Molecular Markers: It's Application in Crop Improvement

Mahipal Singh Kesawat,Basanta Kumar Das 한국작물학회 2009 Journal of crop science and biotechnology Vol.12 No.4

Over the past few decades, plant genomics research has been studied extensively bringing about a revolution in the field of plant biotechnology. Molecular markers, useful for plant genome analysis, have now become an important tool in crop improvement. The development and use of molecular markers for the detection and exploitation of DNA polymorphism is one of the most significant developments in the field of molecular genetics. The presence of various types of molecular markers, and differences in their principles, methodologies and applications require careful consideration in choosing one or more of such methods. No molecular markers are available yet that fulfill all requirements needed by researchers. In this article we attempt to review most of the available DNA markers that can be routinely employed in various aspects of plant genome analysis such as characterization of genetic variability, genome fingerprinting, genome mapping, gene localization, analysis of genome evolution, population genetics, taxonomy, plant breeding, and diagnostics. The emerging patterns make up a unique feature of the analyzed individual and are currently considered to be the ultimate tool for biological individualization. Over the past few decades, plant genomics research has been studied extensively bringing about a revolution in the field of plant biotechnology. Molecular markers, useful for plant genome analysis, have now become an important tool in crop improvement. The development and use of molecular markers for the detection and exploitation of DNA polymorphism is one of the most significant developments in the field of molecular genetics. The presence of various types of molecular markers, and differences in their principles, methodologies and applications require careful consideration in choosing one or more of such methods. No molecular markers are available yet that fulfill all requirements needed by researchers. In this article we attempt to review most of the available DNA markers that can be routinely employed in various aspects of plant genome analysis such as characterization of genetic variability, genome fingerprinting, genome mapping, gene localization, analysis of genome evolution, population genetics, taxonomy, plant breeding, and diagnostics. The emerging patterns make up a unique feature of the analyzed individual and are currently considered to be the ultimate tool for biological individualization.

Molecular Markers: It's Application in Crop Improvement

Kesawat, Mahipal Singh,Das, Basanta Kumar 한국작물학회 2009 Journal of crop science and biotechnology Vol.12 No.4

Over the past few decades, plant genomics research has been studied extensively bringing about a revolution in the field of plant biotechnology. Molecular markers, useful for plant genome analysis, have now become an important tool in crop improvement. The development and use of molecular markers for the detection and exploitation of DNA polymorphism is one of the most significant developments in the field of molecular genetics. The presence of various types of molecular markers, and differences in their principles, methodologies and applications require careful consideration in choosing one or more of such methods. No molecular markers are available yet that fulfill all requirements needed by researchers. In this article we attempt to review most of the available DNA markers that can be routinely employed in various aspects of plant genome analysis such as characterization of genetic variability, genome fingerprinting, genome mapping, gene localization, analysis of genome evolution, population genetics, taxonomy, plant breeding, and diagnostics. The emerging patterns make up a unique feature of the analyzed individual and are currently considered to be the ultimate tool for biological individualization.

Isolation and Characterization of Lipopolysaccharides from Different Rhizobial Isolates

Mahipal Singh Kesawat,Basanta Kumar Das,GR Bhaganagare,Vinay Sharma,Manorama 한국작물학회 2009 Journal of crop science and biotechnology Vol.12 No.3

Formation of nodules on roots or in stems (in some cases) of leguminous plants is the unique ability of gram-negative bacteria, Rhizobia, which converts atmospheric nitrogen into usable forms by the host plant. Lipopolysaccharide (LPS) is the outer membrane component of the gram-negative bacteria, known to be an essential factor in host recognition, specificity, and initial infection processes. In the present study, we extracted lipopolysaccharides from different rhizobial isolates by a modified phenol-water method and partially characterized by polyacrylamide gel electrophoresis with silver staining. The results showed two separate banding regions, LPS-I and LPS-II. The high molecular weight and electrophoretic mobility of LPS-I region resembles that of lysozyme, used as a standard marker. The LPS-II region has a low molecular weight and electrophoretic mobility greater than that of lysozyme. The LPS-II region was due to incomplete LPS, which either lacks the entire O-antigen repeating unit or contains only one or two repeating units. The banding patterns of LPS vary among the different rhizobial isolates. Results revealed that the type of LPS structure and banding regions greatly facilitate the further characterization of the LPS modifications required for symbiosis. Formation of nodules on roots or in stems (in some cases) of leguminous plants is the unique ability of gram-negative bacteria, Rhizobia, which converts atmospheric nitrogen into usable forms by the host plant. Lipopolysaccharide (LPS) is the outer membrane component of the gram-negative bacteria, known to be an essential factor in host recognition, specificity, and initial infection processes. In the present study, we extracted lipopolysaccharides from different rhizobial isolates by a modified phenol-water method and partially characterized by polyacrylamide gel electrophoresis with silver staining. The results showed two separate banding regions, LPS-I and LPS-II. The high molecular weight and electrophoretic mobility of LPS-I region resembles that of lysozyme, used as a standard marker. The LPS-II region has a low molecular weight and electrophoretic mobility greater than that of lysozyme. The LPS-II region was due to incomplete LPS, which either lacks the entire O-antigen repeating unit or contains only one or two repeating units. The banding patterns of LPS vary among the different rhizobial isolates. Results revealed that the type of LPS structure and banding regions greatly facilitate the further characterization of the LPS modifications required for symbiosis.

