Genetics and genomics of moso bamboo (Phyllostachys edulis) : Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry

Sustainable goals for contemporary world seek viable solutions for interconnected challenges, particularly in the fields of food and energy security and climate change. We present bamboo, one of the versatile plant species on earth, as an ideal candidate for bioeconomy for meeting some of these challenges. With its potential realized, particularly in the industrial sector, countries such as China are going extensive with bamboo development and cultivation to support a myriad of industrial uses. These include timber, fiber, biofuel, paper, food, and medicinal industries. Bamboo is an ecologically viable choice, having better adaptation to wider environments than do other grasses, and can help to restore degraded lands and mitigate climate change. Bamboo, as a crop species, has not become amenable to genetic improvement, due to its long breeding cycle, perennial nature, and monocarpic behavior. One of the commonly used species, moso bamboo (Phyllostachys edulis) is a potential candidate that qualifies as industrial bamboo. With its whole-genome information released, genetic manipulations of moso bamboo offer tremendous potential to meet the industrial expectations either in quality or in quantity. Further, bamboo cultivation can expect several natural hindrances through biotic and abiotic stresses, which needs viable solutions such as genetic resistance. Taking a pragmatic view of these future requirements, we have compiled the present status of bamboo physiology, genetics, genomics, and biotechnology, particularly of moso bamboo, to drive various implications in meeting industrial and cultivation requirements. We also discuss challenges underway, caveats, and contextual opportunities concerning sustainable development.Peer reviewe

The role of LTR retrotransposons in plant genetic engineering : How to control their transposition in the genome

Key message We briefly discuss that the similarity of LTR retrotransposons to retroviruses is a great opportunity for the development of a genetic engineering tool that exploits intragenic elements in the plant genome for plant genetic improvement. Long terminal repeat (LTR) retrotransposons are very similar to retroviruses but do not have the property of being infectious. While spreading between its host cells, a retrovirus inserts a DNA copy of its genome into the cells. The ability of retroviruses to cause infection with genome integration allows genes to be delivered to cells and tissues. Retrovirus vectors are, however, only specific to animals and insects, and, thus, are not relevant to plant genetic engineering. However, the similarity of LTR retrotransposons to retroviruses is an opportunity to explore the former as a tool for genetic engineering. Although recent long-read sequencing technologies have advanced the knowledge about transposable elements (TEs), the integration of TEs is still unable either to control them or to direct them to specific genomic locations. The use of existing intragenic elements to achieve the desired genome composition is better than using artificial constructs like vectors, but it is not yet clear how to control the process. Moreover, most LTR retrotransposons are inactive and unable to produce complete proteins. They are also highly mutable. In addition, it is impossible to find a full active copy of a LTR retrotransposon out of thousands of its own copies. Theoretically, if these elements were directly controlled and turned on or off using certain epigenetic mechanisms (inducing by stress or infection), LTR retrotransposons could be a great opportunity to develop a genetic engineering tool using intragenic elements in the plant genome. In this review, the recent developments in uncovering the nature of LTR retrotransposons and the possibility of using these intragenic elements as a tool for plant genetic engineering are briefly discussed.Peer reviewe

A glossy mutant in onion (Allium cepa L.) shows decreased expression of wax biosynthesis genes

Cuticular wax is a characteristic feature of land plants that provides protection against both biotic and abiotic stresses. In this study, a glossy mutant lacking an epicuticular wax layer was identified in the γ-irradiated M2 mutant population of the onion cultivar Bhima Super. The inheritance of the mutant’s glossy phenotype was determined to be recessive and single locus. Scanning electron microscopy analysis showed poor accumulation of wax crystals in the glossy mutant, concentrated near the stomata. The plant height, number of leaves per plant, and stomatal parameters of the mutant were similar to the wild-type. RNA-seq was used to comprehend the expression variations of waxy cuticle-related genes in the glossy mutant and its wild-type waxy cultivars. Differential gene expression analysis of the RNA-seq data revealed that the genes involved in wax biosynthesis, such as AcCER1, AcCER26, AcMAH1, and AcWSD1, were downregulated by 2.72, 1.74, 2.59 and 2.12-fold, respectively, in the glossy mutant respectively. The expression patterns of these four unigenes were validated using semi-quantitative RT-PCR. The glossy mutant displayed a substantial 3.5-fold reduction in cuticular wax load compared to the wild-type due to the significant downregulation of these wax biosynthesis genes. These findings represent early advancements in understanding the molecular mechanisms of wax biosynthesis in onions. Furthermore, they provide a foundation for utilizing the glossy mutant trait in breeding programmes to enhance stress and pest resilience

Study of evaluation of groundwater in Gadilam basin using hydrogeochemical and isotope data

Gadilam river basin has gained its importance due to the presence of Neyveli Lignite open cast mines and other industrial complexes. It is also due to extensive depressurization of Cuddalore aquifer, and bore wells for New Veeranam Scheme are constructed downstream of the basin. Geochemical indicators of groundwater were used to identify the chemical processes that control hydrogeochemistry. Chemical parameters of groundwater such as pH, electrical conductivity, total dissolved solids, sodium (Na+), potassium (K+), calcium (Ca+), magnesium (Mg+), bicarbonate (HCO-3 ), sulfate (SO-4 ),phosphate (PO-4 ), and silica (H4SiO4) were determined. Interpretation of hydrogeochemical data suggests that leaching of ions followed by weathering and anthropogenic impact controls the chemistry of the groundwater. Isotopic study reveals that recharge from meteoric source in sedimentary terrain and rock-water interaction with significant evaporation prevails in hard rock region

