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Strillacci MG, Punturiero C, Milanesi R, Bernini F, Mason T, Bagnato A. Antibiotic treatments and somatic cell count as phenotype to map QTL for mastitis susceptibility in Holstein cattle breed. Italian Journal of Animal Science 2023. [DOI: 10.1080/1828051x.2023.2175498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Affiliation(s)
| | - Chiara Punturiero
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, Lodi, Italy
| | - Raffaella Milanesi
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, Lodi, Italy
| | - Francesca Bernini
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, Lodi, Italy
| | - Tiziano Mason
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, Lodi, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, Lodi, Italy
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Perga S, Biolatti C, Martini I, Rossi F, Benso A, Acutis PL, Bagnato A, Cognata D, Caroggio P, Peletto S, Modesto P. Application of Microsatellites to Trace the Dairy Products Back to the Farm of Origin. Foods 2023; 12:4131. [PMID: 38002189 PMCID: PMC10670529 DOI: 10.3390/foods12224131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
The increasing number of food frauds, mainly targeting high quality products, is a rising concern among producers and authorities appointed to food controls. Therefore, the development or implementation of methods to reveal frauds is desired. The genetic traceability of traditional or high-quality dairy products (i.e., products of protected designation of origin, PDO) represents a challenging issue due to the technical problems that arise. The aim of the study was to set up a genetic tool for the origin traceability of dairy products. We investigated the use of Short Tandem Repeats (STRs) to assign milk and cheese to the corresponding producer. Two farms were included in the study, and the blood of the cows, bulk milk, and derived cheese were sampled monthly for one year. Twenty STRs were selected and Polymerase Chain Reactions for each locus were carried out. The results showed that bulk milk and derived cheese express an STR profile composed of a subset of STRs of the lactating animals. A bioinformatics tool was used for the exclusion analysis. The study allowed the identification of a panel of 20 markers useful for the traceability of milk and cheeses, and its effectiveness in the traceability of dairy products obtained from small producers was demonstrated.
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Affiliation(s)
- Simona Perga
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy; (S.P.); (C.B.); (I.M.); (P.L.A.); (S.P.)
| | - Cristina Biolatti
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy; (S.P.); (C.B.); (I.M.); (P.L.A.); (S.P.)
| | - Isabella Martini
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy; (S.P.); (C.B.); (I.M.); (P.L.A.); (S.P.)
| | - Francesco Rossi
- Computer and Control Engineering Department, Polytechnic of Turin, 10100 Turin, Italy (A.B.)
| | - Alfredo Benso
- Computer and Control Engineering Department, Polytechnic of Turin, 10100 Turin, Italy (A.B.)
| | - Pier Luigi Acutis
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy; (S.P.); (C.B.); (I.M.); (P.L.A.); (S.P.)
| | - Alessandro Bagnato
- Department of Veterinary and Animal Science, Università degli Studi di Milano, 26900 Lodi, Italy;
| | | | - Piero Caroggio
- Azienda Sanitaria Locale 1 Imperiese, 18100 Imperia, Italy;
| | - Simone Peletto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy; (S.P.); (C.B.); (I.M.); (P.L.A.); (S.P.)
| | - Paola Modesto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Turin, Italy; (S.P.); (C.B.); (I.M.); (P.L.A.); (S.P.)
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Giovannini S, Strillacci MG, Bagnato A, Albertini E, Sarti FM. Genetic and Phenotypic Characteristics of Belted Pig Breeds: A Review. Animals (Basel) 2023; 13:3072. [PMID: 37835678 PMCID: PMC10571877 DOI: 10.3390/ani13193072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Belted pig breeds have unique, distinguishing phenotypic characteristics. This review summarises the current knowledge on pig breeds displaying a belted coat pattern. Belts of different widths and positions around the animal's trunk characterise specific pig breeds from all around the world. All the breeds included in the present paper have been searched through the FAO domestic animal diversity information system (DAD-IS), Every country was checked to identify all breeds described as having black or red piebald coat pattern variations. Advances in genomic technologies have made it possible to identify the specific genes and genetic markers associated with the belted phenotype and explore the genetic relationships between different local breeds. Thus, the origin, history, and production traits of these breeds, together with all the genomic information related to the mechanism of skin pigmentation, are discussed. By increasing our understanding of these breeds, we can appreciate the richness of our biological and cultural heritage and work to preserve the biodiversity of the world's animals.
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Affiliation(s)
- Samira Giovannini
- Department of Agricultural, Food and Environmental Sciences, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy; (E.A.); (F.M.S.)
| | - Maria Giuseppina Strillacci
- Department of Veterinary and Animal Science, Università degli Studi di Milano, Via Dell’Università 6, 26900 Lodi, Italy; (M.G.S.); (A.B.)
| | - Alessandro Bagnato
- Department of Veterinary and Animal Science, Università degli Studi di Milano, Via Dell’Università 6, 26900 Lodi, Italy; (M.G.S.); (A.B.)
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy; (E.A.); (F.M.S.)
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy; (E.A.); (F.M.S.)
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4
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Signer-Hasler H, Casanova L, Barenco A, Maitre B, Bagnato A, Vevey M, Berger B, Simčič M, Boichon D, Capitan A, Medugorac I, Bennewitz J, Mészáros G, Sölkner J, Drögemüller C, Flury C. Genomic regions underlying positive selection in local, Alpine cattle breeds. Anim Genet 2023; 54:239-253. [PMID: 36737525 DOI: 10.1111/age.13295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
We used genome-wide SNP data from 18 local cattle breeds from six countries of the Alpine region to characterize population structure and identify genomic regions underlying positive selection. The geographically close breeds Evolèner, Eringer, Valdostana Pezzata Nera, and Valdostana Castana were found to differ from all other Alpine breeds. In addition, three breeds, Simmental, and Original Braunvieh from Switzerland and Pinzgauer from Austria built three separate clusters. Of the 18 breeds studied, the intra-alpine Swiss breed Evolèner had the highest average inbreeding based on runs of homozygosity (FROH ) and the highest average genomic relationship within the breed. In contrast, Slovenian Cika cattle had the lowest average genomic inbreeding and the lowest average genomic relationship within the breed. We found selection signatures on chromosome 6 near known genes such as KIT and LCORL explaining variation in coat color and body size in cattle. The most prominent selection signatures were similar regardless of marker density and the breeds in the data set. In addition, using available high-density SNP data from 14 of the breeds we identified 47 genome regions as ROH islands. The proportion of homozygous animals was higher in all studied animals of local breeds than in Holstein and Brown Swiss cattle, the two most important commercial breeds in the Alpine region. We report ROH islands near genes related to thermoregulation, coat color, production, and stature. The results of this study serve as a basis for the search for causal variants underlying adaptation to the alpine environment and other specific characteristics selected during the evolution of local Alpine cattle breeds.