One gene member of the ADP-ribosylation factor family is heat-inducible and enhances seed germination in Nicotiana tabacum

김동균,Mahipal Singh Kesawat,홍추봉 한국유전학회 2017 Genes & Genomics Vol.39 No.12

ADP ribosylation factors (ARFs), one group within the Ras superfamily of GTP-binding proteins, are ubiquitous within the eukaryotic kingdom. The functions of ARFs are extensive, and include regulatory roles in vesicular transportation, lipid metabolism, and microtubule dynamics, and the cellular processes related to these roles. Most ARFs have been identified from mammalian species and yeast; although little is known about the functional importance of ARFs in plants, it seems to be equally diverse and significant. We have been working on plant responses under heat stress, and showed that heat-shock can induce seed germination (Koo et al. in Plant Physiol 167:1030– 1038, 2015). In the present study, we report nine ARF gene family members from tobacco (Nicotiana tabacum), all belonging to the same group (Class 1) in the phylogenetic analysis. One family member, NtARF1, was induced under high-temperature stress. To elucidate the biological function of NtARF1, we generated transgenic tobacco plants overexpressing NtARF1 and the seeds of these transgenic tobacco plants germinated earlier than the seeds of nontransgenic tobacco plants. We also classified ARF family genes in plant species through systematic genomic DNA sequence data-mining, focusing on the fully sequenced and extensively annotated genomes of Arabidopsis thaliana, Brachypodium distachyon, Medicago truncatula, Mimulus guttatus, Nicotiana benthamiana, Setaria italica, Solanum lycopercisum, and Solanum tuberosum, and of some major crops including rice, soybean, corn, and tobacco. The Class 1 of our phylogenetics analysis comprised the highest number of ARFs among the four groups obtained for all plant species analyzed, especially for crop plant species.

Assessment of nifH Diversity in Rhizobial Isolates of Different Origin and the Role of Antioxidant in Respiratory Protection

Govindraj Ramakantrao Bhaganagare,Mahipal Singh Kesawat,Basanta Kumar Das,Arumuganainar Suresh,Babasaheb Shivmurti Surwase,Manorama 한국작물학회 2013 Journal of crop science and biotechnology Vol.16 No.1

Rhizobia diversity is considered as one of the most useful resources for bioprospecting due to their symbiotic nitrogen-fixing ability with members of Leguminosae. The highly conserved nature of the nitrogenase reductase gene (nifH) makes it an ideal molecular tool to determine the potential for biological nitrogen fixation in any environment. In the present investigation, 250 rhizobial strains were isolated from legumes belonging to different geographical locations of Chhattisgarh, India. Genetic diversity of the nitrogenfixing bacterial community was analyzed using the nifH gene-specific primer. The polymorphism was found among the nitrogen-fixing population of different sources and origin but not in same source of rhizobia. Further, the symbiotic plasmid DNA was characterized on the basis of size and copy number of plasmids. The plasmid number varying from one to three in different rhizobial isolates had a size greater than 23 kb, while in some rhizobial isolates plasmids were absent. In addition, to examine the role of ascorbate in respiratory protection, the clear black spot margin of ascorbate was observed in the endodermis region of the nodule whereas scarcely dispersed in the infected region. Therefore, our findings demonstrated that knowing the rhizobial nifH gene diversity along with copy number of the plasmid is important for strain identification, deciding its fertility, productivity standards, and potential of biological nitrogen fixation across the geographical region.

