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Longeri M, Chiodi A, Brilli M, Piazza A, Lyons LA, Sofronidis G, Cozzi MC, Bazzocchi C. Targeted genotyping by sequencing: a new way to genome profile the cat. Anim Genet 2019; 50:718-725. [PMID: 31512748 PMCID: PMC6899796 DOI: 10.1111/age.12838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2019] [Indexed: 01/01/2023]
Abstract
Targeted GBS is a recent approach for obtaining an effective characterization for hundreds to thousands of markers. The high throughput of next-generation sequencing technologies, moreover, allows sample multiplexing. The aims of this study were to (i) define a panel of single nucleotide polymorphisms (SNPs) in the cat, (ii) use GBS for profiling 16 cats, and (iii) evaluate the performance with respect to the inference using standard approaches at different coverage thresholds, thereby providing useful information for designing similar experiments. Probes for sequencing 230 variants were designed based on the Felis_catus_8.0. 8.0 genome. The regions comprised anonymous and non-anonymous SNPs. Sixteen cat samples were analysed, some of which had already been genotyped in a large group of loci and one having been whole-genome sequenced in the 99_Lives Cat Genome Sequencing Project. The accuracy of the method was assessed by comparing the GBS results with the genotypes already available. Overall, GBS achieved good performance, with 92-96% correct assignments, depending on the coverage threshold used to define the set of trustable genotypes. Analyses confirmed that (i) the reliability of the inference of each genotype depends on the coverage at that locus and (ii) the fraction of target loci whose genotype can be inferred correctly is a function of the total coverage. GBS proves to be a valid alternative to other methods. Data suggested a depth of less than 11× is required for greater than 95% accuracy. However, sequencing depth must be adapted to the total size of the targets to ensure proper genotype inference.
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Affiliation(s)
- M. Longeri
- Department of Veterinary MedicineUniversity of MilanMilano20133Italy
| | - A. Chiodi
- Department of Earth and Environmental SciencesUniversity of PaviaPavia27100Italy
| | - M. Brilli
- Department of BiosciencesUniversity of MilanMilano20133Italy
- Paediatric Clinical Research Centre “Romeo ed Enrica Invernizzi”University of MilanMilano20157Italy
| | - A. Piazza
- Paediatric Clinical Research Centre “Romeo ed Enrica Invernizzi”University of MilanMilano20157Italy
- Department of Biomedical and Clinical Sciences “L. Sacco”University of MilanMilano20157Italy
| | - L. A. Lyons
- Department of Veterinary Medicine and SurgeryCollege of Veterinary MedicineUniversity of MissouriColumbiaMO65211USA
| | - G. Sofronidis
- Orivet Genetic Pet CareSuite 102/163-169 Inkerman StreetSt. KildaVic.3182Australia
| | - M. C. Cozzi
- Department of Veterinary MedicineUniversity of MilanMilano20133Italy
| | - C. Bazzocchi
- Department of Veterinary MedicineUniversity of MilanMilano20133Italy
- Paediatric Clinical Research Centre “Romeo ed Enrica Invernizzi”University of MilanMilano20157Italy
- Coordinated Research Centre “EpiSoMI”University of MilanMilano20133Italy
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Strillacci MG, Vega-Murillo VE, Román-Ponce SI, López FJR, Cozzi MC, Gorla E, Cerolini S, Bertolini F, Fontanesi L, Bagnato A. Looking at genetic structure and selection signatures of the Mexican chicken population using single nucleotide polymorphism markers. Poult Sci 2018; 97:791-802. [PMID: 29272469 DOI: 10.3382/ps/pex374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/18/2017] [Indexed: 11/20/2022] Open
Abstract
Genetic variation enables both adaptive evolutionary changes and artificial selection. Genetic makeup of populations is the result of a long-term process of selection and adaptation to specific environments and ecosystems. The aim of this study was to characterize the genetic variability of México's chicken population to reveal any underlying population structure. A total of 213 chickens were sampled in different rural production units located in 25 states of México. Genotypes were obtained using the Affymetrix Axiom® 600 K Chicken Genotyping Array. The Identity by Descent (IBD) and the principal components analysis (PCA) were performed by SVS software on pruned single nucleotide polymorphisms (SNPs).ADMIXTURE analyses identified 3 ancestors and the proportion of the genetic contribution of each of them has been determined in each individual. The results of the Neighbor-Joining (NJ) analysis resulted consistent with those obtained by the PCA. All methods utilized in this study did not allow a classification of Mexican chicken in distinct clusters or groups. A total of 3,059 run of homozygosity (ROH) were identified and, being mainly short in length (<4 Mb), these regions are indicative of a low inbreeding level in the population. Finally, findings from the ROH analysis indicated the presence of natural selective pressure in the population of Mexican chicken.The study indicates that the Mexican chicken clearly appear to be a unique creole chicken population that was not subjected to a specific artificial selection. Results provide a genetic knowledge that can be used as a basis for the genetic management of a unique and very large creole population, especially in the view of using it in production of hybrids to increase the productivity and economic revenue of family farming agriculture, which is widely present in México.
