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. 2023 Jul;102(7):102692.
doi: 10.1016/j.psj.2023.102692. Epub 2023 Apr 5.

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

Marco Tolone  1 , Maria Teresa Sardina  1 , Andrea Criscione  2 , Emiliano Lasagna  3 , Gabriele Senczuk  4 , Ilaria Rizzuto  1 , Silvia Riggio  1 , Angelo Moscarelli  1 , Vito Macaluso  1 , Rosalia Di Gerlando  1 , Martino Cassandro  5 , Baldassare Portolano  1 , Salvatore Mastrangelo  6
Affiliations

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

Marco Tolone et al. Poult Sci. 2023 Jul.

Abstract

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 Axiom600KChicken Genotyping Array, were used with the aim to investigate the genetic diversity, the runs of homozygosity (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 temperatures. 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 proximity 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 genomic structure, highlighting the presence of 2 subpopulations 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 substructure that characterizes the Val Platani chicken is probably the consequence of the combined effects of genetic drift, small population size, reproductive isolation, and inbreeding. These findings contribute to the understanding of genetic diversity and population structure, and represent a starting point for designing programs to monitor and safeguard these local genetic resources, in order to define a possible official recognition program as breeds.

Keywords: SNP; conservation; genetic diversity; inbreeding; local population.

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Figures

Figure 1
Figure 1
Manhattan plot of frequency (%) of a single nucleotide polymorphism (SNP) in run of homozygosity (ROH) islands in (A) Val Platani (VPL) and (B) Cornuta (COS) chicken populations.
Figure 2
Figure 2
Genetic relatedness of chicken populations inferred by multidimensional scaling (MDS) approach and using (A) all of the individuals and (B) the breed-average coordinates of eigenvalues of C1 and C2. For a full definition of populations, see Table S1.
Figure 3
Figure 3
Neighbor-net graph based on Reynolds genetic distances of all chicken populations. For a full definition of populations, see Table S1.
Figure 4
Figure 4
Model-based clustering of chicken populations from K = 2 to K = 15. For a full definition of populations, see Table S1.
Figure 5
Figure 5
TREEMIX analysis with the most supported number of migration events (m = 1). For the full definition of populations, see Table S1.
See this image and copyright information in PMC

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