Biology subjects

Badmi, R.

Publications and source records attributed to Badmi, R..

5 recordsLinked to original sources

bioRxiv2021

Biomass formation and sugar release efficiency of Populus modified by altered expression of a NAC transcription factor

Woody biomass is an important feedstock for biofuel production. Manipulation of wood properties that enable efficient conversion of biomass to biofuel reduces cost of biofuel production. Wood cell wall composition is regulated at several levels that involve expression of transcription factors such as wood-/secondary cell wall-associated NAC domains (WND or SND). In Arabidopsis thaliana, SND1 regulates cell wall composition through activation of its down-stream targets such as MYBs. The functional aspects of SND1 homologs in the woody Populus have been studied through transgenic manipulation. In this study, we investigated the role of PdWND1B, Populus SND1 sequence ortholog, in wood formation using transgenic manipulation through over-expression or silencing under the control of a vascular-specific 4-coumarate-CoA ligase (4CL) promoter. As compared to control plants, PdWND1B-RNAi plants were shorter in height, with significantly reduced stem diameter and dry biomass, whereas there were no significant differences in growth and productivity of PdWND1B over-expression plants. Conversely, PdWND1B over-expression lines showed a significant reduction in cellulose and increase in lignin content, whereas there was no significant impact on lignin content of down-regulated lines. Stem carbohydrate composition analysis revealed a decrease in glucose, mannose, arabinose, and galactose, but an increase in xylose in the over-expression lines. Transcriptome analysis revealed upregulation of several downstream transcription factors and secondary cell wall related structural genes in the PdWND1B over-expression lines that corresponded to significant phenotypic changes in cell wall chemistry observed in PdWND1B overexpression lines. Relative to the control, glucose release and ethanol production from stem biomass was significantly reduced in over-expression lines but appeared enhanced in the RNAi lines. Our results show that PdWND1B is an important factor determining biomass productivity, cell wall chemistry and its conversion to biofuels in Populus.

plant biology↗

bioRxiv2020

Comparative transcriptomics identifies Botrytis cinerea induced conserved defences across different tissues of Fragaria vesca

Grey mould is one of the most devastating plant diseases that causes huge losses to the agricultural sector worldwide. Botrytis cinerea, the causal pathogen of grey mould, is a generalist necrotrophic fungus with the ability to infect over 1000 species and influence a broad array of hosts physiological responses. B. cinerea is capable of infecting a wide variety of tissues such as leaves, stem, flowers and fruits that adds to the already complex problem in controlling its spread. Understanding the pathogen induced transcriptional reprogramming in different tissues is important to identify key genes for targeted gene modifications. Identifying the genes that are common between different tissue infections will reveal similarities and differences between these pathogen-tissue pairs. In this study, the transcriptomic datasets of Botrytis infected white berries of Fragaria vesca (WhiteBc) and Botrytis infected red berries of F. vesca (RedBc) were (re)mapped to the latest F. vesca transcriptome to enable direct comparisons with the Botrytis infected F. vesca leaves (LeafBc). The genes involved in MAP kinase signalling, pathogenesis-related, allergens, cell-wall defences, detoxification and secondary metabolites were Common Responsive and Upregulated (CoReUp) between LeafBc, WhiteBc and RedBc, suggesting their important roles against B. cinerea infection in all three tissues. These insights maybe helpful for generating B. cinerea resistant varieties of strawberry.

plant biology↗

bioRxiv2020

Comparative transcriptomics reveal conserved modules of plant defence against different pathogens in Strawberry

Strawberry (Fragaria xananassa) is an economically important high-value crop that is susceptible to three most devastating pathogens with different lifestyles - a necrotrophic fungus Botrytis cinerea causing grey mold, a hemibiotrophic oomycete Phytophthora cactorum causing crown/root rot, and a biotrophic fungus Podosphaera aphanis causing powdery mildew. Studies on individual plant-pathogen interactions are only sufficient for developing disease resistant strawberry varieties to a particular pathogen. However, each of these pathogens have the potential to co-infect strawberry at a given point of time. Therefore, understanding how these pathogens manipulate strawberrys defences and how it responds to these pathogens is essential for developing broad-spectrum disease resistant varieties. Here, in the diploid model Fragaria vesca, we performed comparative transcriptome analysis between each of these pathogen infections to identify 501 Common Responsive (CoRe) genes targeted against these pathogens. Furthermore, about 80% of these CoRe set are upregulated upon infection by all three pathogens indicating a similar transcriptional response of F. vesca independent of pathogens lifestyle. These upregulated CoRe set include genes from well-known defence responsive pathways such as calcium and MAP kinase signalling, WRKY transcription factors, pathogenesis-related allergen genes and hormone and terpene biosynthetic genes. These novel insights into F. vescas defences might serve as a basis for engineering plants with broad spectrum resistance.