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Affiliation(s)
- Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Zollikofen, Switzerland
| | | | | | - Blaise Maitre
- Schweizerischer Eringerviehzuchtverband, Sion, Switzerland
| | | | | | | | - Mojca Simčič
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Aurélien Capitan
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried/Planegg, Germany
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences, Vienna, Wien, Austria
| | - Johann Sölkner
- University of Natural Resources and Life Sciences, Vienna, Wien, Austria
| | - Cord Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Zollikofen, Switzerland
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5
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Shen QK, Peng MS, Adeola AC, Kui L, Duan S, Miao YW, Eltayeb NM, Lichoti JK, Otecko NO, Strillacci MG, Gorla E, Bagnato A, Charles OS, Sanke OJ, Dawuda PM, Okeyoyin AO, Musina J, Njoroge P, Agwanda B, Kusza S, Nanaei HA, Pedar R, Xu MM, Du Y, Nneji LM, Murphy RW, Wang MS, Esmailizadeh A, Dong Y, Ommeh SC, Zhang YP. Erratum to: Genomic analyses unveil helmeted guinea fowl (Numida meleagris) domestication in West Africa. Genome Biol Evol 2021; 13:6355925. [PMID: 34417609 PMCID: PMC8379371 DOI: 10.1093/gbe/evab174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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6
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Krasniqi E, Sacconi A, Marinelli D, Pizzuti L, Mazzotta M, Sergi D, Capomolla E, Donzelli S, Carosi M, Bagnato A, Gamucci T, Tomao S, Natoli C, Marchetti P, Grassadonia A, Tinari N, De Tursi M, Vizza E, Ciliberto G, Landi L, Cappuzzo F, Barba M, Blandino G, Vici P. MicroRNA-based signatures impacting clinical course and biology of ovarian cancer: a miRNOmics study. Biomark Res 2021; 9:57. [PMID: 34256855 PMCID: PMC8276429 DOI: 10.1186/s40364-021-00289-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Background In Western countries, ovarian cancer (OC) still represents the leading cause of gynecological cancer-related deaths, despite the remarkable gains in therapeutical options. Novel biomarkers of early diagnosis, prognosis definition and prediction of treatment outcomes are of pivotal importance. Prior studies have shown the potentials of micro-ribonucleic acids (miRNAs) as biomarkers for OC and other cancers. Methods We focused on the prognostic and/or predictive potential of miRNAs in OC by conducting a comprehensive array profiling of miRNA expression levels in ovarian tissue samples from 17 non-neoplastic controls, and 60 tumor samples from OC patients treated at the Regina Elena National Cancer Institute (IRE). A set of 54 miRNAs with differential expression in tumor versus normal samples (T/N-deregulated) was identified in the IRE cohort and validated against data from the Cancer Genoma Atlas (TCGA) related to 563 OC patients and 8 non-neoplastic controls. The prognostic/predictive role of the selected 54 biomarkers was tested in reference to survival endpoints and platinum resistance (P-res). Results In the IRE cohort, downregulation of the 2 miRNA-signature including miR-99a-5p and miR-320a held a negative prognostic relevance, while upregulation of miR-224-5p was predictive of less favorable event free survival (EFS) and P-res. Data from the TCGA showed that downregulation of 5 miRNAs, i.e., miR-150, miR-30d, miR-342, miR-424, and miR-502, was associated with more favorable EFS and overall survival outcomes, while miR-200a upregulation was predictive of P-res. The 9 miRNAs globally identified were all included into a single biologic signature, which was tested in enrichment analysis using predicted/validated miRNA target genes, followed by network representation of the miRNA-mRNA interactions. Conclusions Specific dysregulated microRNA sets in tumor tissue showed predictive/prognostic value in OC, and resulted in a promising biological signature for this disease. Supplementary Information The online version contains supplementary material available at 10.1186/s40364-021-00289-6.
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Affiliation(s)
- E Krasniqi
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - A Sacconi
- UOSD Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - D Marinelli
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, Medical Oncology Unit, Sapienza University, Via di Grottarossa 1035/1039, 00189, Rome, Italy
| | - L Pizzuti
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - M Mazzotta
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - D Sergi
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - E Capomolla
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - S Donzelli
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - M Carosi
- Pathology Department IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - A Bagnato
- Preclinical Models and New Therapeutic Agents Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - T Gamucci
- Medical Oncology, Sandro Pertini Hospital, Via dei Monti Tiburtini 385, 00157, Rome, Italy
| | - S Tomao
- Department of Radiological Oncological and Pathological Sciences, Division of Medical Oncology A, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - C Natoli
- Department of Medical, Oral & Biotechnological Sciences, University G. D'Annunzio, Via dei Vestini, 31, 66100, Chieti, Italy
| | - P Marchetti
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, Medical Oncology Unit, Sapienza University, Via di Grottarossa 1035/1039, 00189, Rome, Italy
| | - A Grassadonia
- Department of Medical, Oral & Biotechnological Sciences, University G. D'Annunzio, Via dei Vestini, 31, 66100, Chieti, Italy
| | - N Tinari
- Department of Medical, Oral & Biotechnological Sciences, University G. D'Annunzio, Via dei Vestini, 31, 66100, Chieti, Italy
| | - M De Tursi
- Department of Medical, Oral & Biotechnological Sciences, University G. D'Annunzio, Via dei Vestini, 31, 66100, Chieti, Italy
| | - E Vizza
- Department of Oncological Surgery, Gynecologic Oncologic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - G Ciliberto
- Scientific Direction, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - L Landi
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - F Cappuzzo
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - M Barba
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
| | - G Blandino
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
| | - P Vici
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
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Shen QK, Peng MS, Adeola AC, Kui L, Duan S, Miao YW, Eltayeb NM, Lichoti JK, Otecko NO, Strillacci MG, Gorla E, Bagnato A, Charles OS, Sanke OJ, Dawuda PM, Okeyoyin AO, Musina J, Njoroge P, Agwanda B, Kusza S, Nanaei HA, Pedar R, Xu MM, Du Y, Nneji LM, Murphy RW, Wang MS, Esmailizadeh A, Dong Y, Ommeh SC, Zhang YP. Genomic Analyses of Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa. Genome Biol Evol 2021; 13:6261762. [PMID: 34009300 PMCID: PMC8214406 DOI: 10.1093/gbe/evab090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 12/22/2022] Open
Abstract
Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.
