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Molecular Characterization and Morphological Clustering of Exotic Early Maturing Rice (oryza Sativa L.) Lines

M. M. Sarker
Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh-2202

L. Hassan
Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh-2202

M. M. Rashid
Farm Management Division, Bangladesh Rice Research Institute, Gazipur-1701

S. Seraj
Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh-2202

Abstract/ Executive Summary:

Characterization and variability analysis is important for the improvement of crop plant. This study aimed to evaluate the morphological and molecular variation of exotic early maturing rice (Oryza sativa L.) lines. A total of 32 exotic rice lines collected from different locations were genotyped and clustered using selected SSR markers. Based on morphological dendrogram, the lines were grouped into three clusters viz.I, II and III. Cluster I, cluster II and cluster III had 12, 11, 9 lines respectively. The results showed that the varieties were closely related belonging to the same cluster. DNA Markers namely Simple Sequence Repeats (SSR) is a useful tool for assessing genetic variations and resolving cultivar identities. Positive correlations were found between gene diversity, number of allele, the allele size range and the maximum number of repeats. Among the primers used RM147 identified more number of alleles and average PIC was 0.88. The UPGMA dendrogram based on Nei’s (1972) genetic distance grouped the 32 rice lines into three major clusters. This result indicates that the line which formed grouped together, they are less diverse. A significant level of polymorphism based on morphological and molecular levels was observed. Being grouped into three clusters C1-4-11-7P-2P-1P and IR 79201-49-1-1-1 could be utilized as potential parents for the improvement of yield in early maturing rice lines.

Keywords: Early maturing rice, SSR markers, Cluster analysis, Genetic diversity

Location: Bangladesh Institute of Nuclear Agriculture , Mymensingh

Start Date: 00-00-2012

End Date: 00-00-2013

Program Area: Variety and Species

Commodity: Rice

Objectives:

To evaluate the morphological and molecular variation among 32 exotic early maturing rice lines.

Methodology:

The current research was carried out at Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh- 2202, during 2012 and 2013 seasons at Breeding field and Biotechnology laboratory. Thirty two rice lines with diverse genetic background were used in this study. Of which thirty one were International Network for Genetic Evaluation of Rice (INGER) early maturing rice lines and one Bangladesh Institute of Nuclear Agriculture (BINA) developed short duration variety ‘Binadhan-7’ was used as check. The experiment was laid out in a RCBD with three replications. The row to row and plant to plant distances were 20 cm and 15 cm, respectively. The following data Plant height (cm), Days to flowering, Days to maturity, Total tillers and effective tillers hill^-1, Filled and unfilled grains panicle^-1, 1000 seed weight (g), Yield plant^-1 (g) were collected from field from randomly selected 5 plants of each unit plot. Modified CTAB mini prep was used for DNA extraction for 21day-old seedling (IRRI, 1997). Parental polymorphism survey was done with eight SSR markers. Out of 5 markers, three polymorphic SSR markers viz., RM147, RM202 and RM215 were showed polymorphic and clear bands. Each PCR reaction carried out with 15.0μl reactions containing 1.5 μl 10 X buffer, 0.75 μl dNTPs, 1μl primer forward, 1μl primer reverse, 0.5 μl taq polymerase, 8.25 μl ddH2O and 2.0 μl of each template DNA samples. PCR profile was maintained as initial denaturation at 94^oC for 5 min, followed by 34 cycles of denaturation at 94^oC for 1 min, annealing at 55^oC for 1 min and polymerization at 72^oC for 2 min; and final extension by 7 min at 72^oC. Then electrophoresis in 1.5% agarose gel was done after polymorphism in the PCR products and stained in ethidium bromide. Five primers of random sequence were screened for amplification of the DNA sequences. A final subset of three primers exhibiting good quality banding patterns and sufficient variability were selected for further analysis. Morphological cluster were constructed by using Stat Graphics Plus for Windows 3.0 (Statistical Graphics Crop. Rockville, USA). Molecular weights for microsatellite products were estimated with AlphaEaseFC 4 software. The summary statistics including the number of alleles per locus, major allele frequency, genetic diversity and polymorphism information content (PIC) values were determined by using POWER MARKER (version 3.23). The unweighted pair-group method with arithmetic mean (UPGMA) dendrogram was drawn by using the software TREEVIEW.

Source of Information: J. Bangladesh Agril. Univ. 11(2): 233–240, 2013 ISSN 1810-3030

Article Link (Online Journal):

Funding Source:

Total Budget (Tk.) :

Achievement/Findings:

Varieties were closely related belonging to the same cluster. DNA Markers namely Simple Sequence Repeats (SSR) is a useful tool for assessing genetic variations and resolving cultivar identities. Positive correlations were found between gene diversity, number of allele, the allele size range and the maximum number of repeats. Among the primers used RM147 identified more number of alleles and average PIC was 0.88.The UPGMA dendrogram based on Nei’s (1972) genetic distance grouped the 32 rice lines into three major clusters. This result indicates that the line which formed grouped together, they are less diverse. A significant level of polymorphism based on morphological and molecular levels was observed. Being grouped into three clusters C1-4-11-7P-2P-1P and IR 79201-49-1-1-1 could be utilized as potential parents for the improvement of yield in early maturing rice lines.

Knowledge Management: Journal