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

Identifying Simple Sequence Repeat (ssr) Marker Linked to Mite Tolerance in Jute Species

SHAMIMA ISLAM KEKA
Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka-1000, Bangladesh.

MD. SHAMSUZZAMAN
Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka-1000, Bangladesh.

SULTANA PERVIN
Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka-1000, Bangladesh.

MINHAZ UDDIN PAHLOAN,
Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka-1000, Bangladesh.

MD. MAKSUDER RAHMAN
2Bangladesh Jute Research Institute, Dhaka-1207, Bangladesh.

HASEENA KHAN*
Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh

Abstract/ Executive Summary:

Mite infestation is one of the main factors restricting jute production in Bangladesh. The utilization of jute cultivars tolerant to mite attack can be one of the most economic strategies for expanding jute production. Among jute genotypes, C. olitorius O-7/95 has been reported to be most tolerant to mite attack. SSR or microsatellite markers for jute have been successfully used in distinguishing mite sensitive and tolerant jute varieties. To increase selection efficiency for mite tolerance we have used an F2 population of O-7/95 and O-72 (sensitive to mite attack) to map a number of these microsatellite markers and to determine their linkage with mite tolerant trait. A preliminary genetic linkage map based on 35 F2 populations, was constructed using software MAPMAKER/EXP (ver 3.0b). This map was based on ten SSR markers and a phenotypic marker (M-11) related to mite sensitivity. In this analysis mite resistance has been found to be linked with a SSR marker, M-66 at LOD threshold of 3. This marker has the potential of being useful in Marker Assisted Selection (MAS) in jute breeding programs for selection of lines resistant to mite.

Keywords: Jute, Mite tolerance, SSR marker, Linkage mapping

Location:

Start Date:

End Date:

Program Area: Variety and Species

Commodity: Jute

Objectives:

To (i) determine their linkage to mite resistance trait and their subsequent use in marker aided selection, and (ii) to develop a molecular framework map of jute

Methodology:

Extraction of DNA: Seeds of jute cultivars, O-72 and O-7/95 and leaf tissues of the F2 population were obtained from the Bangladesh Jute Research Institute (BJRI). For the isolation of total genomic DNA from the leaf tissues of F2 as well as from the seeds of O-72 and O-7/95, CTAB method without phenol was chosen because this method gave good yields of total genomic DNA of high molecular weight (Delaporta et al. 1983). The genomic DNAs along with λ DNA were run on a 0.8% agarose gel which was stained by ethidium bromide solution and visualized using UV illumination and documented by Kodak Biodoc system. The DNAs were quantified by comparing with fluorescence of known concentration of λ DNA. The final DNA concentration of each template stock was adjusted to 50 ng/μl. Microsatellite primers: Linkage analysis of 35 F2 jute DNA samples was carried out by ten microsatellite primers. The microsatellite enriched library was constructed commercially from Vizon Sci. Inc., BC Research Complex 3650, Westbrook Mall, Vancouver, British Columbia, Canada. Clones containing simple sequence repeats were sequenced and from these sequences the microsatellite sites were identified and SSR primers were designed. Primers were designed manually using the following standard rule: (i) 20-25 nucleotides in length, (ii) 40-60% GC content, and non-complementary 3´ nucleotides, (iii) the expected sizes of the amplification products to be between 115 and 300 bps and (iv) annealing temperatures to be between approximately 58-61°C with no greater than 3°C difference in Tm between primers of each pair. PCR amplification: PCR amplification was conducted with 25 μl reaction mixtures containing 50 ng of jute genomic DNA, 10 μM of each primer pair, 10X PCR buffer, 50 mM MgCl₂, 2 mM dNTPs, 0.2 unit Taq DNA polymerase using a GeneAmp® PCR system 9700 (Applied Biosystems). The amplification was programmed as follows: Preheating for 5 min at 95°C; 35 cycles, each for 30 s at 95°C (denaturation), 40 s at the annealing temperature of a particular primer pair, and 30 s at 72°C (extension) and a final extension at 72°C for 5 min, followed by cooling at 4°C for infinite period. For different primers different annealing temperatures were employed. For SSR primers the optimum annealing temperature used was between 55 and 62⁰C. Linkage map construction: The linkage map of jute genome was constructed using software MAPMAKER version 3.0 (stat soft 1994) considering 10 SSR markers and one phenotypic marker with 35 individuals of an F2 population. A logarithm of the odds ratio (LOD) score of 3.0 and a maximum distance of 50 cM was considered for linkage analysis. A raw data was prepared for construction of a linkage map. This raw format contained the polymorphic bands which were scored as A, B, H and null (-).

Source of Information: Bangladesh J. Bot. 37(2): 161-171, 2008 (December)

Article Link (Online Journal):

Funding Source:

Total Budget (Tk.) :

Achievement/Findings:

Results of present work indicate that there are good prospects for detecting QTLs and using marker-assisted selection in a jute breeding programme, provided in future the population size is increased to over 250 and more SSR markers are used. In this study PCR-based markers have been successfully used in establishing linkage between some SSR markers and demonstrating linkage of one of these SSR markers to resistance to jute yellow mite, a major jute pest.

Knowledge Management: Journal