Hostname: page-component-78c5997874-s2hrs Total loading time: 0 Render date: 2024-11-19T13:16:57.708Z Has data issue: false hasContentIssue false
  • English
  • Français

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]
Get access

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 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abebe, AS, Mikko, S and Johansson, AM 2015. Genetic diversity of five local Swedish chicken breeds detected by microsatellite markers. PLoS One 10, e0120580.Google Scholar
Alexander, DH, Novembre, J and Lange, K 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19, 1655–1664.Google Scholar
Al-Qamashoui, B, Simianer, H, Kadim, I and Weigend, S 2014. Assessment of genetic diversity and conservation priority of Omani local chickens using microsatellite markers. Tropical Animal Health and Production 46, 747–752.Google Scholar
Bagnato, A, Strillacci, MG, Pellegrino, L, Schiavini, F, Frigo, E, Rossoni, A, Fontanesi, L, Maltecca, C, Prinsen, RTMM and Dolezal, MA 2015. Identification and validation of copy number variants in Italian Brown Swiss dairy cattle using Illumina Bovine SNP50 Beadchip. Italian Journal of Animal Science 14, 552–558.CrossRefGoogle Scholar
Ceccobelli, S, Di Lorenzo, P, Lancioni, H, Monteagudo Ibáñez, LV, Tejedor, M, Castellini, C, Landi, V, Martínez Martínez, A, Delgado Bermejo, JV, Vega Pla, JL, Leon Jurado, JM, García, M, Attard, G, Grimal, A, Stojanovic, S, Kume, K, Panella, F, Weigend, SGND and Lasagna, E 2015. Genetic diversity and phylogeographic structure of sixteen Mediterranean chicken breeds assessed with microsatellites and mitochondrial DNA. Livestock Science 175, 27–36.CrossRefGoogle Scholar
Ceppolina, S 2015. Standard Italiano delle Razze Avicole. FIAV Publisher, Sacile (PN), Italy.Google Scholar
Food and Agricultural Organization (FAO) of United Nation 2009. Status and trends report on animal genetic resources – 2008. CGRFA/WG-AnGR-5/09/Inf. 7. FAO Publisher, Rome, Italy.Google Scholar
Frankham, R, Ballou, JD and Briscoe, D A 2004. A primer of conservation genetics. Cambridge University Press, Cambridge, UK.Google Scholar
Gazave, E, Darré, F, Morcillo-Suarez, C, Petit-Marty, N, Carreño, A, Marigorta, UM, Ryder, OA, Blancher, A, Rocchi, M, Bosch, E, Baker, C, Marquès-Bonet, T, Eichler, EE and Navarro, A 2011. Copy number variation analysis in the great apes reveals species-specific patterns of structural variation. Genome Research 21, 1626–1639.Google Scholar
Hammond, K 1996. The status of global farm animal genetic resources. Paper Presented at the Symposium on the Economics of Valuation and Conservation of Genetic Resources for Agriculture, Centre for International Studies on Economic Growth, 13–15 May, Tor Vergata University, Rome, Italy.Google Scholar
Han, R, Yang, P, Tian, Y, Wang, D, Zhang, Z, Wang, L, Li, Z, Jiang, R and Kang, X 2014. Identification and functional characterization of copy number variations in diverse chicken breeds. BMC Genomics 15, 934.CrossRefGoogle ScholarPubMed
Makina, SO, Muchadeyi, FC, van Marle-Köster, E, MacNeil, MD and Maiwashe, A 2014. Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel. Frontiers in Genetics 5, 333.Google Scholar
Mills, RE, Walter, K, Stewart, C, Handsaker, RE, Chen, K, Alkan, C, Abyzov, A, Yoon, SC, Ye, K, Cheetham, RK, Chinwalla, A, Conrad, DF, Fu, Y, Grubert, F, Hajirasouliha, I, Hormozdiari, F, Iakoucheva, LM, Iqbal, Z, Kang, S, Kidd, JM, Konkel, MK, Korn, J, Khurana, E, Kural, D, Lam, HY, Leng, J, Li, R, Li, Y, Lin, CY, Luo, R, Mu, XJ, Nemesh, J, Peckham, HE, Rausch, T, Scally, A, Shi, X, Stromberg, MP, Stütz, AM, Urban, AE, Walker, JA, Wu, J, Zhang, Y, Zhang, ZD, Batzer, MA, Ding, L, Marth, GT, McVean, G, Sebat, J, Snyder, M, Wang, J, Ye, K, Eichler, EE, Gerstein, MB, Hurles, ME, Lee, C, McCarroll, SA and Korbel, JO, and 1000 Genomes Project 2011. Mapping copy number variation by population-scale genome sequencing. Nature 470, 59–65.Google Scholar
Mosca, F, Madeddu, M, Mangiagalli, MG, Colombo, E, Cozzi, MC, Zaniboni, L and Cerolini, S 2015. Bird density, stress markers and growth performance in the Italian chicken breed Milanino. Journal of Applied Poultry Research 24, 529–535.CrossRefGoogle Scholar
Muir, WM, Wong, GK, Zhang, Y, Wang, J, Groenen, MA, Crooijmans, RP, Megens, H J, Zhang, H, Okimoto, R, Vereijken, A, Jungerius, A, Albers, GA, Lawley, CT, Delany, ME, MacEachern, S and Cheng, HH 2008. Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. PNAS 105, 17312–17317.Google Scholar