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Affiliation(s)
- Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Centre for Biotechnology Research, Bayero University, Kano, Nigeria
| | - Ling Kui
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Yong-Wang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Nada M Eltayeb
- Department of Animal breeding and Reproduction Technology, College of Animal Production, University of Bahri, Khartoum, Sudan
| | - Jacqueline K Lichoti
- State Department of Livestock, Ministry of Agriculture Livestock Fisheries and Irrigation, Nairobi, Kenya
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | | | - Erica Gorla
- Department of Veterinary Medicine, Università degli Studi di Milano, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Italy
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture, Makurdi, Nigeria
| | - Agboola O Okeyoyin
- National Park Service Headquarter, Federal Capital Territory, Abuja, Nigeria
| | - John Musina
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Peter Njoroge
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, Hungary
| | | | - Rana Pedar
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran
| | - Ming-Min Xu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yuan Du
- Nowbio Biotechnology Company, Kunming, China
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya
| | - Robert W Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, California, USA.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, California, USA
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran
| | - Yang Dong
- College of Biological Big Data, Yunnan Agriculture University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.,Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Sheila C Ommeh
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya.,Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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Strillacci MG, Moradi-Shahrbabak H, Davoudi P, Ghoreishifar SM, Mokhber M, Masroure AJ, Bagnato A. A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes. BMC Genomics 2021; 22:305. [PMID: 33902439 PMCID: PMC8077898 DOI: 10.1186/s12864-021-07604-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/11/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND In Iran, river buffalo is of great importance. It plays an important role in the economy of the Country, because its adaptation to harsh climate conditions and long productive lifespan permitting its farming across the Country and to convert low-quality feed into valuable milk. The genetic variability in Iranian buffalo breeds have been recently studied using SNPs genotyping data, but a whole genome Copy Number Variants (CNVs) mapping was not available. The aim of this study was to perform a genome wide CNV scan in 361 buffaloes of the three Iranian river breeds (Azeri, Khuzestani and Mazandarani) through the analysis of data obtained using the Axiom® Buffalo Genotyping Array 90 K. RESULTS CNVs detection resulted in a total of 9550 CNVs and 302 CNVRs identified in at least 5% of samples within breed, covering around 1.97% of the buffalo genome. and A total of 22 CNVRs were identified in all breeds and a different proportion of regions were in common among the three populations. Within the more represented CNVRs (n = 302) mapped a total of 409 buffalo genes, some of which resulted associated with morphological, healthy, milk, meat and reproductive traits, according to Animal Genome Cattle database. CONCLUSIONS This work provides a step forward in the interpretation of genomic variation within and among the buffalo populations, releasing a first map of CNVs and providing insights about their recent selection and adaptation to environment. The presence of the set of genes and QTL traits harbored in the CNVRs could be possibly linked with the buffalo's natural adaptive history together to a recent selection for milk used as primary food source from this species.
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Affiliation(s)
- Maria G. Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy
| | - Hossein Moradi-Shahrbabak
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167 Iran
| | - Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N5E3 Canada
| | - Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167 Iran
| | - Mahdi Mokhber
- Department of Animal Science, Faculty of Agriculture and Natural resources, Urmia University, 11Km Sero Road, P. O. Box: 165, Urmia, 57561-51818 Iran
| | - Anoar Jamai Masroure
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy
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Strillacci MG, Vevey M, Blanchet V, Mantovani R, Sartori C, Bagnato A. The Genomic Variation in the Aosta Cattle Breeds Raised in an Extensive Alpine Farming System. Animals (Basel) 2020; 10:ani10122385. [PMID: 33322839 PMCID: PMC7764440 DOI: 10.3390/ani10122385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/28/2022] Open
Abstract
The Aosta Red Pied (Valdostana Pezzata Rossa (VRP)), the Aosta Black Pied (Valdostana Pezzata Nera (VBP)) and the Aosta Chestnut (Valdostana Castana (CAS)) are dual-purpose cattle breeds (meat and milk), very well adapted to the harsh environmental conditions of alpine territories: their farming is in fact characterized by summer pasture at very high altitude. A total of 728 individuals were genotyped with the GeenSeek Genomic Profiler® (GGP) Bovine 150K Illumina SNP chip as a part of the DUALBREEDING-PSRN Italian-funded research project. The genetic diversity among populations showed that the three breeds are distinct populations based on the FST values, ADMIXTURE and Principal Component Analysis (PCA) results. Runs of Homozygosity (ROH) were obtained for the three populations to disclose recent autozygosity. The genomic inbreeding based on the ROH was calculated and coupled with information derived from the F (inbreeding coefficient) and FST parameters. The mean FROH values were low: CAS = 0.06, VBP = 0.05 and VRP = 0.07, while the average F values were -0.003, -0.01 and -0.003, respectively. The annotation and enrichment analysis, performed in the identified most frequent ROH (TOP_ROH), showed genes that can be linked to the resilience capacity of these populations to harsh environmental farming conditions, and to the peculiar characteristics searched for by farmers in each breed.
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Affiliation(s)
- Maria Giuseppina Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 20133 Milano, Italy;
| | - Mario Vevey
- Associazione Nazionale Bovini di Razza Valdostana, Fraz. Favret, 5, 11020 Gressan, Italy; (M.V.); (V.B.)
| | - Veruska Blanchet
- Associazione Nazionale Bovini di Razza Valdostana, Fraz. Favret, 5, 11020 Gressan, Italy; (M.V.); (V.B.)
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Università degli Studi di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (R.M.); (C.S.)
| | - Cristina Sartori
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Università degli Studi di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (R.M.); (C.S.)