plant biology↗

bioRxiv2019

Induced and primed defence responses of Fragaria vesca to Botrytis cinerea infection

1.Strawberry is a high-value crop that suffers huge losses from diseases such as grey mould caused by the necrotrophic fungal pathogen Botrytis cinerea. Pesticides are heavily used to protect the strawberry crop, which raises environmental and human health concerns and promotes the evolution of pesticide resistant strains. Upregulating or priming the plants defences may be a more environmentally sustainable way of increasing disease resistance. Using Fragaria vesca as a model for the commercially grown octaploid strawberry Fragaria x ananassa, we investigated the transcriptional reprogramming of strawberry upon B. cinerea infection and the effectiveness of four priming chemicals in protecting strawberry against grey mould. First, we found that the transcriptional reprogramming of strawberry upon B. cinerea infection overlapped substantially with the transcriptome responses induced by Phytophthora cactorum (Toljamo et al., 2016), including the genes involved in jasmonic acid (JA), salicylic acid (SA), ethylene (ET) and terpenoid pathways. Furthermore, we investigated the effectiveness of previously identified priming chemicals in protecting strawberry against B. cinerea. The level of upregulated or primed resistance depended on the priming chemical itself ({beta}-aminobutyric acid (BABA), methyl jasmonate (MeJ), (R)-{beta}-homoserine (RBH), prohexadione-calcium (ProCa)) and the application method used (foliar spray, soil drench, seed treatment). Overall, RBH effectively primed strawberry defences against B. cinerea, whereas BABA and ProCa were not effective and MeJ showed mixed effects. Our results not only identify ways to effectively upregulate or prime strawberry defences against B. cinerea, but also provide novel insights about strawberry defences that may be applied in future crop protection schemes.

plant biology↗

bioRxiv2018

Dynamic regulation of HYL1 provides new insights into its multifaceted role in Arabidopsis

MicroRNAs (miRNAs) are 21 to 24 nucleotide non-coding RNAs that regulate gene expression. Biogenesis of miRNAs is fine-tuned by specialized microprocessor complex, the regulation of which is being continuously understood. Recruitment of HYL1 to the microprocessor complex is crucial for accurate primary-miRNA (pri-miRNA) processing and accumulation of mature miRNA in Arabidopsis thaliana. HYL1 is a double-stranded RNA binding protein also termed as DRB1, has two double-stranded RNA binding domain at N-terminal and a highly disordered C-terminal region. Also, the biological activity of HYL1 is dynamically regulated through transition from hyperphosphorylation to hypophosphorylation state. HYL1 is known to be phosphorylated by a MAP kinase MPK3 and SnRK2. However, the precise role of its phosphorylation are still unknown. Recently, the stability of HYL1 protein has been shown to be regulated by an unknown protease X. However, the identity of the protease and its molecular mechanisms are poorly understood. Here, we describe, three functionally important facets of HYL1, which provide a better picture of its association with molecular processes. First, we identified a conserved MPK3 phosphorylation site on HYL1 and its possible role in the miRNA biogenesis. Secondly, the C-terminal region of HYL1 displays tendencies to bind dsDNA. Lastly, the role of C-terminal region of HYL1 in the regulation of its protein stability and the regulation of miRNA biogenesis is documented. We show the unexplored role of C-terminal and hypothesize the novel functions of HYL1 in addition to miRNA biogenesis. We anticipate that the data presented in this study, will open a new dimension of understanding the role of double stranded RNA binding proteins in diverse biological processes of plants and animal.

plant biology↗