Abstract
This study aims at investigating genomic diversity of several turkey populations using Copy Number Variants (CNVs). A total of 115 individuals from six Italian breeds (Colle Euganei, Bronzato Comune Italiano, Parma e Piacenza, Brianzolo, Nero d’Italia, and Ermellinato di Rovigo), seven Narragansett, 38 commercial hybrids, and 30 Mexican turkeys, were genotyped with the Affymetrix 600K single nucleotide polymorphism (SNP) turkey array. The CNV calling was performed with the Hidden Markov Model of PennCNV software and with the Copy Number Analysis Module of SVS 8.4 by Golden Helix®. CNV were summarized into CNV regions (CNVRs) at population level using BEDTools. Variability among populations has been addressed by hierarchical clustering (pvclust R package) and by principal component analysis (PCA). A total of 2,987 CNVs were identified covering 4.65% of the autosomes of the Turkey_5.0/melGal5 assembly. The CNVRs identified in at least two individuals were 362—189 gains, 116 losses, and 57 complexes. Among these regions the 51% contain annotated genes. This study is the first CNV mapping of turkey population using 600K chip. CNVs clustered the individuals according to population and their geographical origin. CNVs are known to be indicators also of adaptation, as some researches in different species are suggesting.
Highlights
The domestication of the wild turkey appears to occur in Mexico between 200 B.C. and 700 A.D. (Crawford, 1992)
At present in Europe there is a clear differentiation in several turkey breeds, indicating that farmers and breeders have selected the turkey populations according to a directional goal for more than 5 centuries
A total of 115 biological samples from individuals belonging to six Italian breeds (Colle Euganei: CoEu – 22; Bronzato Comune Italiano: BrCI – 5; Parma e Piacenza: PrPc – 15; Brianzolo: BR – 32; Nero d’Italia: NI – 31; Ermellinato di Rovigo: ErRo – 10), 7 Narragansett turkeys, 38 commercial hybrids (HYB), 30 Mexican turkeys (MEX) were available from previous collections or deriving from other research projects and part of the University of Milan repository of animal samples
Summary
The domestication of the wild turkey appears to occur in Mexico between 200 B.C. and 700 A.D. (Crawford, 1992). The domestication of the wild turkey appears to occur in Mexico between 200 B.C. and 700 A.D. The domesticated turkey has been introduced in Europe from Mexico and Central America starting in late 15th century (Schorger, 1996) by the Spanish conquerors. The diffusion of the turkey population in the European territory was very fast, close to 50 km per year as indicated by Crawford (1992). The rapid diffusion in Europe was possibly facilitated because of their farming, as turkey was appreciated for its meat (Schorger, 1996). Since the 15th century, the populations of European and Mexican turkey evolved independently for more than 500 years. At present in Europe there is a clear differentiation in several turkey breeds, indicating that farmers and breeders have selected the turkey populations according to a directional goal for more than 5 centuries
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