الفهرس 
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Abstract
Summary The current study is the first that assessed the genetic diversity of a wide spectrum of Egyptian chickens kept as genetic resources in Al-Azzab Integrated Poultry Project interrogating genome wide 29 microsatellite loci. We aimed to understand their genetic structure necessary for the prospective conservation and breeding strategies. The blood samples were collected randomly from 251 chickens pertained to ten chicken strains kept in Al-Azzab station-4. The strains studied were the native Dandarawi and Fayoumi (two selected lines), Sinai mongrel chicken and six synthetic breeds including Doki-4, Inshas, Golden-Montazah, Silver-Montazah, Gimmizah and Bandara. DNA was extracted from EDTA-blood using standard salt out method. A marker set of 29 autosomal microsatellites, reference samples and seven multiplex PCR reactions were used as given on the AVIANDIV website (http://aviandiv.tzv.fal.de/ html).
DNA fragments were scored on 6% polyacrylamide gel using the LI-COR automated DNA analyser. Genotyping data were analysed using software packages including: GenAlEx 6, GENEPOP, FSTAT, Statistical Analysis System (SAS), PHYLIP, TREEVIEW version 1.6.6, SPLITSTREE4, STRUCTURE, CLUMPP and DISTRUCT. Within and between-population marker estimated kinships (MEK) and MEK-based distances were estimated according to Eding & Meuwissen (2001; 2003).
It was found a total of 209 distinct alleles were observed across the studied populations, and 33 of them (15.8%) were unique mostly to synthetic breeds especially Gimmizah. That case reflects melting of genetic entities of pure strains due to extensive hybridization. The average values of observed and effective alleles / locus were 7.2 and 3.4. The least genetically diverse population was Fayoumi GG line with mean number of alleles 4.2±0.34, PIC value of 0.44±0.03, observed and expected heterozygosity values of 0.48±0.04 and 0.48±0.03). Inshas showed the highest genetic polymorphism in current study (MNA= 5.4±0.49, PIC= 0.62±0.03, HO= 0.67±0.04, HE= 0.67±0.03).
Non-significant deviation from the Hardy-Weinberg equilibrium were observed at each locus-population combination, showing overall low deficiency of heterozygotes (FIS= 0.02± 0.01), except for MCW80 which skewed significantly from HWE in Fayoumi GG, Gimmizah and Silver-Montazah. However, Fayoumi PP and Gimmizah showed highest levels of inbreeding (> 0.06). The global heterozygote deficiency in the Egyptian chickens (FIT ± SE) was 0.09 ± 0.01. About 7% and 8% of total genetic variance was due to between-population differences (FST) including and without synthetic breeds, respectively.
Nei’s and Reynolds genetic distances clarified moderate genetic variation between Egyptian strains if compared to other studies with mean values ±SD of 0.15±0.05, 0.09±0.04, respectively. The MEK findings were very high between studied chickens among other studies (averaged with 0.18±0.1). This could insist that Egyptian chickens might be exposed to substantial gene flows in between or have limited common ancestral origin(s). The phylogenetic trees and STRUCTURE showed consistent cluster pattern. There were three distinct clusters identified involving: Fayoumi-lines and Doki-4; Dandarawi; and Gimmizah in addition to a mosaic admixed cluster encompassing Sinai and other synthetic breeds.
Eventually, Egyptian chickens showed a high intra- and inter-population genetic diversity and thus, are in an urgent appeal to be conserved. Cluster analysis indicated that Fayoumi, Dandarawi, Gimmizah and Sinai are at highest priority for conservation due to their genetic distinctiveness and national importance.