Shoot transcriptome revealed widespread differential expression and potential molecular mechanisms of chickpea (Cicer arietinum L.) against Fusarium wilt

Introduction

The yield of chickpea is severely hampered by infection wilt caused by several races of Fusarium oxysporum f. sp. ciceris (Foc).

Methods

To understand the underlying molecular mechanisms of resistance against Foc4 Fusarium wilt, RNA sequencing-based shoot transcriptome data of two contrasting chickpea genotypes, namely KWR 108 (resistant) and GL 13001 (susceptible), were generated and analyzed.

Results and Discussion

The shoot transcriptome data showed 1,103 and 1,221 significant DEGs in chickpea genotypes KWR 108 and GL 13001, respectively. Among these, 495 and 608 genes were significantly down and up-regulated in genotypes KWR 108, and 427 and 794 genes were significantly down and up-regulated in genotype GL 13001. The gene ontology (GO) analysis of significant DEGs was performed and the GO of the top 50 DEGs in two contrasting chickpea genotypes showed the highest cellular components as membrane and nucleus, and molecular functions including nucleotide binding, metal ion binding, transferase, kinase, and oxidoreductase activity involved in biological processes such as phosphorylation, oxidation-reduction, cell redox homeostasis process, and DNA repair. Compared to the susceptible genotype which showed significant up-regulation of genes involved in processes like DNA repair, the significantly up-regulated DEGs of the resistant genotypes were involved in processes like energy metabolism and environmental adaptation, particularly host-pathogen interaction. This indicates an efficient utilization of environmental adaptation pathways, energy homeostasis, and stable DNA molecules as the strategy to cope with Fusarium wilt infection in chickpea. The findings of the study will be useful in targeting the genes in designing gene-based markers for association mapping with the traits of interest in chickpea under Fusarium wilt which could be efficiently utilized in marker-assisted breeding of chickpea, particularly against Foc4 Fusarium wilt.

Molecular Evaluation of COVID-19 in Pandemic Era

COVID-19 (SARS-CoV-2) has recently emerged as an ongoing pandemic disease or probably syndemic and became the latest threat to global health. The main route of transmission of virus droplet start with respiratory problems coughing, sneezing, fever during infection period, which may end up with death, if not treated. Many emerging epidemiological factors have made COVID-19 as global alarming disease. To control the outbreak of COVID-19, a critical management along with quarantine measure is applicable, which requires early detection of infection. The early detection of COVID-19 infection is playing a vital role in controlling of progression of illness and limiting viral spread within the population. Therefore, reliable, highly specific and sensitive diagnosis techniques are necessary for its early detection.  Among several detection techniques, qRT-PCR is the rapidly employed, sensitive and widely accepted technique. In present review, different molecular techniques with emphasis on qRT-PCR for early diagnosis of emerging COVID-19 will be discussed.

RNA Interference: A Versatile Tool for Functional Genomics and Unraveling the Genes Required for Viral Disease Resistance in Plants

Virus-induced gene silencing (VIGS) is a powerful reverse genetics technology used to unravel the functions of genes. It uses viruses as vectors to carry targeted plant genes. The virus vector is used to induce RNA-mediated silencing of a gene or genes in the host plant. The process of silencing is triggered by dsRNA molecules, the mechanism is explained in this chapter. Over the years a large number of viruses have been modified for use as VIGS vectors and a list of these vectors is also included. As the name suggests, virus-induced gene silencing uses the host plant’s natural defense mechanisms against viral infection to silence plant genes. VIGS is methodologically simple and is widely used to determine gene functions, including disease resistance, abiotic stress, biosynthesis of secondary metabolites and signal transduction pathways. Here, we made an attempt to describe the basic underlying molecular mechanism of VIGS, the methodology and various experimental requirements, as well as its advantages and disadvantages. Finally, we discuss the future prospects of VIGS in relation to CRISPR/Cas9 technology. Besides using it to overexpress or silence genes, VIGS has emerged as the preferred delivery system for the cutting edge CRISPR/Cas9 genome editing technology.

Heterologous expression and characterization of recombinant OsCDR1, a rice aspartic proteinase involved in disease resistance

The Oryza sativa constitutive disease resistance 1 (OsCDR1) gene product is an aspartic proteinase that has been implicated in disease resistance signaling. This apoplastic enzyme is a member of the group of 'atypical' plant aspartic proteinases. Recombinant OsCDR1 expressed in Escherichia coli exhibited protease activity against succinylated-casein substrate. Inactivating the enzyme through modification of an aspartate residue present in the deduced active site completely abolished its proteinase activity. Infiltration of the OsCDR1 fusion protein into leaves of Arabidopsis plants induced PR2 transcripts in both the infiltrated leaf (primary) and in non-treated secondary leaves while the inactive recombinant protein failed to induce either local or systemic PR2. These findings demonstrate that OsCDR1 is capable of inducing systemic defense responses in plants.

Overexpression of rice (Oryza sativa L.) OsCDR1 leads to constitutive activation of defense responses in rice and Arabidopsis

Plant aspartic proteases (AP) play key roles in the regulation of biological processes, such as the recognition of pathogens and pests and the induction of effective defense responses. A large number of AP (>400) have been identified in silico in the rice genome. None have previously been isolated and functionally characterized for their involvement in disease resistance. We describe here the isolation and characterization of a gene (OsCDR1) from rice which encodes a predicted aspartate protease. Expression of OsCDR1 was activated upon treatments with benzothiadiazole and salicylic acid, which are signal molecules in plant disease resistance responses. Ectopic expression of OsCDR1 in Arabidopsis and rice conferred enhanced resistance against bacterial and fungal pathogens. The enhanced disease resistance observed in transgenic plants was correlated with induction of pathogenesis-related gene expression and was shown by mutational analysis to be dependent on AP activity of the transgene-encoded product. OsCDR1 accumulates in intercellular fluids (IF) in transgenic plants. Infiltration of IF from transgenic Arabidopsis plants into leaves of wild-type (WT) Arabidopsis induced the systemic defense response. These results demonstrate the conservation of CDR1 function between rice and Arabidopsis during the disease resistance response.

Airborne dust particle counting techniques

The paper briefly describes an electro-optical system for counting of dust particles, which is based on the scattering phenomena. Utilizing the scattering of light by various size particles present in the environment, various particle counting techniques have been developed in order to measure the scattered intensity of light. Light scatters in all directions but much more in the so-called near forward direction 17( composite function) off axis, at 163( composite function) from the light source in the visible range. On the basis of two techniques, the right angle and forward angle scattering, opto-mechanical systems have been developed which measure scattered intensity and particulate matter. The forward scattering Nephelometer is more sensitive and therefore is more suitable for pollution monitoring than the right angle scattering Nephelometer. Whereas the right angle scattering Nephelometer has the utility in extremely low concentration in ppb level owing to the excellent light trap efficiency in comparison to forward scattering Nephelometer. In this paper measurement techniques and measurement results associated with design and development of a real time particle analyser are also discussed.