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Abstract Egypt is famous for its vast desert spaces. About 4/5 the total area is desert. Only about one-fifth of the total area is cultivated land. In the western desert of Egypt there are a series of oases which stretching longitudinally from the north to the far south in a line almost parallel to the Nile valley. This represents natural depressions rich in natural springs and wells which are used in agriculture. One of the advantages of this desert is the presence of wild flora species adapted to a biotic and biotic stresses. Despite the rarity of wild plant cover in such region, this existing flora is a treasure of genetic resources. Most of these flora species are considered as the ancestors of domesticated plants, others have medicinal benefits either on the popular level or on the documented medicinal treatments The Genetic description and phylogeny of some Egyptian Acacia species and subspecies was investigated in present study by calculating the morphological variation among Acacia species, detecting biochemical markers based on peroxidase activity and proline content in Acacia species, estimate the level of polymorphism among Acacia species using RABD-PCR markers and determining the genetic relationships between these species based on the genetic distances. The present research was carried out at the Faculty of Agriculture, Saba Basha, Alexandria University and Faculty of Agriculture, Ain Shames University, Egypt during the seasons of 2011 up to 2013 to study the morphological, biochemical and molecular genetic markers of some selected Acacia genotypes as a tool for genetic description for these genotypes. Leaves of Acacia genotypes: Acacia tortilis ssp. radiana, Acacia farnesiana, Acacia stenophylla, Acacia sclerosperma, Acacia saligna were collected completely randomly from 20 individuals of Acacia tree natural habitats along different localities in Egypt i.e. Abis station Farm, Faculty of Agriculture Saba Basha., Borg Al-Arab, Marsa Matroh City and EL-Gara (Siwa Oasis). Four samples were taken for each parameter. The following morphological parameters were measured as follow in vegetative parts of the tree: leaf length (cm), pinna’s length (cm), 72 leaflet’s length (mm), spine length (mm) In addition, some qualitative characters such as the shape of the crown, Growth form: either tree or shrub as shown, number of stems from ground level Proline was determined by 3% Aqueous Sulfosalicylic Acid, Acid Ninhydrin:1.25 gm Ninhydrin ,30 ml glacial acetic acid,20 ml 6M phosphoric acid .The mixture was warmed with agitation until dissolved then kept cool at 40C until use. Five RAPD primers has been developed, in which DNA is amplified by the polymerase chain reaction (PCR) using arbitrary short (10 nucleotides) primers . Concerning to spine length (mm) data indicated clearly high significant variations among different species. The highest values was recorded to Acacia tortilis ssp. Radiana collected from (Siwa Oasis), followed by Acacia tortilis ssp. Radiana (collected from Borg Al-Arab city) in means 28.75 and 19.25 mm, in respect. The lowest mean value was recorded to Acacia farnesiana in mean 6.50 mm with LSD =1.36. No spines were found in the other three species Acacia saligna, A. sclerosperma and A. stenophylla. Data showed inverse relationship between the spine and pinna length, epically in the desert localities. The results showed that Acacia tortilis ssp. Radiana collected from Siwa and Borg Al-Arab, have the lowest value of pinna length (0.68 and 0.98cm), respectively, compared with the highest value to (4.28 cm) in Acacia farnesiana. For Leaf length (cm) data showed that Acacia sclerosperma and Acacia saligna have the highest mean values; 23.28 cm and 26.08 cm, in respect. While the lowest leaf length was recorded to Acacia tortilis ssp. Radiana collected from (Siwa) (2.85 cm), followed by Acacia tortilis ssp. Radiana (collected from Borg Al-Arab) by mean (3.15 cm) and finally Acacia farnesiana in mean 3.80 cm. No significant differences were observed among species the means ranged from 2.0 to 2.50 mm in the Acacia tortilis ssp. Radiana collected from (Siwa=2mm), followed by Acacia tortilis ssp. Radiana (collected from Borg Al-Arab=2.50) and Acacia farnesiana=2.25mm. Based on the qualitative data, high similarities were found between Acacia farnesiana and Acacia tortilis ssp. Radiana in leaves type it were pinnately compound . On the other hand, Acacia saligna, Acacia |