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Analysis of Genetic Diversity and Population Structure of Some Bangladeshi Rice Landraces and Hyv

M. M. Hassan
Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, Bangladesh

A. K. M. Shamsuddin
Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh

M. M. Islam
Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh, Bangladesh

K. Khatun
Department of Biotechnology, Patuakhali Science and Technology University, Dumki, Patuakhali, Bangladesh

J. Halder
Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh, Bangladesh

Abstract/ Executive Summary:

Information on the patterns of genetic variation and population structure is essential for rational use and efficient management of germplasms. It helps in monitoring germplasm and can also be used to predict potential genetic gains. Therefore, in the present study genetic diversity of 59 rice genotypes were assessed using 8 simple sequence repeat (SSR) primers. By the DNA profiling, a total of 114 alleles were detected. Allele number per/locus ranged from 9 to 27, with an average of 14.25. Average polymorphism information content (PIC) value was 0.857 with lowest 0.767 to highest 0.857. Mean gene diversity over all SSR loci was 0.870 with a range from 0.792 to 0.948. Fst values for each locus varied from 0.071 to 0.262. Genetic distance between the variety pair ranged from 0.33 to 1.0. The lowest genetic distance was found between Rajashili and Kumragori. Cluster and principal coordinate analysis (PCoA) analysis revealed similar pattern of variation. Marker RM11300 was found most polymorphic and robust among the accessions and can be widely used for rice germplasm characterization. The exclusive variability and unique feature of germplasm found in this study can be a gateway for both domestic and global rice improvement.

Keywords: Rice; Genetic diversity; SSR; DNA fingerprinting; Cluster analysis; AMOVA.

Location: Plant biotechnology laboratory of plant breeding division of Bangladesh Institute of Nuclear Agriculture (BINA)

Start Date: 00-06-2010

End Date: 00-12-2011

Program Area: Conservation and Biodiversity

Commodity: Rice

Objectives:

In the present study 59 rice genotypes were evaluated with 8 simple sequence repeats marker for exploring the available variability.

Methodology:

The experiment was conducted in the plant biotechnology laboratory of plant breeding division of Bangladesh Institute of Nuclear Agriculture (BINA) from June 2010 to December 2011. Fifty nine rice genotypes comprising of land races, high yielding varieties and advanced breeding lines were selected for the experiment. The genotypes were collected from the Genetic Resources and Seed division of Bangladesh Rice Research Institute (BRRI) and from gene bank of Bangladesh Institute of Nuclear Agriculture (BINA). A list of the genotypes used in the study. SSR analysis: Fresh leaves from 20-days old seedlings were used for DNA extraction followed by CTAB mini-prep method. Eight selected SSR primers from rice chromosomes 1, 2 and 12 were used for the survey. The total PCR reaction volume was 15 μl, composed of 2.0 μl genomic DNA, 1.5 μl 10X PCR buffer (Tris with 15 mM MgCl₂, Conc. 10X), 0.75 μl dNTPs, 1.0 μl forward primer, 1.0 μl reverse primer, 0.5 μl Taq DNA polymerase (conc. 5 U/μl) and 8.25 μl sterile deionized water. Samples were subjected to the following thermal profile for amplification in a thermocycler, after the initial 7 min at 95°C, SSR marker amplification comprised 10–15 touchdown cycles of 94°C for 30s, annealing for 30s, decreasing the temperature by 0.5°C per cycle until the specified annealing temperature was reached (55^oC for all the markers), and 72°C for 30s. This was then followed by 25–35 cycles of amplification with the specified annealing temperature, and a final extension at 72°C for 10 min. After amplification, the PCR tube was stored at 4°C until electrophoresis. Visualization of amplification products were accomplished on a 3% agarose gel in 0.5 X TBE buffer. The agarose gels were stained with ethidium bromide solution for 20-25 min. The stained agarose gel was illuminated by UV-trans-illuminator and photographed for assessing the DNA profiles. Analysis of SSR data The allele size at each microsatellite locus was scored in base pairs by using Alpha EaseFC 4 software. The summary statistics including the number of alleles per locus, gene diversity and polymorphism information content (PIC) values were determined using the software POWER MARKER version 3.25. Allele molecular weight data were also used to determine the genetic distance for phylogeny reconstruction based on the UPGMA method as implemented in POWER MARKER with the tree viewed using TREEVIEW. Principal Coordinate (PCoA) and AMOVA analysis was performed using the program GENALEX 6.4.

Source of Information: J. Sci. Res. 4(3), 757-767 (2012)

Article Link (Online Journal):

Funding Source:

Total Budget (Tk.) :

Achievement/Findings:

Bangladeshi rice cultivars used in the present study have not been examined previously in terms of genetic diversity using molecular markers. The SSR analysis of rice landrace and HYV in this study indicated sufficient polymorphism to fully differentiate the inter- and intra-population diversity. The study also confirmed the value of microsatellite loci for genetic diversity studies of rice landraces found in earlier studies. The diversity and the unique features of the Bangladeshi rice-landrace collections examined in this study could be quite relevant to both domestic and global rice development.

Knowledge Management: Journal