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Affiliation(s)
- M G Strillacci
- Department of Veterinary Medicine, Universitá degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
| | - V E Vega-Murillo
- Campo Experimental La Posta, INIFAP, km 22.5 Carretera Federal Veracruz-Córdoba, Paso del Toro, Municipio de Medellín, 94277, Veracruz, México
| | - S I Román-Ponce
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales y Agropecuarias (INIFAP), Km. 1 Carretera a Colón, Auchitlán, 76280, Querétaro, México
| | - F J Ruiz López
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales y Agropecuarias (INIFAP), Km. 1 Carretera a Colón, Auchitlán, 76280, Querétaro, México
| | - M C Cozzi
- Department of Veterinary Medicine, Universitá degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
| | - E Gorla
- Department of Veterinary Medicine, Universitá degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
| | - S Cerolini
- Department of Veterinary Medicine, Universitá degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
| | - F Bertolini
- Department of Agricultural and Food Sciences - Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy.,Department of Animal Science, Iowa State University, 1221 Kildee Hall, Ames, IA 50011
| | - L Fontanesi
- Department of Agricultural and Food Sciences - Division of Animal Sciences, University of Bologna, Viale Fanin 46, Bologna, Italy
| | - A Bagnato
- Department of Veterinary Medicine, Universitá degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
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Gorla E, Cozzi MC, Román-Ponce SI, Ruiz López FJ, Vega-Murillo VE, Cerolini S, Bagnato A, Strillacci MG. Genomic variability in Mexican chicken population using copy number variants. BMC Genet 2017; 18:61. [PMID: 28673234 PMCID: PMC5496433 DOI: 10.1186/s12863-017-0524-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations. The aim of this study was to investigate genetic variability in the Mexican Creole chicken population using CNVs. RESULTS The Hidden Markov Model of the PennCNV software detected a total of 1924 CNVs in the genome of the 256 samples processed with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix). The mapped CNVs comprised 1538 gains and 386 losses, resulting at population level in 1216 CNV regions (CNVRs), of which 959 gains, 226 losses and 31 complex (i.e. containing both losses and gains). The CNVRs covered a total of 47 Mb of the whole genome sequence length, corresponding to 5.12% of the chicken galGal4 autosome assembly. CONCLUSIONS This study allowed a deep insight into the structural variation in the genome of unselected Mexican chicken population, which up to now has not been genetically characterized. The genomic study disclosed that the population, even if presenting extreme morphological variation, cannot be organized in differentiated genetic subpopulations. Finally this study provides a chicken CNV map based on the 600 K SNP chip array jointly with a genome-wide gene copy number estimates in a native unselected for more than 500 years chicken population.
