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Spoon : in vitro and in silico PCR analysis tool for gene discovery , genome-walking and fine mapping

Spoon is C-PERL-based software for performing in silico PCR on PCR primers and genomic sequences. Spoon software simulates PCR reaction by running an approximate-match searching analysis on a user-entered primer pairs against the provided sequences. It reports amplimers close or adjoin genes, SNPs, SSR and other user-provided genomic elements. It also reports PCR amplimers that are shared between in vitro and in silico PCR results in order to select the most appropriate amplimers for gene discovery. Spoon could be used for comparing physical and genetic maps and to study the primer set genome coverage for PCR-walking and NGS sequencing filling gaps using Sanger sequencing. It also reports chromosomal anchored markers, which could be used for linkage and association mapping. In addition to human-readable output files, Spoon creates Circos configurations illustrates different in silico results, which will give the user the ability to merge different bioinformatics tools results with/without slight reformatting.
Team Manager :-
                           Dr. Shafik D. Ibrahim
                           This email address is being protected from spambots. You need JavaScript enabled to view it.

Figure 1




Sex Determination in Date Palm

The date palm (Phoenix dactylifera L.), 2n=36, is a dioecious long-lived monocotyledonous plant, with separate male and female trees. The dioecy represents the major challenge in development of breeding programs as it is impossible to distinguish tree gander till they flower approximately five to eight years after planting. Date palm is an important economic crop in Egypt where the world’s largest producer over the last two years is Egypt with 1,470,000 mt. To date, sex-differentiation mechanism is still uncertain and there is no reliable way to determine the sex of date palm plants before reproductive age across all cultivars.

Research Team : Prof. Dr. Sami S. Adawy , Dr. Mohamed Atia Omar


1- Sex-Differentiation Based on Fluorescence In Situ Hybridization (FISH) with 5S and 45S rDNA of Egyptian Date Palm  Trees


This study aimed to develop a sex-specific fluorescence in situ hybridization (FISH) markers with 5S and 45S rDNA in Egyptian date palm trees (cv. Zaghloul and Siwi).The results successfully revealed clear differences between males and females belonging to both cv. Zaghloul and Siwi by using 45S rDNA FISH. The fluorescence in situ hybridization (FISH) with 45S rDNA localized two clear telomeric intermediate-signals in female trees belonging to cv. Zaghloul and Siwi. While, it exhibited three clear telomeric intermediate-signals in male trees belonging to cv. Zaghloul and Siwi. On the other hand, results of fluorescence in situ hybridization (FISH) with 5S rDNA didn’t reveal any clear differences between males and females belonging to cv. Siwi. Based on the above results, we hypothesize that the third signal (unpaired signal) of 45S rDNA probe characterized in both Siwi and Zaghloul males is located on a male chromosome (Y chromosome). This finding can be utilized and used as cytological marker to differentiate between male and female trees in Egyptian date palm at an early stage.

2- Novel Set of Sex-Specific PCR-Based Markers Reveals New Hypothesis of Sex Differentiation in Date Palm


This study employed three effective gene-targeting marker approaches (SCoT, CDDP and ITAP) in additions to AFLP, in an attempt to develop a novel set of reliable sex-specific PCR-based markers can helping in early gender determination in Egyptian date palm trees. Four SCoT, two CDDP, one ITAP and one AFLP primer/primer combination exhibited differential bands between males and females under study. These differential bands were sequenced. BLAST analysis results indicated that the eleven sequences generated from different gene-targeting marker systems (SCoT, CDDP and ITAP) revealed main similarity with master transcription factors, transcriptional activators/repressors and regulatory proteins involved in plant hormone signal transduction pathways, plant development and biosynthesis of secondary metabolites in date palm or oil palm. We speculated that kind of similarity is not just a coincidence. These results revealed hypothesis that sex differentiation is a complex but well-organized process that involves endogenous and exogenous factors regulate and control the changes in gene expression, physiology, metabolism and architecture of the plant. These results indicate that sex-differentiation process have to be addressed at system biology level for deep and better understanding.
