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 20133 Milano, Italy;
- Correspondence: ; Tel.: +39-02-5033-4583
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Boccardo A, Marelli SP, Pravettoni D, Bagnato A, Busca GA, Strillacci MG. The German Shorthair Pointer Dog Breed ( Canis lupus familiaris): Genomic Inbreeding and Variability. Animals (Basel) 2020; 10:ani10030498. [PMID: 32192001 PMCID: PMC7143860 DOI: 10.3390/ani10030498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 12/22/2022] Open
Abstract
The German Shorthaired Pointer (GSHP) is a breed worldwide known for its hunting versatility. Dogs of this breed are appreciated as valuable companions, effective trackers, field trailers and obedience athletes. The aim of the present work is to describe the genomic architecture of the GSHP breed and to analyze inbreeding levels under a genomic and a genealogic perspective. A total of 34 samples were collected (24 Italian, 10 USA), and the genomic and pedigree coefficients of inbreeding have been calculated. A total of 3183 runs of homozygosity (ROH) across all 34 dogs have been identified. The minimum and maximum number of Single Nucleotide Polymorphisms (SNPs) defining all ROH are 40 and 3060. The mean number of ROH for the sample was 93.6. ROH were found on all chromosomes. A total of 854 SNPs (TOP_SNPs) defined 11 ROH island regions (TOP_ROH), in which some gene already associated with behavioral and morphological canine traits was annotated. The proportion of averaged observed homozygotes estimated on total number of SNPs was 0.70. The genomic inbreeding coefficient based on ROH was 0.17. The mean inbreeding based on genealogical information resulted 0.023. The results describe a low inbred population with quite a good level of genetic variability.
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Affiliation(s)
- Antonio Boccardo
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy (S.P.M.); (D.P.)
| | - Stefano Paolo Marelli
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy (S.P.M.); (D.P.)
| | - Davide Pravettoni
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy (S.P.M.); (D.P.)
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy (S.P.M.); (D.P.)
| | - Giuseppe Achille Busca
- Centro Clinico-Veterinario e Zootecnico-Sperimentale, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy;
| | - Maria Giuseppina Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy (S.P.M.); (D.P.)
- Correspondence: ; Tel.: +39-02-50334582
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11
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Marelli SP, Beccaglia M, Bagnato A, Strillacci MG. Canine fertility: The consequences of selection for special traits. Reprod Domest Anim 2020; 55 Suppl 2:4-9. [PMID: 31913541 DOI: 10.1111/rda.13586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/05/2019] [Accepted: 11/08/2019] [Indexed: 01/07/2023]
Abstract
Pedigree dogs and cats are bred aiming to conform breed standards with very poor consideration for breeding stock fertility. At the same time, the genetic asset underlining reproductive traits could be effectively analysed like in other species under selection. The definition of selection targets is very important in breeding protocols determination. The aim of the present work is to present an overview of the different correlations between reproduction and genetics, starting from selection procedure and inbreeding coefficient moving to genomic and the application of SNPs and GWAS on population study and identification of genes involved in phenotypical variation of reproductive traits in dogs. Particular relevance has been given to the concept of inbreeding which effects on canine reproduction have been presented. The use of genomic information in inbreeding coefficient calculation can be considered an improved effective procedure in the evaluation of the genetic variability loss in canine population and its negative effects on reproductive traits.
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Affiliation(s)
- Stefano P Marelli
- Department of Veterinary Medicine - DIMEVET, University of Milan, Milano, Italy
| | | | - Alessandro Bagnato
- Department of Veterinary Medicine - DIMEVET, University of Milan, Milano, Italy
| | - Maria G Strillacci
- Department of Veterinary Medicine - DIMEVET, University of Milan, Milano, Italy
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12
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Strillacci MG, Gorla E, Ríos-Utrera A, Vega-Murillo VE, Montaño-Bermudez M, Garcia-Ruiz A, Cerolini S, Román-Ponce SI, Bagnato A. Copy Number Variation Mapping and Genomic Variation of Autochthonous and Commercial Turkey Populations. Front Genet 2019; 10:982. [PMID: 31737031 PMCID: PMC6828962 DOI: 10.3389/fgene.2019.00982] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/13/2019] [Indexed: 01/02/2023] Open
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.
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Affiliation(s)
- Maria G Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Milano, Italy
| | - Erica Gorla
- Department of Veterinary Medicine, Università degli Studi di Milano, Milano, Italy
| | - Angel Ríos-Utrera
- Campo Experimental La Posta, INIFAP, Municipio de Medellín, Veracruz, Mexico
| | | | - Moises Montaño-Bermudez
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, INIFAP, Auchitlán, Querétaro, Mexico
| | - Adriana Garcia-Ruiz
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, INIFAP, Auchitlán, Querétaro, Mexico
| | - Silvia Cerolini
- Department of Veterinary Medicine, Università degli Studi di Milano, Milano, Italy
| | - Sergio I Román-Ponce
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, INIFAP, Auchitlán, Querétaro, Mexico
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Milano, Italy
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Scienski K, Ialacci A, Bagnato A, Reginelli D, Durán-Aguilar M, Giuseppina Strillacci M. Genetic variability in a Holstein population using SNP markers and their use for monitoring mating strategies. REV MEX CIENC PECU 2019. [DOI: 10.22319/rmcp.v10i3.4842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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González-Ruiz S, Strillacci MG, Durán-Aguilar M, Cantó-Alarcón GJ, Herrera-Rodríguez SE, Bagnato A, Guzmán LF, Milián-Suazo F, Román-Ponce SI. Genome-Wide Association Study in Mexican Holstein Cattle Reveals Novel Quantitative Trait Loci Regions and Confirms Mapped Loci for Resistance to Bovine Tuberculosis. Animals (Basel) 2019; 9:ani9090636. [PMID: 31480266 PMCID: PMC6769677 DOI: 10.3390/ani9090636] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/23/2019] [Accepted: 08/24/2019] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Bovine tuberculosis is an infectious disease of cattle caused by Mycobacterium bovis characterized by the formation of tubercles in any organ or tissue. Bovine tuberculosis represents a significant veterinary and public health problem in many parts of the world. It is zoonotic, transmitted to humans through consumption of infected milk and other cattle products. Although many factors influence infection and progression of the disease, there must be an important host genetic component that explains why some animals get sick and others remain healty. We present evidence of genetic variants associated with resistance to tuberculosis in Mexican Holstein dairy cattle using a case-control approach with a selective DNA pooling. Here, we identified novel quantitative trait loci regions harboring genes involved in Mycobacterium spp. immune response. This is a first screening about resistance to tuberculosis infection on Mexican Holstein cattle based on a dense single nucleotide polymorphism chip. The identified genes belong to both, the already known, and the undisclosed quantitative trait loci regions. Abstract Bovine tuberculosis (bTB) is a disease of cattle that represents a risk to public health and causes severe economic losses to the livestock industry. Recently, genetic studies, like genome-wide association studies (GWAS) have greatly improved the investigation of complex diseases identifying thousands of disease-associated genomic variants. Here, we present evidence of genetic variants associated with resistance to TB in Mexican dairy cattle using a case-control approach with a selective DNA pooling experimental design. A total of 154 QTLRs (quantitative trait loci regions) at 10% PFP (proportion of false positives), 42 at 5% PFP and 5 at 1% PFP have been identified, which harbored 172 annotated genes. On BTA13, five new QTLRs were identified in the MACROD2 and KIF16B genes, supporting their involvement in resistance to bTB. Six QTLRs harbor seven annotated genes that have been previously reported as involved in immune response against Mycobacterium spp: BTA (Bos taurus autosome) 1 (CD80), BTA3 (CTSS), BTA 3 (FCGR1A), BTA 23 (HFE), BTA 25 (IL21R), and BTA 29 (ANO9 and SIGIRR). We identified novel QTLRs harboring genes involved in Mycobacterium spp. immune response. This is a first screening for resistance to TB infection on Mexican dairy cattle based on a dense SNP (Single Nucleotide Polymorphism) chip.
