Posts

Vol.7 No.2 – 5: Genetic variations in some Egyptian Zea mexicana genotypes based on RAPD and AFLP markers

/0 Comments/in , , /by

By: K.H. Radwan1,2*, G.A. Abdelfattah1,3, M.A. Badawi1,4, E. M. Zayed5, M.M. Tarrd6. Manal M. S. El-Baghdady1, Reem M. Abd El-Maksoud1

1. Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza -12619, Egypt

2. National biotechnology Network of Expertise, ASRT, Egypt.

3. Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, KSA

4. Dép. des Sciences Biologiques, Univ. du Québec à Montréal, Montréal, QC H3C 3P8, Canada

5. Cell Study Research Department (CSRD), Field Crops Research Institute, Agriculture Research Center (ARC), Giza 12619, Egypt

6. Forage Crops Research Department (FCRD), Field Crops Research Institute, Agriculture Research Center (ARC), Giza-12619, Egypt.

Abstract

Maize-Teosinte hybrids are of significant interest to maize breeders as a resource of genetic diversity during the maize domestication process as a genetic pool for maize improvement. This study examines the genetic diversity and population structure of 16 Zea mexicana populations which are currently active in Zea breeding programs in Egypt using Random Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) markers. RAPD analysis (14 primers) produced 141 bands; out of which, 102 (72.3%) were polymorphic. On the other hand, AFLP (5 primer combinations) yielded 276 peaks including 267 (96.7%) polymorphic ones with an average of 53.4 peaks per primer combination. A total of 11 unique RAPD markers were created by 6 primers and identified 8 genotypes. The five primer combinations generated 56 unique amplicons that successfully distinguished 12 out of the 16 genotypes tested. Furthermore, the number of observed alleles (Na), effective multiplex ratio (EMR), and polymorphic information content (PIC) indices showed higher values for AFLP (2.00, 53.4, and 0.21) than for RAPD (1.67, 7.3, and 0.15). Cluster analysis based on Nei and Li genetic distance and an Unweighted Pair Group Method with Arithmetic Mean (UPGMA) revealed 5 main clusters representing the 16 Zea mexicana confirming the population structure analysis obtained. High variability of the studied teosinte genotypes using RAPD and AFLP markers will provide valuable tools for Zea mexicana breeding programs in Egypt.

Genetic variations in some Egyptian Zea mexicana genotypes based on RAPD and AFLP Markers-converted

Download PDF

Vol.5 No.4 – 2: Salt Tolerance Associated With Molecular Markers In Alfalfa

/0 Comments/in , , /by

By : 1Clara R. Azzam*,  2 Zainab M. Abd El Naby  and 2 Nabila, A. Mohamed

1Department of Cell Research, Field Crop Res. Inst., Agric. Res. Center, Giza, Egypt

2 Department of Forage Research, Field Crop Res. Inst., Agric. Res. Center, Giza, Egypt

Abstract

Background: Breeding for salinity tolerance in open-pollinated crops depends on broad genetic variation in order to selection for vigorous plants under salinity stress. Objective: To compare yield of some local alfalfa cultivars under saline and non-saline soils and to develop molecular genetic markers associated with salt tolerance using RAPD and ISSR analysis, thereby providing a basis for alfalfa salt-tolerance breeding and research. Methods: A two years field trial was carried out during 2013/14 and 2014/15 in Galbana Village at Sahl El-Tina site., North Sinai Governorate with 13 cuts after establishing period. Three local parental cultivars, nine selected population for salt stress under different stress levels (three initial EC’s: 8.73, 10.63 and 12.43 dSm-1), a new tolerant pop, and three exotic varieties were included in the experiment under initial EC’s (10.83). Results: Under Egyptian conditions local cultivars: Siwa and Ismaelia were qualified as more adapted to salinity stress conditions than the exotic cultivars. New tolerant pop. ranked as the top yielding across all tested parental populations followed by Siwa and Ismaelia tolerant selected populations. New valley population had the lowest fresh, dry and protein yield over all studied populations. The tolerant selected populations were out yielded than their parental cultivars. A total of 16 alfalfa populations were analyzed at the molecular level to develop molecular markers associated with salt tolerance using seven RAPD and five ISSR primers. All primers succeeded to generate reproducible polymorphic DNA products. RAPD primers produced eight positive specific markers and six negative specific markers for salt tolerance in alfalfa population Sinai-1, while ISSR primers produced 12 positive specific markers and six negative specific markers for salt tolerance in alfalfa. The dendrograms were generated using pooled RAPD, ISSR and the combined analysis of their data divided the alfalfa populations into two main clusters. The first cluster consisted of population Sinai 1 alone, while the second one contains all other evaluated populations. Conclusion: The new tolerant pop. could be considered as a new promising population and more adapted to salt stress.

