genome scan inference to the genetic evaluation of selected and randombred chicken populations

ABSTRACT

The genome scans were obtained for three lines of chickens genotyping for homozygous nakednecks [line N], homozygous normal feathering [line F] and their randombred population [line C]. Lines N and F have undergone massive selection for two generations for increased 6-week body weight. The objective of the study was to evaluate the genetic changes associated with selection or random breeding. Six pooled DNA samples within line and generation were scanned by five decamer RAPD-PCR primers. The averages of allelic bands were 11, 10.6, and 9.6 bands for lines N, F and C, respectively. Bands with polymorphic nature were detected and averaged 71.5, 66.7 and 59.3% of the total allelic bands in the respective lines. The monomorphic alleles averaged 3.3, 8.2 and 8.6%, and line-specific bands were also observed and averaged 9.7, 10.8, and 6.2%. The line-specific bands were mainly attributed to selection and poorly to the random genetic drift. The recognition of monomorphic and line-specific allelic bands revealed the reliable contribution of genome scanning in recognition of line specificity. The change in allele frequency over two selected generations in lines N and F demonstrated allelic bands with downward trend and others with upward trend, concluding that genomic alleles may be employed to monitor the changes in allele frequency over subsequent generations. Allelic coalescence points were estimated and the copies descended from ancestral alleles to the second generation were estimated to be 29.56, 28.20 and 37.56% of the total allelic bands scored in lines N, F and C. Number of gene trees were formed due to the accumulation of transmitted ancestral alleles and totaled 22, 12, and 15 in the respective lines. The estimation of rate of coalescence points and tracing ancestral alleles is of significance for small-sized selected and inbred populations. The results of genomic variability reported in lines N and F indicated that a further selection progress is anticipated in each. The genetic distance between lines N and F after two generations of selection was 1.03, and both were genetically distant from line C by 1.15 and 0.81. The results denote to the significance of genome scanning in the evaluation of breeding programs