High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources

Italy counts a large number of local chicken populations, some without a recognized genetic structure, such as Val Platani (VPL) and Cornuta (COS), which represent noteworthy local genetic resources. In this study, the genotype data of 34 COS and 42 VPL, obtained with the Affymetrix Axiom600K-Chicken Genotyping Array, were used with the aim to investigate the genetic diversity, the runs of homozygos-ity (ROH) pattern, as well as the population structure and relationship within the framework of other local Italian and commercial chickens. The genetic diversity indices, estimated using different approaches, displayed moderate levels of genetic diversity in both populations. The identified ROH hotspots harbored genes related to immune response and adaptation to local hot tempera-tures. The results on genetic relationship and population structure reported a clear clustering of the populations according to their geographic origin. The COS formed a nonoverlapping genomic cluster and clearly separated from the other populations, but showed evident proxim-ity to the Siciliana breed (SIC). The VPL highlighted intermediate relationships between the COS-SIC group and the rest of the sample, but closer to the other Italian local chickens. Moreover, VPL showed a complex geno-mic structure, highlighting the presence of 2 subpopula-tions that match with the different source of the samples. The results obtained from the survey on genetic differentiation underline the hypothesis that Cornuta is a population with a defined genetic structure. The sub-structure that characterizes the Val Platani chicken is probably the consequence of the combined effects of genetic drift, small population size, reproductive isola-tion, and inbreeding. These findings contribute to the understanding of genetic diversity and population struc-ture, and represent a starting point for designing pro-grams to monitor and safeguard these local genetic resources, in order to define a possible official recognition program as breeds.