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Affiliation(s)
- Sara González-Ruiz
- Doctorado en Ciencias Biológicas, Universidad Autónoma de Querétaro, Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Querétaro C.P. 76230, Mexico
| | - Maria G Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Via Trentacoste, 2, 20134 Milano, Italy.
| | - Marina Durán-Aguilar
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Querétaro C.P. 76230, Mexico
| | - Germinal J Cantó-Alarcón
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Querétaro C.P. 76230, Mexico
| | - Sara E Herrera-Rodríguez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Guadalajara C.P. 44270, Mexico
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Via Trentacoste, 2, 20134 Milano, Italy
| | - Luis F Guzmán
- Centro Nacional de Recursos Genéticos, INIFAP, Tepatitlán de Morelos 47600, Mexico
| | - Feliciano Milián-Suazo
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, Querétaro C.P. 76230, Mexico
| | - Sergio I Román-Ponce
- Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento animal, INIFAP, SAGARPA, Km. 1 Carretera a Colón, Ajuchitlán, Colón, Querétaro C.P. 76280, Mexico.
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Di Gerlando R, Sutera AM, Mastrangelo S, Tolone M, Portolano B, Sottile G, Bagnato A, Strillacci MG, Sardina MT. Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep. PLoS One 2019; 14:e0215204. [PMID: 31013280 PMCID: PMC6478285 DOI: 10.1371/journal.pone.0215204] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 03/28/2019] [Indexed: 11/19/2022] Open
Abstract
Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 CNVRs after aggregating overlapping CNVs. Thirty-one CNVRs were significantly associated with one or more traits included in the analysis. All CNVRs, except those on OAR19, overlapped with quantitative trait loci (QTL), even if they were not directly related to the traits of interest. A total of 222 genes were annotated within the significantly associated CNVRs, most of which played important roles in biological processes related to milk production and health-related traits. Identification of the genes in the CNVRs associated with the studied traits will provide the basis for further investigation of their role in the metabolic pathways related to milk production and health traits.
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Affiliation(s)
- Rosalia Di Gerlando
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Anna Maria Sutera
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Salvatore Mastrangelo
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Marco Tolone
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Baldassare Portolano
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Gianluca Sottile
- Università degli Studi di Palermo, Dipartimento di Scienze Economiche, Aziendali e Statistiche, Italy
| | - Alessandro Bagnato
- Università degli Studi di Milano, Dipartimento di Medicina Veterinaria, Italy
| | | | - Maria Teresa Sardina
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
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Genova F, Longeri M, Lyons LA, Bagnato A, Strillacci MG. First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data. BMC Genomics 2018; 19:895. [PMID: 30526495 PMCID: PMC6288940 DOI: 10.1186/s12864-018-5297-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/21/2018] [Indexed: 01/09/2023] Open
Abstract
Background Copy Number Variations (CNVs) have becoming very significant variants, representing a major source of genomic variation. CNVs involvement in phenotypic expression and different diseases has been widely demonstrated in humans as well as in many domestic animals. However, genome wide investigation on these structural variations is still missing in Felis catus. The present work is the first CNV mapping from a large data set of Next Generation Sequencing (NGS) data in the domestic cat, performed within the 99 Lives Consortium. Results Reads have been mapped on the reference assembly_6.2 by Maverix Biomics. CNV detection with cn.MOPS and CNVnator detected 592 CNVs. These CNVs were used to obtain 154 CNV Regions (CNVRs) with BedTools, including 62 singletons. CNVRs covered 0.26% of the total cat genome with 129 losses, 19 gains and 6 complexes. Cluster Analysis and Principal Component Analysis of the detected CNVRs showed that breeds tend to cluster together as well as cats sharing the same geographical origins. The 46 genes identified within the CNVRs were annotated. Conclusion This study has improved the genomic characterization of 14 cat breeds and has provided CNVs information that can be used for studies of traits in cats. It can be considered a sound starting point for genomic CNVs identification in this species. Electronic supplementary material The online version of this article (10.1186/s12864-018-5297-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- F Genova
- Department of Veterinary Medicine, University of Milan, 20122, Milan, Italy
| | - M Longeri
- Department of Veterinary Medicine, University of Milan, 20122, Milan, Italy
| | - L A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - A Bagnato
- Department of Veterinary Medicine, University of Milan, 20122, Milan, Italy
| | | | - M G Strillacci
- Department of Veterinary Medicine, University of Milan, 20122, Milan, Italy.
