New microsatellite markers for assessment of genetic diversity in date palm (Phoenix dactylifera L.)

3 Biotech 09/2011; 1(2):91-97. DOI: 10.1007/s13205-011-0010-z
Source: PubMed


New primer pairs of genomic DNA microsatellite markers were tested to assess the genetic diversity of eleven date palm genotypes. The results indicated that out of thirty, only seven primers (23.3%) failed to amplify the expected PCR fragments, while thirteen primers (43.3%) amplified monomorphic banding patterns and the remaining ten primers (33.4%) generated polymorphic banding patterns. A total of 77 alleles have been observed with a mean of 7.7 alleles per locus. The average of gene diversity was 0.80 ranging from 0.6 (in marker DP168) to 0.9 (in two markers DP157 and DP175). These new co-dominant markers will be a starting point for researchers making use of the markers for genetic mapping and diversity analysis of date palm.

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Available from: Khaled Elmeer,
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    • "Several molecular markers have been applied for genetic diversity assessment, such as RAPD (Sedra et al., 1998; Trifi et al., 2000; Al-Khalifa & Askari, 2003; Mirbahar et al., 2014), ISSRs (Zehdi et al., 2002) SSRs (Zehdi et al., 2004; Elmeer et al., 2011) RAMPO (Rhouma et al., 2008) and AFLP (Devanand & Chao, 2003; Bandelj et al., 2004; Rhouma et al., 2007; Khierallah et al., 2011). These nrDNA markers revealed high polymorphism among date palm cultivars but it remained difficult to describe cultivars. "
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    ABSTRACT: Date palm (Phoenix dactylifera L.) is the oldest cultivated fruit tree and it has a great socioeconomic and nutritional value. Breeding programs and conservation rely on genetic characterization and diversity in gene pool. Its genetic diversity has not been focused more in Pakistan yet, therefore the present study aimed at the evaluation of genetic relationship based on chloroplast ribosomal protein gene (rps14). Rps14 gene was amplified and sequenced from selected varieties. Phylogram illustrated over all genetic distance of 0.001 representing close genetic relationship of selected P. dactylifera varieties. Pairwise distance was calculated for rps14 gene and very low genetic diversity values were observed ranging 0.003-0.017. Estimates of average evolutionary divergence of overall sequence pairs and nucleotide diversity were again found very low with 0.008 and 0.007 respectively. Sequences were analyzed by MEGA6, which revealed Pathri, Dhaddy, Makhi and Khudrawi as recent varieties. On the basis of rps14 genetic makeup, it can be suggested that Pakistani date palm varieties show very high degree of similarity.
    Pakistan Journal of Botany 12/2014; 46(6):2095-2100. · 0.82 Impact Factor
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    • "The DNA samples were sent to the University of Georgia for further analysis. The 21 pairs of microsatellite primers used in the current study included primers from earlier reports (Billotte et al. 2004; Elmeer et al. 2011) and new primers designed from the Deglet Noor genomic DNA sequence (Table 1). Fosmid library production and sequencing of random clones from this library were reported earlier (Al-Dous et al. 2011). "
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    ABSTRACT: Date palm (Phoenix dactylifera) has been cultivated since ancient times, but little is known about its genetic diversity and population structure. Examination of 80 date palm accessions grown in the United Arab Emirates, including a collection of varieties from around the world, using 21 microsatellite markers, indicated extensive genetic diversity, with many accessions heterozygous for most markers. The average number of alleles per locus (19), expected heterozygosity (0.7), observed heterozygosity (0.25) and fixation indices (Fst = 0.6, Rst = 0.72) demonstrated significant population structure. Analysis with a model-based Baysian method, STRUCTURE 2.4.1, indicated that the 80 accessions could be broadly divided into nine groups. Independent samples of genotypes with the same name, collected from different experimental stations, usually clustered together. The study was enriched for germplasm from the United Arab Emirates (UAE), and one STRUCTURE-derived grouping consisted mainly of UAE accessions. In a few other clusters, several genotypes from the UAE, Iraq and Oman grouped together. Two clusters included accessions from both North Africa and the Middle East. Many accessions in the STRUCTURE-derived populations appeared to be genetic admixtures. The results indicated a broad dissemination of related germplasms across date-palm growing regions of the world, with very few alleles that still correlate with particular regional germplasms.
    Tropical Plant Biology 03/2014; 7(1):31. DOI:10.1007/s12042-014-9135-7 · 1.52 Impact Factor
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    • "and their outbreak investigations largely depend on efficient isolation , detection and typing methods. A wide range of molecular typing methods have been used to study the genetic relatedness or diversity of bacterial pathogens and even plants (Wassenaar and Newell 2000; Elmeer et al. 2011; Adzitey et al. 2012c, d; Rezk et al. 2012; Tripathi et al. 2012). Genotyping methods such as pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), random amplified polymorphic deoxyribonucleic acid (RAPD), enterobacterial repetitive intergenic consensus (ERIC) and repetitive extragenic palindromic (REP), are among those routinely used to type Salmonellae to study their genetic diversity or relatedness (Chansiripornachai et al. 2000; Khoodoo et al. 2002; Lim et al. 2005; Albufera et al. 2009; Smith et al. 2011; Noble et al. 2012). "
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    ABSTRACT: Salmonella species are important foodborne pathogens that can cause illness and death in humans. The objective of this study was to determine the genetic relatedness of 115 Salmonella strains isolated from ducks and their environment using random amplified polymorphic deoxyribonucleic acid (RAPD). The analysis of Salmonella strains by RAPD produced DNA fingerprints of different sizes for differentiation purposes, and cluster analysis at a coefficient of 0.85 grouped the Salmonella strains into various clusters and singletons. S. Typhimurium were grouped into nine clusters and ten singletons, S. Hadar were grouped into seven clusters and nine singletons, S. Enteritidis were grouped into four clusters and five singletons, S. Braenderup were grouped into five clusters and four singletons, S. Albany were grouped into two clusters and seven singletons, and S. Derby were grouped into two clusters and four singletons at a coefficient of 0.85 with discriminatory index (D) ranging from 0.879 to 0.957. With the exception of S. Typhimurium strains which were grouped into three major groups (genotypes) by RAPD analysis, the rest were grouped into two major genotypes. RAPD was a useful genotyping tool for determining the genetic relatedness of the duck Salmonella strains. Comparison of the genetic relatedness among foodborne pathogens and their sources of isolation are important to trace their source and possibly the source of human infection. Electronic supplementary material The online version of this article (doi:10.1007/s13205-013-0115-7) contains supplementary material, which is available to authorized users.
    12/2013; 3(6). DOI:10.1007/s13205-013-0115-7
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