Indrani Baruah

Bio: Indrani Baruah is an academic researcher from Council of Scientific and Industrial Research. The author has contributed to research in topics: Abiotic component & Biology. The author has an hindex of 3, co-authored 6 publications receiving 46 citations. Previous affiliations of Indrani Baruah include North East Institute of Science and Technology & Academy of Scientific and Innovative Research.

Molecular genetics and functional genomics of abiotic stress-responsive genes in oilseed rape ( Brassica napus L.): a review of recent advances and future

Abstract: Abiotic stresses are the key factors which negatively influence plant development and productivity and are the main cause of extensive agricultural production losses worldwide. Brassica napus is an oilseed crop of global economic significance and major contributor to the total oilseed production, quite often encounters abiotic stresses, resulting in reduced agricultural productivity. Hence, there is an immediate need being felt to raise B. napus cultivars which would be more suitable for various abiotic stress conditions presently and in the years to come. Biotechnology and molecular plant breeding has emerged as an important tool for molecular understanding of plant response to various abiotic stresses. Currently, various stress-responsive genes and mechanisms have been identified and functionally characterized in model plant Arabidopsis and other major crop plants such as Oryza sativa and Zea mays. However, very inadequate success has been achieved in this direction in a major oilseed crop such as B. napus. In this review, we present the latest methods and approaches of studying abiotic stress in B. napus. In this review, we describe the genes functioning as markers for crop breeding and discuss the recent progress and advances in genome editing by break through CRISPR/Cas9 multigene–multiplex approaches for developing multiple abiotic stress tolerance with our on-going research as a scheme. We also throw some light on molecular genetics, plant breeding and abiotic stress biotechnology of B. napus which offer a new prospective on the research directions for the practical plant breeding and functional genomics of B. napus in response to different abiotic stress conditions.

The DEAD-box RNA helicases and multiple abiotic stresses in plants: a systematic review of recent advances and challenges

Abstract: Major crop production does not yet match the population growth rate because multiple abiotic stresses hamper the growth and yield of these crops. Most of the plants can tolerate adverse climatic conditions by performing some adaptive machineries but to certain extent. Till date various biotechnological and molecular breeding research approaches have been directed towards developing resistance to single stress factor. However, development of crop plants resistant to a single stress is not an ideal solution in the current agriculture scenario. Occurrence of multiple stresses at a single point of time makes it difficult to formulate research strategies. Considering the huge loss of crop productivity due to these environmental factors, there is an urgent need to direct our research focus towards developing sustainable multi-stress resistance in plants to counter the adverse effect of climate change on the productivity of crops. RNA helicases are ubiquitous proteins that are found in both prokaryotes and eukaryotes. The largest RNA helicase family comprises the DEAD-box RNA helicases which are involved in many aspects of RNA metabolism and in diverse biological processes in plants including regulation of multiple abiotic stress responses. The DEAD-box RNA helicases can be considered as means to identify pathways involved in multiple abiotic stress tolerance. In this review, we summarize the recent advances in elucidating the functions of the DEAD-box RNA helicases in multiple abiotic stress responses and future challenges. We also briefly discussed about our recent research efforts (published and on-going) in this direction. This review would help to formulate new research endeavours utilizing the DEAD-box helicase genes in development of multiple abiotic stress tolerant plants through genetic engineering and biotechnology. Target specific multiplex and multigene CRISPR/Ca9 genome editing would be ideal approach to edit different abiotic stress responsive DEAD-box RNA helicase genes to develop sustainable multiple abiotic stress tolerance in crop plants.

Genetic Engineering/Genome Editing Approaches to Modulate Signaling Processes in Abiotic Stress Tolerance

Abstract: Drought, salinity, and extreme temperatures are the key abiotic stress factors that negatively influence plant growth, leading to loss of agricultural productivity worldwide. Plants during the course of their evolution develop biochemical and physiological mechanisms to withstand different abiotic stresses. This book chapter describes the plant response to abiotic stress in developing tolerance through stress signaling molecules such as late embryogenesis abundant proteins, HSPs, methylglyoxyl, HyPRPs, aquaporins, and protein kinases. Various genetic engineering approaches to modulate the abiotic stress signaling process in crop plants are also discussed along with recent case studies on transgenics, plant transcription factors, and molecular chaperones. The topic emphasizes ubiquitination pathway genes, epigenetic regulation, small RNAs, and helicases in modulating signaling processes in abiotic stress tolerance. The chapter also focuses on the huge potential of breakthrough CRISPR-Cas9 and CRISPR-Cpf1 genome editing systems in developing sustainable multiple abiotic stress tolerance in crop plants.