Indian Journal of Pediatrics: A Bibliometric Study Based on Scopus Database (1936- 2018)

This study was to examine the research productivity published in the Indian Journal of Pediatrics. The study was conducted based on the citable documents like articles, conference papers and review published in the journal which is indexed in the Scopus Database. The period of study is from 1936 to 2018 ie 83 years. The yearly distribution of publications with growth analysis, authorship pattern with its nature of collaboration, citation analysis with citations per paper, uncited ratio and top 20 authors ranking were statistically analyzed in this study. Further the study analyzed the geographical distribution of literature, highly cited research outputs, most preferred forms of documents, prolific institutions. A total number of 8732 research productivity has been published in the journal between 1936 and 2018 and collaborated research work dominates during the study period. More than two thirds (66.71%) of the total publications received citations with an average of 6.92 citations per paper. The uncited ratio stood at 0.33. The article on “Liver function tests ad their interpretation’ by B. R. Thapa and A.Walia published in the year 2007 is the highest cited paper with 175 citations. The Highest number of publications was contributed by I. C. Verma with 105 publications. S.K. Kabra is the most successful author for his 83 cited publications. The Article form of publications is the most preferable form of publications by the researchers. All India Institute of Medical Sciences, New Delhi is the major contributor among the Institutions and India being the most productive country with 55.88% share of contributions to the journal

Indian Journal of Pediatrics: A Bibliometric Study Based on Scopus Database (1936- 2018)

This study was to examine the research productivity published in the Indian Journal of Pediatrics. The study was conducted based on the citable documents like articles, conference papers and review published in the journal which is indexed in the Scopus Database. The period of study is from 1936 to 2018 ie 83 years. The yearly distribution of publications with growth analysis, authorship pattern with its nature of collaboration, citation analysis with citations per paper, uncited ratio and top 20 authors ranking were statistically analyzed in this study. Further the study analyzed the geographical distribution of literature, highly cited research outputs, most preferred forms of documents, prolific institutions. A total number of 8732 research productivity has been published in the journal between 1936 and 2018 and collaborated research work dominates during the study period. More than two thirds (66.71%) of the total publications received citations with an average of 6.92 citations per paper. The uncited ratio stood at 0.33. The article on “Liver function tests ad their interpretation’ by B. R. Thapa and A.Walia published in the year 2007 is the highest cited paper with 175 citations. The Highest number of publications was contributed by I. C. Verma with 105 publications. S.K. Kabra is the most successful author for his 83 cited publications. The Article form of publications is the most preferable form of publications by the researchers. All India Institute of Medical Sciences, New Delhi is the major contributor among the Institutions and India being the most productive country with 55.88% share of contributions to the journal

Recent advancement of NGS technologies to detect active transposable elements in plants

Unlike peoples’ belief that transposable elements (TEs) are “junk DNAs” or “genomic parasites”, TEs are essential genomic elements that bring about genetic diversity and enable evolution of a species. In fact, transposons are major constituent of chromosome in crop genomes, particularly in major cereal crops, the primary type of which is long terminal repeat (LTR) retrotransposon. Since TE mobilization can be controlled by specific environmental stimulation and as the result can generate novel genetic variations, it has been suggested that controlled mobilization of TEs can be a plausible method for crop breeding. To achieve this goal, series of sequencing techniques have been recently established to identify TEs that are active in mobility. These methods target and detect extrachromosomal DNAs (ecDNAs), which are final products of integration. The newly identified TEs by these methods exhibit strong transpositional activity which can generate novel genetic diversity and provide useful breeding resources

Allelic variations in <i>dnaK</i> of thermotolerant bacilliinhabiting thermal springs

527-531Abiotic stresses including high or low temperature are known to affect productivity in plants as well as microflora, and often heat shock proteins (Hsps) are induced in cells experiencing such heat stress. Hsp 70 which belongs to one of the five major families of Hsps, DnaK family, plays a vital role in the protection and recovery of cells damaged by heat stress. Further, the role of dnak gene encoding a protein related to Hsp70 in thermoregulation has been established already. In this study, we analyzed a set of thermotolerant bacilli for variation in the dnaK gene that codes for DnaK/Hsp70 protein. A part of the dnaK was amplified from seven different bacilli isolated from Manikaran hot springs, Himachal Pradesh, India. Phylogenetic analyses of dnaK in the set of strains generated four clusters, three representing highly thermotolerant strains and one, a moderately thermotolerant strain. However, analyses of deduced amino acid sequences generated only three clusters, two representing highly thermotolerant strains and one representing moderately thermotolerant strain. Comparison of DnaK of highly thermotolerant strain (M5) and moderately thermotolerant strain (M36) revealed polymorphism for 26 amino acids in the ATPase domain and for one amino acid in the substrate binding domain. It can be hypothesized that polymorphism in the DnaK could be linked to the difference in the temperature tolerance limit of the two strains