Article

Molecular marker based (SSR) genetic diversity analysis in deep water rice germplasms of Bangladesh

International Journal of Biosciences 10/2012; 2(10 (2)):64-72.

ABSTRACT

The study was undertaken to assess the genetic diversity among deep water rice genotypes using Simple Sequence Repeat (SSR) markers through marker aided selection (MAS). Twelve deep water rice (Oryza sativa L.) germplasms of Bangladesh was selected for genetic diversity analysis using eighteen SSR markers. Upon PCR amplification the alleles were separated on Polyacrylamide Gel Electrophoresis (PAGE) system. Initial polymorphism detection was conducted using eighteen primer pairs distributed on twelve rice chromosomes. The chosen microsatellite marker panel consisted of RM1, RM452, RM130, RM252, RM13, RM204, RM11, RM25, RM205, RM244, RM206, and RM463 with one representative from each chromosome. A total of 79 alleles were detected with an average of 4.38 alleles per locus. The polymorphism information content (PIC) reflections of alleles diversity frequency among the varieties, which is ranged from 0.477 to 0.782, with an average of 0.634. RM 13 was found as the best marker for identification of genotypes as revealed by PIC values. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram revealed 2 major groups with 4 clusters and the wide range of dissimilarity values (0.14-0.89) which showed a high degree of diversity among the cultivars. The results of the genetic diversity will be useful for the selection of the parents for developing submergence tolerant and flash flood tolerant rice variety through molecular breeding program.

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    • "DNA extraction was done by the modified Cetyl Trimethyl Ammonium Bromide (CTAB) mini-prep method (IRRI, 1997). DNA samples were evaluated both quantitatively and qualitatively using spectrophotometer and λ (lamda) DNA (concentration marker) respectively (Matin et al. 2012 "
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    ABSTRACT: To ensure the productivity of rice in drought condition, ‘NERICA’ varieties of African origin has been introduced in Bangladesh and subsequently mutant lines are also developed for improving the performance further. The present study was undertaken to screen out better drought tolerant mutant lines of NERICA having other desirable traits. Thirteen NARICA mutant lines, four susceptible (BINA dhan8, BINA dhan10, BINA dhan11 and BINA dhan12) and one tolerant (BRRI dhan56) varieties were included in the experiment and selection was based on morphological and molecular characteristics. The plants were grown in pot containing 9 kg of soil and when they were 60 days old, drought was imposed by adding 1L of distilled water at every four days interval till harvesting. The quantity of water applied to control pots was double. The results showed that important yield contributing morphological attributes like days of 50% flowering, plant height, total number of tiller hill-1, panicle length, 100 seed weight, fresh weight of plant and dry weight of plant were significantly positively regulated due to drought in N10/300/P-2(1)-3-5, N1/250/P-6-2-7 and N10/300/P-2(1)-6-13 mutant lines. The findings of genetic diversity analysis through SSR markers RM32, RM202, RM351 and RM510 for N10/300/P-2(1)-3-5, N1/350/P-2-2-6 and N1/250/P-6-2-7 lines appeared to resemble to that of control (BRRI dhan56) from the UPGMA dendrogram. Based on morphological, molecular characteristics and UPGMA dendrogram study, mutant lines N10/300/P-2(1)-3-5 and N1/250/P-6-2-7 lines appeared superior as genetic material for developing better drought tolerant rice varieties.Progressive Agriculture 26:15-21, 2015
    Preview · Article · Aug 2015
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    • "DNA extraction was done by the modified Cetyl Trimethyl Ammonium Bromide (CTAB) mini-prep method (IRRI, 1997). DNA samples were evaluated both quantitatively and qualitatively using spectrophotometer and λ (lamda) DNA (concentration marker) respectively (Matin et al. 2012 "

    Full-text · Article · Jan 2015
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    • "The rapid development of biotechnology allows easy analysis of a large number of loci distributed throughout the genome of plants. Molecular markers have proven to be powerful tool in the assessment of genetic variation and in the elucidation of genetic relationships within and among species (Matin et al., 2012). Molecular markers originate from different parts of the genome including coding and non-coding regions and can cover either the full genome or large genomic segments. "
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    ABSTRACT: Molecular markers are useful tool for assessing genetic variations and resolving genotype identity. In the current study, genetic diversity among 20 rice genotypes was assessed using the random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR). In RAPD analysis, 20 primers generated a total of 116 bands of which 114 were polymorphic. The number of amplification products produced by each primer varied from 4 to 7 with an average of 5.8 bands per primer. Twenty (20) SSR primers generated a total of 65 alleles with an average 3.2 alleles per primer. Genetic diversity of 20 genotypes estimated by polymorphic information content (PIC) value ranged from 0.62 to 0.97 in SSR and 0.33 to 0.88 with RAPD analysis. The cluster dendrogram by SSR revealed two major clusters. Rajeshwari was the only genotype in cluster I. The cluster II further divided into two sub clusters IIA and IIB. II A consisted of 17 genotypes while II B consisted of two genotypes (Apo and Kalakeni). The information generated from this study can be used to maximize selection of diverse parents and broaden the germplasm base for the future rice breeding programs.
    Full-text · Article · Aug 2013
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Questions & Answers about this publication

  • Nayem Zobayer added an answer in Plant Biotechnology:
    Can anyone recommend a Simple Sequence Repeat (SSR) protocol for Monkey orange (Strychnos cocculoides)?
    I am a PhD student working on genetic diversity of Strychnos cocculoides
    Nayem Zobayer
    I worked on Rice with SSR.No idea on Monkey orange though, you can find out something by yourself from it. Hope it will help a bit. Here is the paper,
    https://www.researchgate.net/publication/233859949_Molecular_marker_based_%28SSR%29_genetic_diversity_analysis_in_deep_water_rice_germplasms_of_Bangladesh?ev=prf_pub
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      [Show abstract] [Hide abstract]
      ABSTRACT: The study was undertaken to assess the genetic diversity among deep water rice genotypes using Simple Sequence Repeat (SSR) markers through marker aided selection (MAS). Twelve deep water rice (Oryza sativa L.) germplasms of Bangladesh was selected for genetic diversity analysis using eighteen SSR markers. Upon PCR amplification the alleles were separated on Polyacrylamide Gel Electrophoresis (PAGE) system. Initial polymorphism detection was conducted using eighteen primer pairs distributed on twelve rice chromosomes. The chosen microsatellite marker panel consisted of RM1, RM452, RM130, RM252, RM13, RM204, RM11, RM25, RM205, RM244, RM206, and RM463 with one representative from each chromosome. A total of 79 alleles were detected with an average of 4.38 alleles per locus. The polymorphism information content (PIC) reflections of alleles diversity frequency among the varieties, which is ranged from 0.477 to 0.782, with an average of 0.634. RM 13 was found as the best marker for identification of genotypes as revealed by PIC values. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram revealed 2 major groups with 4 clusters and the wide range of dissimilarity values (0.14-0.89) which showed a high degree of diversity among the cultivars. The results of the genetic diversity will be useful for the selection of the parents for developing submergence tolerant and flash flood tolerant rice variety through molecular breeding program.
      Full-text · Article · Oct 2012