The main duty for AGERI’s Genomics facility is to provide access to the latest technologies and highly specialized equipment in genetic analyses. This enables the utilization of such technologies and instruments to improve productivity and sustainability in the agricultural sectors as well as providing services for the national and regional scientific communities.

Several research activities are carried out in the facility using the available state-of-the-art equipment.

  1.      Egyptian Buffalo Genome Sequencing:

This project was carried out in collaboration with Nile University and ARC’s Animal Production Research Institute. The goal of this research activity was to produce a high resolution draft genome of Egyptian buffalo and to partially annotate the genome to identify genetic features within the sequenced genomes: These features include, but not limited to, identification of genes, regulatory elements, and repeat families. The first draft was completed in 2013 and the high-quality version and the annotation of the genome were finished in early 2015. This activity was the first of its kind to establish a national platform for whole genome sequencing. This was the first activity of its kind in Egypt to integrate multi-disciplinary research institutes to develop a national platform for whole genome sequencing. The outcomes of this project will help improve the productivity of meat and milk in Egyptian buffalo as well as aiding the breeders in selecting the more economical herds.

  1.      Date Palm genome sequencing:

In 2014, the draft genome of 4 Egyptian date palm varieties was finished. The genomes of Zaghloul, Hayani, Amhat and Siwi varieties were sequenced in order to study the genetic variation between theses commercially important varieties as well as laying the foundation for utilizing genomics approaches to improve productivity, decrease crop loss, sex determination and the accurate prediction of varietal genotypes. This activity was carried out in collaboration with the ARC’s Central Laboratory for Date Palm Research and Development.



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During the last century, the Green Revolution has preserved the global population from hunger (the fact that hunger still exists on this planet, is a political, not an agricultural problem). In addition to mineral fertilisers, chemical plant protection, and the use of machines, it has been the progress in breeding that allowed to multiply yields although area did not increase. This intensivity claimed its price, though. Especially in dry regions, inappropriate irrigation has made soils progressively salty (transpiration of water leaves salty residues). The agriculture of the future has to become more sustainable and this requires a more careful use of the precious resource water. To breed plants that consume less water and also can cope with salty soils, has therefore shifted in the focus of global research. Rice as most important staple food is of central interest in this context. In frame of the German-Egypt cooperation projectDesertcereals, funded by the Federal Ministry of Education and Research, we investigate, how rice responds to salt and drought stress. To our surprise, we found that mutants we had developed affected in the synthesis of the central stress hormone jasmonic acid (a kind of plant version for adrenalin) performed superior to normal, non-mutated rice plants. In the search for an explanation we discovered that a precursor of jasmonic acid, OPDA, can cause all sort of damage, when normal plants are challenged by stress. Especially the oxidative equilibrium is messed up leading to an excess of so called reactive oxygen species. The mutants cannot synthetise OPDA and therefore remain “cool” even under stress. Of course it does not make sense to use these mutants for agriculture – the lack of jasmonic acid has also negative impact (for instance a strong reduction in fertility) – but we can now search for alternative strategies to contain OPDA and thus to improve plant performance under salt and drought stress. Our strategy is rather to use molecular breeding, whereby wild relatives of rice, old cultivars or landraces are searched for favourable variants of the relevant genes. Then these variants are introduced by natural crossing into the plant of interest. By means of the molecular information it is possible to identify in the offspring of the cross already in the seedling stage those individuals that are most favourable for the next breeding step. In contrast to traditional breeding, where only time consuming field trials will tell this, it is possible to advance more precisely and therefore more rapidly. In contrast to genetic engineering, no introduction of foreign DNA is required.


113. Hazman M, Hause B, Eiche E, Nick P, Riemann M (2015) Increased tolerance to salt stress in OPDA-deficient rice ALLENE OXIDE CYCLASE mutants is linked to an increased ROS-scavenging activity. J Exp Bot, doi: 10.1093/jxb/erv142 -

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