Agricultural Research Management Information System

Home
Research Summary
Search
About Us
- ARMIS
- Brochure
Contact Us
Report
User Request
Data Input
Help
- Operation Manual
  - PDF
  - Video
- Program Area & Commodity
We have reached 37600 number of research entries at this moment.

- Logout

Research Detail

Home
Research
Detail

Preliminary Progress in Jute (corchorus Species) Genome Analysis

Ahmad S. Islam
Molecular Cell and Developmental Biology, School of Biological Sciences, The University of Texas at Austin, USA

Matthew Taliaferro
Molecular Cell and Developmental Biology, School of Biological Sciences, The University of Texas at Austin, USA

Christopher T. Lee
Molecular Cell and Developmental Biology, School of Biological Sciences, The University of Texas at Austin, USA

Craig Ingram
Molecular Cell and Developmental Biology, School of Biological Sciences, The University of Texas at Austin, USA

Rebecca J. Montalvo
Molecular Cell and Developmental Biology, School of Biological Sciences, The University of Texas at Austin, USA

Gerrit van der Ende
Molecular Cell and Developmental Biology, School of Biological Sciences, The University of Texas at Austin, USA

Shahabudin Alam
DNA Technologies, Gaithersburg, Maryland.

Javed Siddiqui
DNA Technologies, Gaithersburg, Maryland.

Kanagasabapathi Sathasivan
Molecular Cell and Developmental Biology, School of Biological Sciences, The University of Texas at Austin, USA

Abstract/ Executive Summary:

The paper summarizes the progress made in cloning and sequencing a limited number of genes from jute (Corchorus olitorius and C. capsularis) and discusses future applications of jute genome analysis. As of December 2005, slightly over 200 DNA sequences have been deposited in Gen Bank. Although many of these sequences are partial and uncharacterized, this marks the beginning of a major step in unraveling of the hitherto unknown jute genome. We have constructed both cDNA and genomic DNA libraries for C. olitorius var. O4 and C. capsularis var. CVL-1 in the plasmid vectors pSMART and pBluescript, respectively. Random clones were isolated and sequenced. These DNA sequences have been deposited in Gen Bank and analyzed using TAIR (www.arabidopsis.org) for similar sequences in Arabidopsis thaliana and other related plant species. The complete sequence for tRNA-Leu and partial sequence of DNA fragments encoding several proteins, such as RNA polymerase β subunit-1, 18S rRNA, mitochondrial DNA directed RNA polymerase and carboxytransferase β-subunit are reported in this paper. The analysis of DNA sequences of related taxa deposited in Gen Bank is also presented delineating the scope and applications of cloning genes of agronomic importance.

Keywords: Genomic DNA, Corchorus olitorius, C. capsularis, WU-BLAST

Location: The University of Texas at Austin, USA

Start Date:

End Date:

Program Area: Variety and Species

Commodity: Jute

Objectives:

To construct a complete cDNA and genomic DNA libraries of both C. olitorius and C. capsularis

Methodology:

Seeds of C. capsularis var. CVL-1 and of C. olitorius var. O4 were supplied by Bangladesh Jute Research Institute through the courtesy of Haseena Khan, Dhaka University. Seeds from C. olitorius were surface sterilized with 10 % bleach and incubated on a moist filter paper in Petri dishes inside an incubator at room temperature (23°C). Seven-day-old seedlings grown inside Petri dishes were collected and shipped to DNA technologies, Maryland for RNA isolation and cDNA library construction. The sample weight was roughly 1g. Seeds of C. capsularis were surface sterilized in the same manner and planted in the greenhouse under normal lighting and allowed to grow to mature plants. The frozen jute tissues were directly grinded in the RNA isolation solution (Trizol-Invitrogen) in liquid nitrogen. The lysates were centrifuged at 10,000 × g for 10 min to remove unlysed cells and contaminants. The supernatant was mixed with 0.2 volume of chloroform and incubated on ice for 15 min. Jute mRNA was isolated from total RNA using oligo dT cellulose. Briefly, the total RNA was mixed with 10 ml of binding buffer (10 mM Tris pH 7.5, 500 mM NaCl) and heated at 70°C for 5 min. The samples were immediately chilled on ice for 5 min and mixed with oligo dT latex beads. Two μg (micrograms) of mRNA were mixed with oligo dT primer (18 mer) and heated at 65°C for 10 min. The mixture was cooled on ice and the following cDNA synthesis reagents were added: dNTP, RNase inhibitor, first strand cDNA synthesis buffer and superscript reverse transcriptase. For making the library, pSMART vector from Lucigen was used. The sequences and the restriction map of the vector are available in www.lucigen.com. The vector was digested with EcoRI and treated with calf intestinal alkaline phosphatase (CIAP). The other experiment were Genomic DNA library construction, Restriction enzyme digestion of gDNA and size fractionation, Vector preparation, Ligation and electroporation, Quality control (QC) of the library, and Isolation of plasmid DNA.

Source of Information: Plant Tissue Cult. & Biotech. 15(2): 145-156, 2005 (December)

Article Link (Online Journal):

Funding Source:

1.

Budget:

Total Budget (Tk.) :

Achievement/Findings:

The ultimate objective of the present study was to construct a complete cDNA and genomic DNA libraries of both C. olitorius and C. capsularis so that the genes of interest can be cloned and used to transform jute cultivars for obtaining value-added industrial products. Since this enormous task cannot be undertaken without adequate funding and collaboration with institutions willing to work on a tropical crop, we have been studying the partial cDNA and genomic DNA libraries on a limited scale. So far the genes we have isolated are either chloroplast-, ribosomal- or mitochondrial genes or the enzymes that reside in these structures. The main reason for obtaining genes from the above organelles alone is that DNA has so far been isolated from young leaves that contain numerous chloroplasts and mitochondria, and such genes are more abundant than others. No efforts were made so far to select unique DNA fragments. Future analysis will involve screening of the current library with probes of these abundantly expressed genes to avoid repeated sequencing. Also, many of the sequences are partial and full length sequences need to be isolated by cloning the cDNA ends. Further study aims at collecting suitable material from other parts of the plant such as young stem, bark tissue and roots to clone genes controlling many important traits of agronomic importance including those that confer resistance to insects, fungal and viral pathogens, and those for regulating lignin biosynthesis. Both random sequencing and selective cloning strategies will be employed. In addition, tissue specific promoters will be also be cloned for potential genetic improvement. Since the entire jute genome analysis is a major effort, an international collaboration among the scientists from India, Bangladesh, USA and other countries is essential to help accomplish this task. The clones and sequences should be made available for the genetic improvement of jute to ultimately benefit the millions of jute farmers in the long run.

Knowledge Management: Journal