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Genomic and genetic variability of six chicken populations using single nucleotide polymorphism and copy number variants as markers

Published online by Cambridge University Press:  07 November 2016

M. G. Strillacci ,
M. C. Cozzi ,
E. Gorla ,
F. Mosca ,
F. Schiavini ,
S. I. Román-Ponce ,
F. J. Ruiz López ,
A. Schiavone ,
M. Marzoni  and
S. Cerolini
...Show all authors
M. G. Strillacci*
Affiliation:
Department of Veterinary Medicine, Universitá Degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
M. C. Cozzi
Affiliation:
Department of Veterinary Medicine, Universitá Degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
E. Gorla
Affiliation:
Department of Veterinary Medicine, Universitá Degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
F. Mosca
Affiliation:
Department of Veterinary Medicine, Universitá Degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
F. Schiavini
Affiliation:
Department of Health, Animal Science and Food Safety (VESPA), Universitá degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
S. I. Román-Ponce
Affiliation:
Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, INIFAP, Km.1 Carretera a Colón, Auchitlán, 76280 Querétaro, México
F. J. Ruiz López
Affiliation:
Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, INIFAP, Km.1 Carretera a Colón, Auchitlán, 76280 Querétaro, México
A. Schiavone
Affiliation:
Department of Veterinary Science, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
M. Marzoni
Affiliation:
Department of Veterinary Science, Università degli Studi di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
S. Cerolini
Affiliation:
Department of Veterinary Medicine, Universitá Degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
A. Bagnato
Affiliation:
Department of Veterinary Medicine, Universitá Degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
*
†Email: [email protected]
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Abstract

Genomic and genetic variation among six Italian chicken native breeds (Livornese, Mericanel della Brianza, Milanino, Bionda Piemontese, Bianca di Saluzzo and Siciliana) were studied using single nucleotide polymorphism (SNP) and copy number variants (CNV) as markers. A total of 94 DNA samples genotyped with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix) were used in the analyses. The results showed the genetic and genomic variability occurring among the six Italian chicken breeds. The genetic relationship among animals was established with a principal component analysis. The genetic diversity within breeds was calculated using heterozygosity values (expected and observed) and with Wright’s F-statistics. The individual-based CNV calling, based on log R ratio and B-allele frequency values, was done by the Hidden–Markov Model (HMM) of PennCNV software on autosomes. A hierarchical agglomerative clustering was applied in each population according to the absence or presence of definite CNV regions (CNV were grouped by overlapping of at least 1 bp). The CNV map was built on a total of 1003 CNV found in individual samples, after grouping by overlaps, resulting in 564 unique CNV regions (344 gains, 213 losses and 7 complex), for a total of 9.43 Mb of sequence and 1.03% of the chicken assembly autosome. All the approaches using SNP data showed that the Siciliana breed clearly differentiate from other populations, the Livornese breed separates into two distinct groups according to the feather colour (i.e. white and black) and the Bionda Piemontese and Bianca di Saluzzo breeds are closely related. The genetic variability found using SNP is comparable with that found by other authors in the same breeds using microsatellite markers. The CNV markers analysis clearly confirmed the SNP results.

Keywords

single nucleotide polymorphismcopy number variationpoultrybiodiversitygenetic variability
Type
Research Article
Information
animal , Volume 11 , Issue 5 , May 2017 , pp. 737 - 745
Copyright
© The Animal Consortium 2016 

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