Chania

About DPMMD:

Date Palm Molecular Markers Database:        In order to provide useful genomic information for date palm, we have established a database, the Date Palm Molecular Markers Database (http://dpmmd.easyomics.org/). This database includes information on more than 3,611,400 DNA markers (e.g., SSR, SSR-SNPs and SNP markers), genetic linkage maps, KEGG maps, DNA-barcode and all previously published date palm articles in PubMed-indexed journals since 1976 to 2017.



        Keyword searches for the markers, sequence data used for marker development and other information are also available through this database. The Date Palm Molecular Markers Database will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in date palm.

Molecular Markers Database:

        Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, co-dominant inheritance, extensive genomic coverage, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. SSRs are also have extensively been exploited as genetic markers for diverse applications including variety identiļ¬cation, genetic diversity, construction of genetic linkage maps, association mapping, and marker-assisted selection.

        The list of integrated date palm SSRs and Single Nucleotide Polymorphisms (SNPs) were collected from earlier studies (Mokhtar et al., 2016, Al-Dous et al., 2011) and stored in relational database tables of MySQL database. The information of SSR markers was stored in four sub-databases, while, SNP markers was stored in one sub-database. Each SSR or SNP marker was given a unique identifier called Primer-ID. The sub-databases are as follows:

1- Genic Simple Sequence Repeat (Genic-SSRs) sub-database: includes 9,649 Genic-SSR markers. Clik Here

2- Intergenic Simple Sequence Repeat (Intergenic-SSRs) sub-database: which contain 22,772 Intergenic-SSR markers. Clik Here

3- Genic SSR-SNPs (SNPs that are located within the SSR flanking regions) sub-database: includes 21731 Genic SSR-SNPs markers. Clik Here

4- Intergenic SSR-SNPs sub-database: includes 57251 Intergenic SSR-SNPs markers. Clik Here

5- SNPs sub-database: includes 3,500,000 SNPs markers. Clik Here

R-Genes SSR markers:

        One of the great challenges for date palm breeding in the 21st century is to improve yield stability through the development of disease-resistant palm tree by use both genomic information and molecular tools. Here we integrated 42 SSR primers located within 16 different disease resistance genes, previously published by (Mokhtar et al., 2016). These data were summarized Here.

Functional map by KEGG pathway analyses:

        The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database is a useful tool for understanding genes biological functions and their molecular interactions. We integrated in this sub-database, our previous published 896 SSR primers that mapped onto 111 KEGG pathway, in order to make this data publicly available for scientists interested in functional map analysis in date palm. These data were summarized Here.

Date palm genetic linkage maps

        Genetic linkage maps describe the relative locations of genetic markers on chromosomes. Distances between genetic markers are determined by measuring the frequency of meiotic recombination between markers. Genetic linkage maps can be used to identify the location of genes responsible for traits and diseases. Date palm genetic linkage maps are important as a tool can be used in linkage analysis, association studies, and the building of physical maps. The first date palm genetic linkage maps, which were constructed by (Mathew et al., 2014) with the ~4000 DNA markers spanning a total of 1293 cM are also registered and integrated in our database. The information provided on the genetic linkage maps includes the mapped positions of the various markers and the reference sequence for each marker. Here.

Date palm DNA Barcoding

        DNA barcoding is a taxonomic method that uses a short genetic marker in an organism's DNA to identify it as belonging to a particular species. Rather, DNA barcoding can serve a dual purpose as a new tool in the taxonomists toolbox supplementing their knowledge as well as being an innovative device for non-experts who need to make a quick identification. Two gene regions in the chloroplast, matK and rbcL, have been approved as univrsal barcode regions for plants. Here we retrieved all date palm barcodes sequence excited at NCBI database (138 date palm cultivars characterized by use rbcL and matK genes), all collected data has been showing in this page. Here.

Date palm Published Articles in PubMed-indexed Journals

        We collected and integrated all previously published date palm articles (504 articles) excited in all PubMed-indexed journals since 1976 to 2017, all collected articles has been showing in this page. Here.











How to cite:

Morad M. Mokhtar, Sami S. Adawy, Salah El-Din S. El-Assal and Ebtissam H. A. Hussein.  Genic and intergenic SSR database generation, SNPs determination and pathway annotations, in date palm (Phoenix dactylifera L.). PLoS ONE. 2016; 11(7): e0159268. doi:10.1371/journal.pone.0159268   link

Contact:

Morad M. Mokhtar: morad.mokhtar@ageri.sci.eg   link