Mostafa Helal

Microsatellites are important markers for livestock including ducks. The development of microsatellites is expensive and labor-intensive. Meanwhile, the in silico approach for mining for microsatellites became a practicable alternative. Therefore, the current study aimed at comparing whole-genome and chromosome-wise microsatellite mining approaches in Muscovy and Mallard ducks and testing the transferability of markers between them. The GMATA software was used for the in silico study, and validation was performed using 26 primers.

In a research project aiming at the genetic improvement of warm-region originated chickens,
a breeding program was practiced on naturally heat-resistant local population in Egypt and
four lines have been derived. The lines were the homozygous normally-feathered selected
(CE1) and control (CE2) lines, and the homozygous naked-neck selected (CE3) and control
(CE4) lines. Lines CE1 and CE3 have been selected for 6-wk body weight for eight
generations. The objective of this study was to assess the genetic features of the selected lines
at the microsatellite loci recognized by 27 microsatellite primers in generations 6, 7 and 8.
The number of alleles detected by each primer varied from one to seven. The number of
alleles per primer and generation averaged 5.72, 2.35, 5.98 and 2.57 in lines CE1, CE2, CE3
and CE4, respectively. The genetic variability was in general low among lines and ranged
0.17–0.20. Polymorphic information content (PIC) averaged 0.50, .39, 0.55 and 0.50 in lines
CE1, CE2, CE3 and CE4 respectively, and line-specific alleles (LSA) formed 4.3, 0.7, 4.6
and 1.2% of total alleles in corresponding lines. The differences between each selected line
and its control line in PIC and LSA were significant, except between line CE3 and line CE4
in PIC. The results denoted to the possible linkages between the detected microsatellite loci
and QTL for body weight. By generation 8, the genetic distance indices between line CE1
and line CE2 averaged 0.740, and between line CE3 and line CE4 averaged 0.815. The
phylogenetic dendograms revealed the genetic progress of the selected lines over subsequent
generations.

The genome scanning was performed on four chicken populations to estimate the genomic
changes associated with genetic selection. The populations were the local naked-neck line CE3 that
has been selected for 6-wk BW for 6 generations with its genetic control line CE4, and a broiler
dam line D with its genetic control line CD. In lines CE3 and D. The PCR was applied to pooled
DNA samples of each line and sex using seven microsatellite markers. The average number of
alleles per microsatellite locus was 2.14, denoting to the multi-allelic property of the detected loci.
The total number of allelic bands and their frequencies differed among lines and sexes,
demonstrating the genetic composition specificity of each line and the sexual dimorphism. The
variability, heterozygosity and PIC averaged 0.54, 0.68 and 0.81 in line CE3 versus 0.46, 0.52 and
0.57 in line CE4. The moderate variability and moderately high heterozygosity estimates in line
CE3 indicate that there is still much work can be done through selection. The distance between line
CE3 and line CE4 averaged 2.92, and the distance between line D and its control line CD averaged
1.95. These distances reveal the progress of selection practiced in lines CE3 and D, that has been
expressed in shifting the genetic composition of them from those of their control lines CE4 and CD.
The longer distance between line CE3 and line CE4 than that between line D and line CD indicates
the higher selection progress achieved in line CE3 compared to line D.

ABSTRACT This study aimed at elucidating the genetic variation within and between duck populations and estimating the phylogenetic relationships among them. Five duck breeds of two species, Muscovy and Sudani of Cairina species, and White Pekin, Damietti and Khaki Campbell of Anas species, were used. The technique of random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) was applied using five random primers. Individual DNA samples within breed and also a bulk of DNA samples for each breed were used. Primers amplified bands with an overall mean of 8.45 and 8.68 bands for individual and pooled samples, respectively. No significant difference was observed between pooled and individual samples indicating the reliability of mixing DNA samples within breed. High levels of polymorphism and heterozygosity between breeds were obtained. Two primers (OPC-08 and OPC-11), resulted in highly polymorphic markers for duck genomes. Specific bands were obtained for species and also for breeds. The overall mean of genetic variability indices within breed was low to moderate and averaged 0.38, whereas band sharing levels within breed were high and averaged 0.73. Variability estimates between breeds were 0.47 and 0.35 for individual and pooled samples respectively, whereas band sharing estimates were 0.63 and 0.74. Genetic distance indices between breeds ranged between 0.264 and 0.728.