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Strillacci MG, Gorla E, Cozzi MC, Vevey M, Genova F, Scienski K, Longeri M, Bagnato A. A copy number variant scan in the autochthonous Valdostana Red Pied cattle breed and comparison with specialized dairy populations. PLoS One 2018; 13:e0204669. [PMID: 30261013 PMCID: PMC6160104 DOI: 10.1371/journal.pone.0204669] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/12/2018] [Indexed: 11/24/2022] Open
Abstract
Copy number variants (CNVs) are an important source of genomic structural variation, recognized to influence phenotypic variation in many species. Many studies have focused on identifying CNVs within and between human and livestock populations alike, but only few have explored population-genetic properties in cattle based on CNVs derived from a high-density SNP array. We report a high-resolution CNV scan using Illumina’s 777k BovineHD Beadchip for Valdostana Red Pied (VRP), an autochthonous Italian dual-purpose cattle population reared in the Alps that did not undergo strong selection for production traits. After stringent quality control and filtering, CNVs were called across 108 bulls using the PennCNV software. A total of 6,784 CNVs were identified, summarized to 1,723 CNV regions (CNVRs) on 29 autosomes covering a total of ~59 Mb of the UMD3.1 assembly. Among the mapped CNVRs, there were 812 losses, 832 gains and 79 complexes. We subsequently performed a comparison of CNVs detected in the VRP and those available from published studies in the Italian Brown Swiss (IBS) and Mexican Holstein (HOL). A total of 171 CNVRs were common to all three breeds. Between VRP and IBS, 474 regions overlapped, while only 313 overlapped between VRP and HOL, indicating a more similar genetic background among populations with common origins, i.e. the Alps. The principal component, clustering and admixture analyses showed a clear separation of the three breeds into three distinct clusters. In order to describe the distribution of CNVs within and among breeds we used the pair VST statistic, considering only the CNVRs shared to more than 5 individuals (within breed). We identified unique and highly differentiated CNVs (n = 33), some of which could be due to specific breed selection and adaptation. Genes and QTL within these regions were characterized.
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Affiliation(s)
| | - Erica Gorla
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | | | - Mario Vevey
- Associazione Nazionale Allevatori Bovini Di Razza Valdostana, Gressan, Aosta, Italy
| | - Francesca Genova
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Kathy Scienski
- Department of Animal Science, Texas A&M University, College Station, Texas, United States of America
| | - Maria Longeri
- Department of Veterinary Medicine, University of Milan, Milan, Italy
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Cozzi MC, Strillacci MG, Valiati P, Rogliano E, Bagnato A, Longeri M. Genetic variability of Akhal-Teke horses bred in Italy. PeerJ 2018; 6:e4889. [PMID: 30202639 PMCID: PMC6129384 DOI: 10.7717/peerj.4889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/14/2018] [Indexed: 12/13/2022] Open
Abstract
Background The Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences. Methods Seventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences of AKH (56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences. Results Nucleic markers showed a high degree of polymorphism (Ho = 0.642; He = 0.649) and a low inbreeding level (FIS = 0.016) in Italian horses, compared to other AKH populations (ranged from −0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity (π) and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy.
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Affiliation(s)
- Maria C Cozzi
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Maria G Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Paolo Valiati
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Elisa Rogliano
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Maria Longeri
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
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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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20
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Mastrangelo S, Ciani E, Ajmone Marsan P, Bagnato A, Battaglini L, Bozzi R, Carta A, Catillo G, Cassandro M, Casu S, Ciampolini R, Crepaldi P, D'Andrea M, Di Gerlando R, Fontanesi L, Longeri M, Macciotta NP, Mantovani R, Marletta D, Matassino D, Mele M, Pagnacco G, Pieramati C, Portolano B, Sarti FM, Tolone M, Pilla F. Conservation status and historical relatedness of Italian cattle breeds. Genet Sel Evol 2018; 50:35. [PMID: 29940848 PMCID: PMC6019226 DOI: 10.1186/s12711-018-0406-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 06/11/2018] [Indexed: 01/30/2023] Open
Abstract
Background In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Results After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding. Conclusions This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource. Electronic supplementary material The online version of this article (10.1186/s12711-018-0406-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy.
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, 70124, Bari, Italy
| | | | - Alessandro Bagnato
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | - Luca Battaglini
- Dipartimento di Scienze Agrarie Forestali e Alimentari, University of Torino, 10095, Grugliasco, Italy
| | - Riccardo Bozzi
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, University of Firenze, 50144, Florence, Italy
| | - Antonello Carta
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, 07100, Sassari, Italy
| | - Gennaro Catillo
- CREA Research Centre for Animal Production and Acquaculture, CREA, 00015, Monterotondo, Italy
| | - Martino Cassandro
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020, Legnaro, Italy
| | - Sara Casu
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, 07100, Sassari, Italy
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie, University of Pisa, 56100, Pisa, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | | | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Luca Fontanesi
- Dipartimento di Scienze e tecnologie Agroalimentari, University of Bologna, 40127, Bologna, Italy
| | - Maria Longeri
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | | | - Roberto Mantovani
- Dipartimento di Agronomia Animali Alimenti Risorse naturali e Ambiente, University of Padova, 35020, Legnaro, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione, Ambiente, University of Catania, 95125, Catania, Italy
| | - Donato Matassino
- Divulgazione e Applicazione di Biotecniche Innovative, Consorzio per la Sperimentazione, 82100, Benevento, Italy
| | - Marcello Mele
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, 56124, Pisa, Italy
| | - Giulio Pagnacco
- Dipartimento di Medicina Veterinaria, University of Milano, 20133, Milan, Italy
| | - Camillo Pieramati
- Dipartimento di Medicina Veterinaria, University of Perugia, 06126, Perugia, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Francesca M Sarti
- Dipartimento di Scienze Agrarie, Alimentari, Ambientali, University of Perugia, 06121, Perugia, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, University of Molise, 86100, Campobasso, Italy.,Centro Risorse Bio-Culturali e Sviluppo Locale, University of Molise, 86100, Campobasso, Italy
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21
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Vega Murillo VE, Román Ponce SI, Durán Aguilar M, Velez Iquierdo A, Cabrera Torres E, Cantú Covarrubias A, De la Cruz Colín L, Maldonado Jaquez JA, Martínez Velázquez G, Ríos Utrera Á, Bagnato A, Strillacci MG, Montaño Bermúdez M, Ruíz López FJ. Evaluación morfológica de gallinas de traspatio mexicanas (Gallus gallus domesticus). REV MEX CIENC PECU 2018. [DOI: 10.22319/rmcp.v9i2.4484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
El objetivo fue evaluar algunas características morfológicas de gallinas de traspatio (n= 255) provenientes de 65 unidades rurales de producción, localizadas en 52 municipios de 18 estados de la República Mexicana. El modelo estadístico incluyó los efectos de sexo, estado y municipio anidado en estado. El efecto de sexo fue importante para todas las variables analizadas (P<0.0001), excepto para robustez (P=0.33). El efecto de estado fue importante (P<0.0001) para todas las variables analizadas, mientras que municipio solo influyó significativamente a envergadura (P<0.0001), peso corporal (P=0.0271) y solidez (P=0.0267). Los machos tuvieron mayor (P<0.0001) longitud corporal (4.85 cm), envergadura (5.66 cm), circunferencia de la pechuga (2.94 cm), longitud del tarso (1.73 cm), peso corporal (0.65 kg) y solidez (0.99 puntos porcentuales). El peso corporal aumentó 126 g (P<0.01) en machos y 61 g en hembras (P<0.01) por cada centímetro que aumentó la circunferencia de la pechuga. El peso corporal mostró estar moderadamente correlacionado con longitud del cuerpo (r= 0.65), envergadura (r= 0.49) y longitud del tarso (r= 0.67), y altamente correlacionada con circunferencia de la pechuga (r= 0.76) en machos. La gallina de traspatio en México presentó una diferenciación morfológica importante entre machos y hembras para las características estudiadas, excepto para robustez, en la cual no se detectaron diferencias.
