Genomic DNA fingerprinting of indigenous chicken breeds with molecular markers designed on interspersed repeats

In Italy more than fifty different local breeds of chicken (Gallus gallus L.) are known to have been present in the past. The overall situation is now critical since most of these breeds are becoming extinct or threatened and only a few are subject of conservation plans. The use of molecular markers for the analysis of chicken populations could help in characterizing their genetic variation and preserving them from genetic erosion. valuable and irreplaceable sources of chicken germplasm from indigenous populations of the Veneto region were analyzed by means of DNA fingerprinting with molecular markers designed on interspersed mini- and microsatellite repeats. The identification of either among-breed discriminant or breed-specific markers was based on the S-SAP and M-AFLP systems derived from the AFLP technology. Genomic DNA fingerprints were generated in 84 individuals belonging to six local breeds (Ermellinata, Padovana, Pépoi, Polverara, Robusta Lionata and Robusta Maculata) and one commercial line used as reference standard. A number of variation statistics were computed to assess the genetic variability within and relatedness among breeds: the effective number of alleles per locus (ne = 1.570), total and single-breed genetic diversity (HT = 0.366 and HS = 0.209, respectively) and the fixation index (GST = 0.429). The mean genetic similarity coefficients within and between local breeds were 0.769 and 0.628, respectively. Markers useful for the genetic traceability of breeds revealed significant sequence similarities with either genic or intergenic regions of known chromosome position. Sequence tagged site primers were designed for the most discriminant markers in order to develop multiplex non-radioactive genomic PCR assays. Analysis of the population structure along with individual assignment tests successfully identified all breed clusters and subclusters. The vast majority of animals were correctly allocated to their breed of origin, demonstrating the suitability and reliability of the chosen AFLP-derived marker systems for detecting population structure and tracing individual breeds. The local breeds have been preliminarily identified according to sequence-specific SNPs and haplotypes and the polymorphism information content of genomic AFLP-derived markers is reported and critically discussed.