Nicoloso, L, Bomba, L, Colli, L, Negrini, R, Milanesi, M, Mazza, R, Sechi, T, Frattini, S, Talenti, A, Coizet, B, Chessa, S, Marletta, D, D’Andrea, M, Bordonaro, S, Ptak, G, Carta, A, Pagnacco, G, Valentini, A, Pilla, F, Ajmone-Marsan, P and Crepaldi, P, and Italian Goat Consortium 2015. Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip. Genetic Selection Evolution 4, 47–62.Google Scholar
Rambaut, A. 2014. FigTree. Retrieved on 16 January 2016 from http://tree.bio.ed.ac.uk/software/figtree/.Google Scholar
Redon, R, Ishikawa, S, Fitch, KR, Feuk, L, Perry, GH, Andrews, TD, Flegler, H, Shapero, MH, Carson, AR and Chen, W 2006. Global variation in copy number in the human genome. Nature 444, 444–454.Google Scholar
Sartore, S, Sacchi, P, Soglia, D, Maione, S, Schiavone, A, De Marco, M, Ceccobelli, S, Lasagna, E and Rasero, R 2016. Genetic variability of two Italian indigenous chicken breeds inferred from microsatellites marker analysis. British Poultry Science 15, 1–9.Google Scholar
Schiavo, G, Dolezal, MA, Scotti, E, Bertolini, F, Calò, DG, Galimberti, G, Russo, V and Fontanesi, L 2014. Copy number variants in Italian Large White pigs detected using high-density single nucleotide polymorphisms and their association with back fat thickness. Animal Genetics 45, 745–749.Google Scholar
Strillacci, MG, Marelli, SP, Cozzi, MC, Colombo, E, Polli, M, Gualtieri, M, Cristalli, A, Pignattelli, P, Longeri, M and Guidobono Cavalchini, L 2009. Italian autochthonous chicken breeds conservation: evaluation of biodiversity in Valdarnese Bianca breed (Gallus gallus domesticus). Avian Biology Research 2, 229–233.Google Scholar
Suzuki, R and Shimodaira, H 2006. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 12, 1540–1542.Google Scholar
Tadano, R, Nishibori, M, Imamura, Y, Matsuzaki, M, Kinoshita, K, Mizutani, M, Namikawa, T and Tsudzuki, M 2008. High genetic divergence in miniature breeds of Japanese native chickens compared to Red Junglefowl, as revealed by microsatellite analysis. Animal Genetics 39, 71–78.Google Scholar
Tadano, R, Nishibori, M, Nagasaka, N and Tsudzuki, M 2007. Assessing genetic diversity and population structure for commercial chicken lines based on forty microsatellite analyses. Poultry Science 86, 2301–2308.CrossRefGoogle ScholarPubMed
Tian, M, Wang, Y, Gu, X, Feng, C, Fang, S, Hu, X and Li, N 2013. Copy number variants in locally raised Chinese chicken genomes determined using array comparative genomic hybridization. BMC Genomics 14, 262.CrossRefGoogle ScholarPubMed
Wang, K, Li, M, Hadley, D, Liu, R, Glessner, J, Grant, S, Hakonarson, H and Bucan, M 2007. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Research 17, 1665–1674.Google Scholar
Wang, X and Byers, S 2014. Copy number variation in chickens: a review and future prospects. Microarrays 3, 24–38.Google Scholar
Wang, Z, Chen, Q, Yang, Y, Liao, R, Zhao, J, Zhang, Z, Chen, Z, Zhang, X, Xue, M, Yang, H, Zheng, Y, Wang, Q and Pan, Y 2015. Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data. Animal Genetics 46, 697–701.CrossRefGoogle ScholarPubMed
Wilkinson, S, Wiener, P, Teverson, D, Haley, CS and Hocking, PM 2011. Characterization of the genetic diversity, structure and admixture of British chicken breeds. Animal Genetics 43, 552–563.Google Scholar
Xu, L, Hou, Y, Bickhart, DM, Zhou, Y, Hay, EH, Song, J, Sonstegard, TS, Van Tassell, CP and Liu, GE 2016. Population-genetic properties of differentiated copy number variations in cattle. Scientific Reports 6, 23161.Google Scholar
Xu, S, Guputa, S and Jin, L 2010. PEAS V1.0: a package for elementary analysis of SNP data. Molecular Ecology Resources 10, 1085–1088.Google Scholar
Yan, Y, Yang, N, Cheng, HH, Song, J and Qu, L 2015. Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek’s disease. BMC Genomics 16, 843.Google Scholar
Yi, G, Qu, L, Liu, J, Yan, Y, Xu, G and Yang, N 2014. Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing. BMC Genomics 15, 962.CrossRefGoogle ScholarPubMed
Zanetti, E, De Marchi, M, Dalvit, C and Cassandro, M 2010. Genetic characterization of local Italian breeds of chickens undergoing in situ conservation. Poultry Science 89, 420–427.Google Scholar
Zanon, A and Sabbioni, A 2001. Identificazione e salvaguardia genetica delle razze avicole italiane. Annali della Facoltà di Medicina Veterinaria Università di Parma XXI, 117–134.Google Scholar
Supplementary material: File

Strillacci supplementary material

Table S1

Download Strillacci supplementary material(File)
File 84.3 KB
Supplementary material: File

Strillacci supplementary material

Table S2

Download Strillacci supplementary material(File)
File 19.7 KB
Supplementary material: File

Strillacci supplementary material

Table S3

Download Strillacci supplementary material(File)
File 116.3 KB