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Affiliation(s)
- E. Gorla
- Department of Veterinary Medicine, Universitá degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - M. C. Cozzi
- Department of Veterinary Medicine, Universitá degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - S. I. Román-Ponce
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agricola y Pecuarias (INIFAP), Km.1 Carretera a Colón, Auchitlán, 76280 Querétaro, CP Mexico
| | - F. J. Ruiz López
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agricola y Pecuarias (INIFAP), Km.1 Carretera a Colón, Auchitlán, 76280 Querétaro, CP Mexico
| | - V. E. Vega-Murillo
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, Instituto Nacional de Investigaciones Forestales, Agricola y Pecuarias (INIFAP), Melchor Ocampo # 234 Desp. 313, Col. Centro Veracruz, C.P. 91700 Veracruz, Mexico
| | - S. Cerolini
- Department of Veterinary Medicine, Universitá degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - A. Bagnato
- Department of Veterinary Medicine, Universitá degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
| | - M. G. Strillacci
- Department of Veterinary Medicine, Universitá degli Studi di Milano, Via Celoria 10, 20133 Milan, Italy
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Strillacci MG, Frigo E, Canavesi F, Ungar Y, Schiavini F, Zaniboni L, Reghenzani L, Cozzi MC, Samoré AB, Kashi Y, Shimoni E, Tal-Stein R, Soller M, Lipkin E, Bagnato A. Quantitative trait loci mapping for conjugated linoleic acid, vaccenic acid and ∆9-desaturase in Italian Brown Swiss dairy cattle using selective DNA pooling. Anim Genet 2014; 45:485-99. [DOI: 10.1111/age.12174] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 02/04/2023]
Affiliation(s)
- M. G. Strillacci
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - E. Frigo
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - F. Canavesi
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - Y. Ungar
- Israel Institute of Technology (Technion); Department of Biotechnology and Food Engineering; Technion City; Haifa 3200003 Israel
| | - F. Schiavini
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
- Genomic and Bioinformatics Platform; University of Milan; c/o Fondazione Filarete, Viale Ortles 20 Milano 20100 Italy
| | - L. Zaniboni
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - L. Reghenzani
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - M. C. Cozzi
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - A. B. Samoré
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
| | - Y. Kashi
- Israel Institute of Technology (Technion); Department of Biotechnology and Food Engineering; Technion City; Haifa 3200003 Israel
| | - E. Shimoni
- Israel Institute of Technology (Technion); Department of Biotechnology and Food Engineering; Technion City; Haifa 3200003 Israel
| | - R. Tal-Stein
- Department of Genetics; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - M. Soller
- Department of Genetics; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - E. Lipkin
- Department of Genetics; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - A. Bagnato
- Department of Health; Animal Science and Food Safety (VESPA); University of Milan; Via Celoria 10 20133 Milan Italy
- Genomic and Bioinformatics Platform; University of Milan; c/o Fondazione Filarete, Viale Ortles 20 Milano 20100 Italy
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Pertica G, Riva J, Strillacci MG, Cozzi MC, Longeri M, Polli M. Prevalence of inherited junctional epidermolysis bullosa in German shorthaired pointers bred in Italy. Vet Rec 2010; 167:751-2. [PMID: 21257512 DOI: 10.1136/vr.c5178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- G Pertica
- Department of Animal Science, Università degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
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Vacca GM, Daga C, Pazzola M, Carcangiu V, Dettori ML, Cozzi MC. D-loop sequence mitochondrial DNA variability of Sarda goat and other goat breeds and populations reared in the Mediterranean area. J Anim Breed Genet 2010; 127:352-60. [PMID: 20831559 DOI: 10.1111/j.1439-0388.2010.00863.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- G M Vacca
- Department of Animal Biology, University of Sassari, Sassari, Italy Department of Animal Science, University of Milano, Milano, Italy
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Marelli SP, Terova G, Cozzi MC, Lasagna E, Sarti FM, Cavalchini LG. Gene expression of hepatic glucocorticoid receptor NR3C1 and correlation with plasmatic corticosterone in Italian chickens. Anim Biotechnol 2010; 21:140-8. [PMID: 20379891 DOI: 10.1080/10495391003608621] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This study examined breed-specific stress-related hormonal and gene expression profiles in three Italian chicken breeds (Valdarnese Bianca, Bionda Piemontese, Robusta Maculata) reared in controlled conditions. Glucocorticoids work through the glucocorticoid receptor (GR), which modulates target genes transcription. We investigated breed-specific changes in corticosterone (ELISA) and GR expression. GR mRNA levels were analyzed using one-tube, two-temperature real-time PCR for absolute quantification of the gene expression by the standard curve method. Our results show high expression of GR in hepatic tissue. Significant effect of the breed was recorded for plasma corticosterone concentration: Valdarnese Bianca 3.35 ng/mL, Bionda Piemontese 1.73 ng/mL, Robusta Maculata 2.02 ng/mL. Breed specific gene expression has been recorded with a GR ranging from 1.12E+04 (Robusta Maculata) to 1.00E+05 (Bionda Piemontese) mRNA copy number/100 ng total RNA. Negative correlation was found between gene expression and blood corticosterone level.
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Affiliation(s)
- S P Marelli
- Department of Animal Science, University of Milan, Milan, Italy.
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