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22
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Schiavo G, Strillacci MG, Ribani A, Bovo S, Roman-Ponce SI, Cerolini S, Bertolini F, Bagnato A, Fontanesi L. Few mitochondrial DNA sequences are inserted into the turkey (Meleagris gallopavo) nuclear genome: evolutionary analyses and informativity in the domestic lineage. Anim Genet 2018. [PMID: 29521475 DOI: 10.1111/age.12648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mitochondrial DNA (mtDNA) insertions have been detected in the nuclear genome of many eukaryotes. These sequences are pseudogenes originated by horizontal transfer of mtDNA fragments into the nuclear genome, producing nuclear DNA sequences of mitochondrial origin (numt). In this study we determined the frequency and distribution of mtDNA-originated pseudogenes in the turkey (Meleagris gallopavo) nuclear genome. The turkey reference genome (Turkey_2.01) was aligned with the reference linearized mtDNA sequence using last. A total of 32 numt sequences (corresponding to 18 numt regions derived by unique insertional events) were identified in the turkey nuclear genome (size ranging from 66 to 1415 bp; identity against the modern turkey mtDNA corresponding region ranging from 62% to 100%). Numts were distributed in nine chromosomes and in one scaffold. They derived from parts of 10 mtDNA protein-coding genes, ribosomal genes, the control region and 10 tRNA genes. Seven numt regions reported in the turkey genome were identified in orthologues positions in the Gallus gallus genome and therefore were present in the ancestral genome that in the Cretaceous originated the lineages of the modern crown Galliformes. Five recently integrated turkey numts were validated by PCR in 168 turkeys of six different domestic populations. None of the analysed numts were polymorphic (i.e. absence of the inserted sequence, as reported in numts of recent integration in other species), suggesting that the reticulate speciation model is not useful for explaining the origin of the domesticated turkey lineage.
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Affiliation(s)
- G Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - M G Strillacci
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milano, Italy
| | - A Ribani
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - S Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy.,Biocomputing Group, Department of Biological, Geological, and Environmental Sciences, University of Bologna, Via San Giacomo 9/2, 40126, Bologna, Italy
| | - S I Roman-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, Mexico
| | - S Cerolini
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milano, Italy
| | - F Bertolini
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy.,Department of Animal Science, Iowa State University, 2255 Kildee Hall, 50011, Ames, IA, USA
| | - A Bagnato
- Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milano, Italy
| | - L Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
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23
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Bouwman AC, Daetwyler HD, Chamberlain AJ, Ponce CH, Sargolzaei M, Schenkel FS, Sahana G, Govignon-Gion A, Boitard S, Dolezal M, Pausch H, Brøndum RF, Bowman PJ, Thomsen B, Guldbrandtsen B, Lund MS, Servin B, Garrick DJ, Reecy J, Vilkki J, Bagnato A, Wang M, Hoff JL, Schnabel RD, Taylor JF, Vinkhuyzen AAE, Panitz F, Bendixen C, Holm LE, Gredler B, Hozé C, Boussaha M, Sanchez MP, Rocha D, Capitan A, Tribout T, Barbat A, Croiseau P, Drögemüller C, Jagannathan V, Vander Jagt C, Crowley JJ, Bieber A, Purfield DC, Berry DP, Emmerling R, Götz KU, Frischknecht M, Russ I, Sölkner J, Van Tassell CP, Fries R, Stothard P, Veerkamp RF, Boichard D, Goddard ME, Hayes BJ. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals. Nat Genet 2018; 50:362-367. [PMID: 29459679 DOI: 10.1038/s41588-018-0056-5] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/03/2018] [Indexed: 11/09/2022]
Abstract
Stature is affected by many polymorphisms of small effect in humans 1 . In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10-8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP-seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
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Affiliation(s)
- Aniek C Bouwman
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Wageningen, the Netherlands
| | - Hans D Daetwyler
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Amanda J Chamberlain
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia
| | - Carla Hurtado Ponce
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,Faculty of Land and Food Resources, University of Melbourne, Parkville, Victoria, Australia
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada.,The Semex Alliance, Guelph, Ontario, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Simon Boitard
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Marlies Dolezal
- Platform of Bioinformatics and Statistics, University of Veterinary Medicine, Vienna, Austria
| | - Hubert Pausch
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,Chair of Animal Breeding, Technische Universität München, Freising-Weihenstephan, Germany.,Animal Genomics, ETH Zurich, Zurich, Switzerland
| | - Rasmus F Brøndum
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Phil J Bowman
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia
| | - Bo Thomsen
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Mogens S Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet-Tolosan, France
| | - Dorian J Garrick
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Johanna Vilkki
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | | | - Min Wang
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Jesse L Hoff
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Anna A E Vinkhuyzen
- University of Queensland, Institute for Molecular Bioscience, St Lucia, Queensland, Australia.,University of Queensland, Queensland Brain Institute, St Lucia, Queensland, Australia
| | - Frank Panitz
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Christian Bendixen
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Lars-Erik Holm
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | | | - Chris Hozé
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France.,Allice, Paris, France
| | - Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | | | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Aurelien Capitan
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France.,Allice, Paris, France
| | - Thierry Tribout
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Anne Barbat
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Pascal Croiseau
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | | | | | - Christy Vander Jagt
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia
| | | | - Anna Bieber
- Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Deirdre C Purfield
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Ireland
| | - Donagh P Berry
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Ireland
| | - Reiner Emmerling
- Institute of Animal Breeding, Bavarian State Research Centre for Agriculture, Poing, Germany
| | - Kay-Uwe Götz
- Institute of Animal Breeding, Bavarian State Research Centre for Agriculture, Poing, Germany
| | | | | | - Johann Sölkner
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, USA
| | - Ruedi Fries
- Chair of Animal Breeding, Technische Universität München, Freising-Weihenstephan, Germany
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science/Livestock Gentec, University of Alberta, Edmonton, Alberta, Canada
| | - Roel F Veerkamp
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Wageningen, the Netherlands
| | - Didier Boichard
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Mike E Goddard
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,Faculty of Land and Food Resources, University of Melbourne, Parkville, Victoria, Australia
| | - Ben J Hayes
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia. .,Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, University of Queensland, St Lucia, Queensland, Australia.