Salt Tolerance Associated With Molecular Markers In Alfalfa 1-converted

Download PDF

Vol.2 No.4 -4 : Development of cytochrome-c-oxidase 1 specific primers for genetic discrimination of the European eel Anguilla anguilla (Linnaeus, 1758).

/0 Comments/in , , /by

By : Khaled Mohammed-Geba, Sobhy El-Sayed Hassab El-Nabi, Marwa Said El-Desoky

Abstract

The European eel Anguilla anguilla (Anguillidae, Anguilliformes) is amongst the most peculiar, economically-important fish species in the Egyptian and Mediterranean waters. Very rare studies are available about its populations in the Mediterranean. In order to investigate this issue, we designed cytochrome-c-oxidase subunit 1 (COI) gene-specific primers for A. anguilla. These primers targeted the amplification of a 750 bp fragment towards the 5` extremity of COI. The primers were tested for A. anguilla elvers collected from Rachid Estuary in Egypt. They succeeded to amplify the targeted fragment. Using Forensically Informative Nucleotide Sequences (FINS) analysis and BLAST comparisons, the sequences were successfully assigned to A. anguilla, with clear segregation from other Anguilla species. The primers designed and used in this study can be then suggested as successful alternatives for universal primers commonly used in European eel barcoding.

4. Development of cytochrome-c-oxidase 1 specific primers for genetic discrimination of the European eel Anguilla anguilla (Linnaeus, 1758).
Download Issue

Vol.1 No.4 -6 : North African sharptooth catfish Clarias gariepinus In silico analyses for genetic expansion of a peculiarly successful catfish species in and out of its African homelands.

/0 Comments/in , , /by

By : Khaled Mohammed-Geba

Abstract

The African sharptooth catfish Clarias gariepinus originated from Africa, but its sturdiness and resistance to different environmental conditions enabled it to spread to almost all continents of the world. To develop effective conservation strategies for C. gariepinus, the connection patterns of its geographically related and isolated strains should be precisely described. For this purpose, 65 sequences for cytochrome oxidase subunit 1 (CO1) mitochondrial gene were retrieved from GenBank database. Common and unique haplotypes, average numbers of nucleotide substitutions (Dxy), fixation indices (FST), neutrality and expansion, phylogeny, and haplotype network analyses were all identified. 13 different haplotypes were found, most of which are related to an African haplotype mainly found in Nigeria. Other African, Asian, and South American haplotypes were detected, with the South American and some Asian haplotypes showing the greatest diversion from the main African one. The Nigerian population of C. gariepinus seems to be the most rapidly expanding one, due to the highest frequency of singletone haplotypes among all studied populations. Our results agreed with the knowledge about the world-wide propagation of C. gariepinus recorded in the Food and Agriculture Organization introduced aquatic species database and other related reports, what may confirm the effectiveness of such molecular markers and bioinformatic tools for tracking the origin and movement of the C. gariepinus out of Africa.

6. North African sharptooth catfish Clarias gariepinus In silico analyses for genetic expansion of a peculiarly successful catfish species in and out of its African homelands.
Download Issue