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

Molecular Characterization and Genetic Diversity Analysis of Rice (oryza Sativa L.) Using Ssr Markers

M. Mamunur Rahman
Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Japan and Bangladesh Rice Research Institute, Regional Station, Sonagazi, Feni, Bangladesh

M.G. Rasul
Department of Genetics and Plant Breeding, BSMRAU, Gazipur, Bangladesh

M. A. Hossain
Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh

K. M. Iftekharuddaula
Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh

H. Hasegawa
Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Japan

Abstract/ Executive Summary:

Assessment of genetic diversity and molecular characterization among elite rice varieties of Bangladesh is very important for germplasm management, varietal identification, and DNA fingerprinting. Thirty-four microsatellite markers were studied across 21 types of rice to characterize and discriminate among different varieties. The number of alleles per locus ranged from 2 to 11, with an average of 4.18 alleles across 34 loci. A total of 57 rare alleles were detected at 24 loci, whereas 42 unique alleles were detected at 20 loci. The results revealed that 14 rice varieties produced unique alleles that could be used for identification, molecular characterization, and DNA fingerprinting of these varieties. Polymorphic information content (PIC) values ranged from 0.157 to 0.838, with an average of 0.488, which revealed that much variation was present among the studied varieties. The PIC values revealed that RM401 might be the best marker for identification and diversity estimation of rice varieties, followed by RM566, RM3428, RM463, and RM8094 markers. The UPGMA cluster dendrogram created in this study identified five clusters with a similarity coefficient of 0.50. The SSR polymorphism and diversity could likely be attributed to pedigree. In this study, eight SSR markers (RM10713, RM279, RM424, RM6266, RM1155, RM289, RM20224, and RM5371) were identified that produced specific alleles only in the aromatic rice varieties and were useful for varietal identification and DNA fingerprinting of these varieties. The findings of this study should be useful for varietal identification and could help in background selection in backcross breeding programs.

Keywords: Genetic Diversity, Molecular Characterization, Rice, SSR Marker, Breeding

Location: Graduate School of Natural Science and Technology, Kanazawa University, Kakuma,Kanazawa, Japan

Start Date:

End Date:

Program Area: Variety and Species

Commodity: Rice

Objectives:

(1) To assess the genetic variation and diversity of 21 elite Aman rice genotypes,

(2) To determine the genetic relationship among these genotypes for breeding purposes, and

(3) To characterize these rice genotypes.

Methodology:

Plant Materials and Markers

Twenty-one elite and high-yielding rice varieties were studied. Seeds were germinated in germination chambers and, after three days, germinated seedlings were sown in pots. The pots were then kept in a net house. Thirty-four SSR markers distributed across 12 chromosomes were used for diversity analysis. SSR Marker Genotyping DNA was collected from young leaves of 28-day-old seedlings following a modified miniscale protocol. Polymerase chain reaction was performed in a solution of a 10 μl containing 1.5 μl 10x PCR buffer, 1.0 μl dNTPs (0.25 μl each of the dNTPs), 1.0 μl of each of primer (including forward and reverse primer), 0.5 μl taq DNA polymerase, 1.0 μl template DNA, and a suitable amount of double-distilled water. Amplification was carried out using a G-storm PCR machine (Gene Technologies Ltd., England). The initial denaturation was carried out for 5 min at 94^?C. Subsequently, 35 cycles of PCR were performed, and each cycle was completed by denaturation (1 min at 94^?C), annealing (1 min at appropriate temperature), and extension (2 min at 72^?C). A final extension was performed for 7 min at 72^?C. Bromophenol blue (2 μl 5x) was added to each well of the PCR plate, and 3.5 μl of PCR amplification products was loaded in each well of the gel using fine-tipped 10-μl pipettes. A DNA ladder (3.0 μl) was also loaded between two sets of wells loaded with the PCR product. The gel was then run for 45 min to 1.15 hours (depending upon the allele size) at 100 mA current. SYBR-safe staining solution was used for staining the gels. The gels were stained for 30–35 min in the dark and were documented using a UVPRO Alpha Innotech gel documentation unit.

Data Analysis

The molecular weight of each amplified allele was measured in base pairs using the Alpha-Ease FC 5.0 software. The allele frequency data from Power Marker version 3.25 was used to export the data in binary format (allele presence = 1; allele absence = 0) for analysis with Numerical Taxonomy and Multivariate Analysis System (NTSYS-pc) version 2.2. Polymorphic information content (PIC) values were calculated. Summary statistics, including the number of alleles per locus, major allele frequency, gene diversity, and PIC values were determined using PowerMarker version 3.25. For the unrooted phylogenetic tree, genetic distance was calculated, followed by phylogeny reconstruction using neighbor-joining as implemented in PowerMarker, and the tree was viewed via Treeview. A similarity matrix was calculated with the Simqual subprogram using the Dice coefficient, followed by cluster analysis with the SAHN subprogram using the UPGMA clustering method as implemented in NTSYS-pc, and this was used to construct a dendrogram that showed relationships among the genotypes. The similarity matrix was also used for principal coordinate analysis (PCoA) with the DCenter, Eigen, Output, and MXPlot subprograms in the computer program NTSYS-pc.

Source of Information: Journal of Crop Improvement, 26:2, 244-257

Article Link (Online Journal): http://dx.doi.org/10.1080/15427528.2011.627533

Funding Source:

Total Budget (Tk.) :

Achievement/Findings:

The tested samples possessed a high level of microsatellite variation. The markers used here were of value for characterizing rice cultivars, DNA fingerprinting of rice varietiesm and constructing a database for breeding programs, especially in background selections during backcross breeding.

Knowledge Management: Journal