The Genetic Diversity Of Egyptian And Ugandan Indigenous Chicken Populations

A total of 20 microsatellite DNA markers were used to assess the genetic diversity within and among four indigenous chicken populations (322 samples of two indigenous chicken populations each from Egypt and Uganda). The genetic diversity parameters of allele frequency, number of observed alleles (Na), number of effective alleles (Ne), heterozygosity (H), and polymorphic information content (PIC) were calculated. NJ and UPGMA phylogenetic trees were reconstructed using Nei's DS and DA genetic distances. The results were as follows:A total of 208 alleles were detected in the Egyptian and Ugandan chicken populations, of which loci of LEI0094 and LEI0234 had the highest Na of 21 while locus of MCW0248 had 4 alleles, and the highest average number of observed and effective number of alleles were 17.25 and 8.24 for LEI0234, while the lowest were 3.05 and 1.59 for MCW0248. Except for loci of LEI0166, MCW0248, MCW0222, and MCW0014 with PIC values ranging from 0.318 to 0.489, and the PIC values of remaining loci were larger than 0.5, indicating their high polymorphisms. The expected heterozygosity (He) showed a similar pattern with the PIC values across all the loci.All Egyptian and Ugandan populations showed high level of genetic diversity with the highest He as 0.679 for the AG population, while the lowest He as 0.626 for the UT population. Among the populations, there were 4 to 7 loci deviated significantly from the Hardy-Weinberg equilibrium (P < 0.05). About 5.1% genetic variability was derived from the differences among the populations, with all markers contributing to the total genetic differentiation significantly.The patterns of Nei's DS and DA genetic distances between the populations were similar. The UT population had the most distant genetic distance from AF population with the highest DA estimate of 0.107, while AG population and AF population had the closest DA distance of 0.020. Clustering and Principal Component Analyses also revealed similar genetic relationships among the four populations that can be divided into two groups: AG population and AF population were in one group while another group consisted of the UT population and UA population.To verify the quality of genotyping data and understand the property of microsatellite DNA structures for elucidating chicken genetic diversity, the DNA sequence variations of major alleles at two chicken microsatellites of MCW0216 and LEI0234 were assessed through direct sequencing their PCR products of 26 selected chicken blood samples.The results of MCW0216 locus were interesting and useful because they showed very complicated DNA sequence structures within both flanking and repeat regions that validated alleles different from each other by single nucleotides. The three SNPs present within both primer regions for genotyping the MCW0216 locus called for an action to re-design new genotyping primers to avoid allelic drop-out during genotyping exercise.The LEI0234 locus was a complex of either perfect or compound tetra-nucleotide microsatellites, with small-sized alleles with 7 to 18 perfect CTTT repeat units while all big alleles longer than 275 bp were consisted of more than 20 basic CTTT repeats being interrupted by a few CCTT motifs as a stabilizing effecter contributing to the expansion of microsatellite length and allelic polymorphism. The presence of many'cryptic'alleles that were identical in fragment sizes but different in either flanking sequences or repeat unit compositions at both loci further warranted an intensive DNA sequence characterization of major alleles for a correct interpretation of microsatellite data.