akond

Rahman

Ahsan

et al. 2022

BioMed Research International

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Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are known as the three major gene families that act as the critical components of RNA interference or silencing mechanisms through the noncoding small RNA molecules (miRNA and siRNA) to regulate the expressions of protein-coding genes in eukaryotic organisms. However, most of their characteristics including structures, chromosomal location, subcellular locations, regulatory elements, and gene networking were not rigorously studied. Our analysis identified 7 TaDCL, 39 TaAGO, and 16 TaRDR genes as RNA interference (RNAi) genes from the wheat genome. Phylogenetic analysis of predicted RNAi proteins with the RNAi proteins of Arabidopsis and rice showed that the predicted proteins of TaDCL, TaAGO, and TaRDR groups are clustered into four, eight, and four subgroups, respectively. Domain, 3D protein structure, motif, and exon-intron structure analyses showed that these proteins conserve identical characteristics within groups and maintain differences between groups. The nonsynonymous/synonymous mutation ratio Ka / Ks < 1 suggested that these protein sequences conserve some purifying functions. RNAi genes networking with TFs revealed that ERF, MIKC-MADS, C2H2, BBR-BPC, MYB, and Dof are the key transcriptional regulators of the predicted RNAi-related genes. The cis-regulatory element (CREs) analysis detected some important CREs of RNAi genes that are significantly associated with light, stress, and hormone responses. Expression analysis based on an online database exhibited that almost all of the predicted RNAi genes are expressed in different tissues and organs. A case-control study from the gene expression level showed that some RNAi genes significantly responded to the drought and heat stresses. Overall results would therefore provide an excellent basis for in-depth molecular investigation of these genes and their regulatory elements for wheat crop improvement against different stressors.

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“…Based on the two chromosome‐level jute genomes, we compared the expression of transcripts and genes that are related to fibre development in the secondary cell wall with phytohormone, especially gibberellin. Gibberellin, the key plant hormone associated with the reduction of plant height by plant breeders during the Green Revolution in the middle of the 20th century, and the main function of which is to promote cell elongation (Honi et al ., 2020). Thus, transcriptome analysis of stem bark grown under either normal conditions or after GA 3 treatment at the vigorous vegetative stage (60 days after germination) in HM179 and KYCG was conducted to identify candidate genes that are involved in fibre development of bast fiber (Table S11).…”

Section: Resultsmentioning

confidence: 99%

Reference genomes of the two cultivated jute species

Zhang

et al. 2021

Plant Biotechnology Journal

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Summary Cultivated jute, which comprises the two species Corchorus capsularis and C. olitorius, is the second most important natural fibre source after cotton. Here we describe chromosome‐level assemblies of the genomes of both cultivated species. The C. capsularis and C. olitorius assemblies are each comprised of seven pseudo‐chromosomes, with the C. capsularis assembly consisting of 336 Mb with 25,874 genes and the C. olitorius assembly containing 361 Mb with 28 479 genes. Although the two Corchorus genomes exhibit collinearity, the genome of C. olitorius contains 25 Mb of additional sequences than that of C. capsularis with 13 putative inversions, which might give a hint to the difference of phenotypic variants between the two cultivated jute species. Analysis of gene expression in isolated fibre tissues reveals candidate genes involved in fibre development. Our analysis of the population structures of 242 cultivars from C. capsularis and 57 cultivars from C. olitorius by whole‐genome resequencing resulted in post‐domestication bottlenecks occurred ~2000 years ago in these species. We identified hundreds of putative significant marker‐trait associations (MTAs) controlling fibre fineness, cellulose content and lignin content of fibre by integrating data from genome‐wide association studies (GWAS) with data from analyses of selective sweeps due to natural and artificial selection in these two jute species. Among them, we further validated that CcCOBRA1 and CcC4H1 regulate fibre quality in transgenic plants via improving the biosynthesis of the secondary cell wall. Our results yielded important new resources for functional genomics research and genetic improvement in jute and allied fibre crops.

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Genome-wide identification, characterization and expression profiling of gibberellin metabolism genes in jute

Cited by 17 publications

References 64 publications

Plasticity in the Morphology of Growing Bamboo: A Bayesian Analysis of Exogenous Treatment Effects on Plant Height, Internode Length, and Internode Numbers

Plasticity in the Morphology of Growing Bamboo: A Bayesian Analysis of Exogenous Treatment Effects on Plant Height, Internode Length, and Internode Numbers

Comprehensive In Silico Analysis of RNA Silencing‐Related Genes and Their Regulatory Elements in Wheat (Triticum aestivum L.)

Reference genomes of the two cultivated jute species

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