Dissecting the Role of Promoters of Pathogen-sensitive Genes in Plant Defense

Abstract: Plants inherently show resistance to pathogen attack but are susceptible to multiple bacteria, viruses, fungi, and phytoplasmas. Diseases as a result of such infection leads to the deterioration of crop yield. Several pathogen-sensitive gene activities, promoters of such genes, associated transcription factors, and promoter elements responsible for crosstalk between the defense signaling pathways are involved in plant resistance towards a pathogen. Still, only a handful of genes and their promoters related to plant resistance have been identified to date. Such pathogen-sensitive promoters are accountable for elevating the transcriptional activity of certain genes in response to infection. Also, a suitable promoter is a key to devising successful crop improvement strategies as it ensures the optimum expression of the required transgene. The study of the promoters also helps in mining more details about the transcription factors controlling their activities and helps to unveil the involvement of new genes in the pathogen response. Therefore, the only way out to formulate new solutions is by analyzing the molecular aspects of these promoters in detail. In this review, we provided an overview of the promoter motifs and cis-regulatory elements having specific roles in pathogen attack response. To elaborate on the importance and get a vivid picture of the pathogen-sensitive promoter sequences, the key motifs and promoter elements were analyzed with the help of PlantCare and interpreted with available literature. This review intends to provide useful information for reconstructing the gene networks underlying the resistance of plants against pathogens.

Transient Sub-cellular Localization and In Vivo Protein-Protein Interaction Study of Multiple Abiotic Stress-Responsive AteIF4A-III and AtALY4 Proteins in Arabidopsis thaliana

Abstract: Major abiotic stress factors such as drought, salinity, hypoxia, and extreme temperatures along with rapid global climate change have had a huge negative impact on agricultural productivity. Understanding the abiotic stress-responsive molecular mechanisms and its associated proteins is extremely important to advance our knowledge towards developing multiple abiotic stress tolerance in plants. Firstly, basic understanding at transient level would be a vital foundation to accomplish this goal. Therefore, our present study aimed at understanding the sub-cellular localization of Eukaryotic Initiation Factor 4A-III (AteIF4A-III), a key DEAD-box RNA helicase, and Always Early 4 (AtALY4), an mRNA export factor, and their in vivo protein-protein interaction with major abiotic stress–associated proteins under control and multiple abiotic stress conditions. AteIF4A-III and AtALY4 were localized to the nucleus as evident by transient protoplast assay. AteIF4A-III has shown strong interaction with a negative regulator of multiple abiotic stresses, Stress Response Suppressor 1 (AtSTRS1) in Bi-FC assay. Further, the flow cytometry analysis has shown the strong interaction between them. Interestingly, under multiple abiotic stress treatment, the interacting partners were rapidly re-localized from nucleus to cytoplasm and cytoplasmic space. Similar results were observed when N- and C-terminal fusions of AteIF4A-III and AtALY4 treated under multiple abiotic stresses. Our study reveals that AteIF4A-III, AtALY4, and abiotic stress–associated protein AtSTRS1 are among the key proteins associated with multiple abiotic stress responses in plants.

Osmoprotection in plants under abiotic stresses: new insights into a classical phenomenon

Abstract: Plant osmoprotectants protect against abiotic stresses. Introgression of osmoprotectant genes into crop plants via genetic engineering is an important strategy in developing more productive plants. Plants employ adaptive mechanisms to survive various abiotic stresses. One mechanism, the osmoprotection system, utilizes various groups of low molecular weight compounds, collectively known as osmoprotectants, to mitigate the negative effect of abiotic stresses. Osmoprotectants may include amino acids, polyamines, quaternary ammonium compounds and sugars. These nontoxic compounds stabilize cellular structures and enzymes, act as metabolic signals, and scavenge reactive oxygen species produced under stressful conditions. The advent of recent drastic fluctuations in the global climate necessitates the development of plants better adapted to abiotic stresses. The introgression of genes related to osmoprotectant biosynthesis from one plant to another by genetic engineering is a unique strategy bypassing laborious conventional and classical breeding programs. Herein, we review recent literature related to osmoprotectants and transgenic plants engineered with specific osmoprotectant properties.