Functional Analysis of the Hydrophilic Loop in Intracellular Trafficking of <i>Arabidopsis</i> PIN-FORMED Proteins

Ganguly, Anindya,Park, Minho,Kesawat, Mahipal Singh,Cho, Hyung-Taeg American Society of Plant Biologists 2014 The Plant cell Vol.26 No.4

<P>The auxin efflux carrier PIN2 has a long hydrophilic loop (HL); when transplanted into PIN5 (a short-HL PIN), this HL confers the PIN5:PIN2-HL fusion protein with the capacity for phosphorylation and plasma membrane (PM) targeting but not for PIN2-like polarity. Moreover, depending on cell type, PIN5 can show internal, PM, or polar localization in the PM.</P>

Assessment of nifH Diversity in Rhizobial Isolates of Different Origin and the Role of Antioxidant in Respiratory Protection

Bhaganagare, Govindraj Ramakantrao,Kesawat, Mahipal Singh,Das, Basanta Kumar,Suresh, Arumuganainar,Surwase, Babasaheb Shivmurti,Manorama, Manorama 한국작물학회 2013 Journal of crop science and biotechnology Vol.16 No.1

Rhizobia diversity is considered as one of the most useful resources for bioprospecting due to their symbiotic nitrogen-fixing ability with members of Leguminosae. The highly conserved nature of the nitrogenase reductase gene (nifH) makes it an ideal molecular tool to determine the potential for biological nitrogen fixation in any environment. In the present investigation, 250 rhizobial strains were isolated from legumes belonging to different geographical locations of Chhattisgarh, India. Genetic diversity of the nitrogen-fixing bacterial community was analyzed using the nifH gene-specific primer. The polymorphism was found among the nitrogen-fixing population of different sources and origin but not in same source of rhizobia. Further, the symbiotic plasmid DNA was characterized on the basis of size and copy number of plasmids. The plasmid number varying from one to three in different rhizobial isolates had a size greater than 23 kb, while in some rhizobial isolates plasmids were absent. In addition, to examine the role of ascorbate in respiratory protection, the clear black spot margin of ascorbate was observed in the endodermis region of the nodule whereas scarcely dispersed in the infected region. Therefore, our findings demonstrated that knowing the rhizobial nifH gene diversity along with copy number of the plasmid is important for strain identification, deciding its fertility, productivity standards, and potential of biological nitrogen fixation across the geographical region.

MS2 Labeling of Endogenous Beta-Actin mRNA Does Not Result in Stabilization of Degradation Intermediates

김송희,Melissa Vieira,김혜진,Mahipal Singh Kesawat,박혜윤 한국분자세포생물학회 2019 Molecules and cells Vol.42 No.4

The binding of MS2 bacteriophage coat protein (MCP) to MS2 binding site (MBS) RNA stem-loop sequences has been widely used to label mRNA for live-cell imaging at singlemolecule resolution. However, concerns have been raised recently from studies with budding yeast showing aberrant mRNA metabolism following the MS2-GFP labeling. To investigate the degradation pattern of MS2-GFP-labeled mRNA in mammalian cells and tissues, we used Northern blot analysis of β-actin mRNA extracted from the Actb-MBS knock-in and MBS×MCP hybrid mouse models. In the immortalized mouse embryonic cell lines and various organ tissues derived from the mouse models, we found no noticeable accumulation of decay products of β-actin mRNA compared with the wild-type mice. Our results suggest that accumulation of MBS RNA decay fragments does not always happen depending on the mRNA species and the model organisms used.

MS2 Labeling of Endogenous Beta-Actin mRNA Does Not Result in Stabilization of Degradation Intermediates

Kim, Songhee H.,Vieira, Melissa,Kim, Hye-Jin,Kesawat, Mahipal Singh,Park, Hye Yoon Korean Society for Molecular and Cellular Biology 2019 Molecules and cells Vol.42 No.4

The binding of MS2 bacteriophage coat protein (MCP) to MS2 binding site (MBS) RNA stem-loop sequences has been widely used to label mRNA for live-cell imaging at single-molecule resolution. However, concerns have been raised recently from studies with budding yeast showing aberrant mRNA metabolism following the MS2-GFP labeling. To investigate the degradation pattern of MS2-GFP-labeled mRNA in mammalian cells and tissues, we used Northern blot analysis of ${\beta}$-actin mRNA extracted from the Actb-MBS knock-in and $MBS{\times}MCP$ hybrid mouse models. In the immortalized mouse embryonic cell lines and various organ tissues derived from the mouse models, we found no noticeable accumulation of decay products of ${\beta}$-actin mRNA compared with the wild-type mice. Our results suggest that accumulation of MBS RNA decay fragments does not always happen depending on the mRNA species and the model organisms used.