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.

5 Bookmarks
 · 
605 Views
  • [Show abstract] [Hide abstract]
    ABSTRACT: The growing number of rice microsatellite markers warrants a comprehensive comparison of allelic variability between the markers developed using different methods, with various sequence repeat motifs, and from coding and non-coding portions of the genome. We have performed such a comparison over a set of 323 microsatellite markers; 194 were derived from genomic library screening and 129 were derived from the analysis of rice-expressed sequence tags (ESTs) available in public DNA databases. We have evaluated the frequency of polymorphism between parental pairs of six inter- subspecific crosses and one inter-specific cross widely used for mapping in rice. Microsatellites derived from genomic libraries detected a higher level of polymorphism than those derived from ESTs contained in the GenBank database (83.8% versus 54.0%). Similarly, the other measures of genetic variability [the number of alleles per locus, polymorphism information content (PIC), and allele size ranges] were all higher in genomic library-derived microsatellites than in their EST-database counterparts. The highest overall degree of genetic diversity was seen in GA-containing microsatellites of genomic library origin, while the most conserved markers contained CCG- or CAG-trinucleotide motifs and were developed from GenBank sequences. Preferential location of specific motifs in coding versus non-coding regions of known genes was related to observed levels of microsatellite diversity. A strong positive correlation was observed between the maximum length of a microsatellite motif and the standard deviation of the molecular-weight of amplified fragments. The reliability of molecular weight standard deviation (SDmw) as an indicator of genetic variability of microsatellite loci is discussed.
    Theoretical and Applied Genetics 02/2000; 100(5):713-722. · 3.66 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The existence of Oryza glumaepatula is threatened by devastation and, thus, the implementation of conservation strategies is extremely relevant. This study aimed to characterize the genetic variability and estimate population parameters of 30 O. glumaepatula populations from three Brazilian biomes using 10 microsatellite markers. The levels of allelic variability for the SSR loci presented a mean of 10.3 alleles per locus and a value of 0.10 for the average allelic frequency value. The expected total heterozygosity (H(e)) ranged from 0.63 to 0.86. For the 30 populations tested, the mean observed (H(o)) and expected heterozygosities (H(e)) were 0.03 and 0.11 within population, respectively, indicating an excess of homozygotes resulting from the preferentially self-pollinating reproduction habit. The estimated fixation index ( (IS) ) was 0.79 that differed significantly from zero, indicating high inbreeding within each O. glumaepatula population. The total inbreeding of the species ((IT) ) was 0.98 and the genetic diversity indexes among populations, (ST) and (ST), were 0.85 and 0.90, respectively, indicating high genetic variability among them. Thus, especially for populations located in regions threatened with devastation, it is urgent that in situ preservation conditions should be created or that collections be made for ex situ preservation to prevent loss of the species genetic variability.
    Genetica 12/2005; 125(2-3):115-23. · 1.68 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT:  Ninety-four newly developed microsatellite markers were integrated into existing RFLP framework maps of four rice populations, including two doubled haploid, a recombinant inbred, and an interspecific backcross population. These simple sequence repeats (SSR) were predominantly poly(GA) motifs, targetted because of their abundance in rice. They were isolated from a previously described sheared library and a newly constructed enzyme-digested library. Differences in the average length of poly(GA) tracts were observed for clones isolated from the two libraries. The length of GA motifs averaged 21 repeat units for clones isolated from the Tsp-509-digested library, while motifs averaged 17 units for clones from the sheared library. There was no evidence of clustering of microsatellite markers near centromeres or telomeres. Mapping of the 94 newly developed markers as well as of 27 previously reported microsatellites provided genome-wide coverage of the 12 chromosomes, with an average distance of 1 SSLP (simple sequence repeat polymorphism) per 16–20 cM.
    Theoretical and Applied Genetics 08/1997; 95(4):553-567. · 3.66 Impact Factor

Full-text

View
98 Downloads
Available from
May 20, 2014