Ethylene Response Factor (ERF) Family Proteins in Abiotic Stresses and CRISPR–Cas9 Genome Editing of ERFs for Multiple Abiotic Stress Tolerance in Crop Plants: A Review

Abstract: Abiotic stresses such as extreme heat, cold, drought, and salt have brought alteration in plant growth and development, threatening crop yield and quality leading to global food insecurity. Many factors plays crucial role in regulating various plant growth and developmental processes during abiotic stresses. Ethylene response factors (ERFs) are AP2/ERF superfamily proteins belonging to the largest family of transcription factors known to participate during multiple abiotic stress tolerance such as salt, drought, heat, and cold with well-conserved DNA-binding domain. Several extensive studies were conducted on many ERF family proteins in plant species through over-expression and transgenics. However, studies on ERF family proteins with negative regulatory functions are very few. In this review article, we have summarized the mechanism and role of recently studied AP2/ERF-type transcription factors in different abiotic stress responses. We have comprehensively discussed the application of advanced ground-breaking genome engineering tool, CRISPR/Cas9, to edit specific ERFs. We have also highlighted our on-going and published R&D efforts on multiplex CRISPR/Cas9 genome editing of negative regulatory genes for multiple abiotic stress responses in plant and crop models. The overall aim of this review is to highlight the importance of CRISPR/Cas9 and ERFs in developing sustainable multiple abiotic stress tolerance in crop plants.

Trichoderma parareesei Favors the Tolerance of Rapeseed (Brassica napus L.) to Salinity and Drought Due to a Chorismate Mutase

Abstract: Both drought and salinity represent the greatest plant abiotic stresses in crops. Increasing plant tolerance against these environmental conditions must be a key strategy in the development of future agriculture. The genus of Trichoderma filament fungi includes several species widely used as biocontrol agents for plant diseases but also some with the ability to increase plant tolerance against abiotic stresses. In this sense, using the species T. parareesei and T. harzianum, we have verified the differences between the two after their application in rapeseed (Brassica napus) root inoculation, with T. parareesei being a more efficient alternative to increase rapeseed productivity under drought or salinity conditions. In addition, we have determined the role that T. parareesei chorismate mutase plays in its ability to promote tolerance to salinity and drought in plants by increasing the expression of genes related to the hormonal pathways of abscisic acid (ABA) under drought stress, and ethylene (ET) under salt stress.

A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes

Abstract: Single-nucleotide polymorphisms (SNPs)are molecular markers based on nucleotide variation and can be used for genotyping assays across populations and to track genomic inheritance. SNPs offer a comprehensive genotyping alternative to whole-genome sequencing for both agricultural and research purposes including molecular breeding and diagnostics, genome evolution and genetic diversity analyses, genetic mapping, and trait association studies. Here genomic SNPs were discovered between four cultivars of the important amphidiploid oilseed species Brassica napus and used to develop a B. napus Infinium™ array containing 5,306 SNPs randomly dispersed across the genome. Assay success was high, with >94 % of these producing a reproducible, polymorphic genotype in the 1,070 samples screened. Although the assay was designed to B. napus , successful SNP amplification was achieved in the B. napus progenitor species, Brassica rapa and Brassica oleracea , and to a lesser extent in the related species Brassica nigra . Phylogenetic analysis was consistent with the expected relationships between B. napus individuals. This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species. It also demonstrates the utility of this assay in genotyping resistance genes on chromosome A7, which segregate amongst the 1,070 samples.

Salt Stress in Brassica: Effects, Tolerance Mechanisms, and Management

Abstract: Brassica genus includes several agronomically important brassica species, and their yield performance is being affected by salt stress. Salt stress considerably reduces Brassica species growth and development by disrupting photosynthesis, leaf gas exchange, vegetative, and reproductive growth. Nonetheless, Brassica exhibits numerous salt stress tolerating mechanisms, and by targeting such potential traits, further improvement in overall salt stress tolerance in brassica can be achieved. Brassica can tolerate salt stress by accumulating organic and inorganic osmolytes, efficient Na+ exclusion, and better K+ retention ability. Recent studies have also proposed a strong role of ROS as a signaling element to enhance salt stress tolerance in Brassica. Thus, the response and tolerance mechanisms are profiled, and the possible management options to mitigate the severity of salt stress are also reviewed.