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24
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Peletto S, Strillacci M, Capucchio M, Biasibetti E, Modesto P, Acutis P, Bagnato A. Genetic basis of Lipomatous Myopathy in Piedmontese beef cattle. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.09.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Scotti E, Fontanesi L, Schiavini F, La Mattina V, Bagnato A, Russo V. DGAT1 p.K232A polymorphism in dairy and dual purpose Italian cattle breeds. Italian Journal of Animal Science 2017. [DOI: 10.4081/ijas.2010.e16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Emilio Scotti
- Dipartimento di Protezione e Valorizzazione Agroalimentare. Università di Bologna, Reggio Emilia, Italy
| | - Luca Fontanesi
- Dipartimento di Protezione e Valorizzazione Agroalimentare. Università di Bologna, Reggio Emilia, Italy
| | - Fausta Schiavini
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare. Università di Milano, Italy
| | - Valeria La Mattina
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare. Università di Milano, Italy
| | - Alessandro Bagnato
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare. Università di Milano, Italy
| | - Vincenzo Russo
- Dipartimento di Protezione e Valorizzazione Agroalimentare. Università di Bologna, Reggio Emilia, Italy
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26
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Frischknecht M, Meuwissen THE, Bapst B, Seefried FR, Flury C, Garrick D, Signer-Hasler H, Stricker C, Bieber A, Fries R, Russ I, Sölkner J, Bagnato A, Gredler-Grandl B. Short communication: Genomic prediction using imputed whole-genome sequence variants in Brown Swiss Cattle. J Dairy Sci 2017; 101:1292-1296. [PMID: 29153527 DOI: 10.3168/jds.2017-12890] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 09/28/2017] [Indexed: 01/27/2023]
Abstract
The accuracy of genomic prediction determines response to selection. It has been hypothesized that accuracy of genomic breeding values can be increased by a higher density of variants. We used imputed whole-genome sequence data and various single nucleotide polymorphism (SNP) selection criteria to estimate genomic breeding values in Brown Swiss cattle. The extreme scenarios were 50K SNP chip data and whole-genome sequence data with intermediate scenarios using linkage disequilibrium-pruned whole-genome sequence variants, only variants predicted to be missense, or the top 50K variants from genome-wide association studies. We estimated genomic breeding values for 3 traits (somatic cell score, nonreturn rate in heifers, and stature) and found differences in accuracy levels between traits. However, among different SNP sets, accuracy was very similar. In our analyses, sequence data led to a marginal increase in accuracy for 1 trait and was lower than 50K for the other traits. We concluded that the inclusion of imputed whole-genome sequence data does not lead to increased accuracy of genomic prediction with the methods.
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Affiliation(s)
- Mirjam Frischknecht
- Qualitas AG, Zug 6300, Switzerland; School of Agricultural, Forest and Food Sciences (HAFL), Bern University of Applied Sciences, Zollikofen 3052, Switzerland.
| | - Theodorus H E Meuwissen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Science, Ås 1432, Norway
| | | | | | - Christine Flury
- School of Agricultural, Forest and Food Sciences (HAFL), Bern University of Applied Sciences, Zollikofen 3052, Switzerland
| | - Dorian Garrick
- Institute of Veterinary, Animal & Biomedical Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences (HAFL), Bern University of Applied Sciences, Zollikofen 3052, Switzerland
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- Interbull Center, Uppsala 75007, Sweden
| | - Anna Bieber
- Department of Animal Sciences, Research Institute of Organic Agriculture (FiBL), Frick 5070, Switzerland
| | - Ruedi Fries
- Chair of Animal Breeding, Technische Universität München, Freising-Weihenstephan 85354, Germany
| | - Ingolf Russ
- Tierzuchtforschung e.V., Poing-Grub 85586, Germany
| | - Johann Sölkner
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Wien 1180, Austria
| | - Alessandro Bagnato
- Department of Veterinary Sciences and Technologies for Food Safety, University of Milan, Milano 20133, Italy
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Cozzi MC, Colombo E, Zaniboni L, Madeddu M, Mosca F, Strillacci MG, Longeri M, Bagnato A, Cerolini S. Phenotypic and genetic characterization of the Italian bantam chicken breed Mericanel della Brianza. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Baldari S, Annibale V, Lastoria S, Tucci M, Borsatti E, Monari F, Paganelli G, Verri E, Muto P, Panareo S, Mosca A, Storto G, Bagnato A, Farsad M, Bilancia D, Marchetti P, Sternberg C, Procopio G, Seregni E, Valdagni R. Patient (pt) characteristics and treatment patterns in the radium (Ra)-223 REASSURE observational study. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx423.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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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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Cozzi MC, Valiati P, Cherchi R, Gorla E, Prinsen RTMM, Longeri M, Bagnato A, Strillacci MG. Mitochondrial DNA genetic diversity in six Italian donkey breeds (Equus asinus). Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:409-418. [PMID: 28278690 DOI: 10.1080/24701394.2017.1292505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Donkeys have played an important role in agricultural land practices and in human historical periods of recent past and, still today, are used as a working power in several world areas. The objective of this study was to identify genetic variability in six Italian donkey breeds using mtDNA D-loop. Fifteen haplotypes, grouped in three haplogroups, were identified. The genetic indices were informative and showed a high population genetic variability. The results of AMOVA analyses based on geographic structuring of Italian populations highlighted that the majority of the observed variance is due to differences among samples within breeds. Comparison among Italian haplotypes and mtDNA D-loop sequences belonging to European domestic and Ethiopian donkeys and wild asses, clearly define two clades referred to Nubian lineage. The results can be useful to complement safeguard planes for donkey breeds that are considered to extinction endangered.
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Affiliation(s)
- Maria Cristina Cozzi
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
| | - Paolo Valiati
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
| | - Raffaele Cherchi
- b Agenzia per la ricerca in agricoltura-AGRIS Sardegna , Sassari , Italy
| | - Erica Gorla
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
| | | | - Maria Longeri
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
| | - Alessandro Bagnato
- a Department of Veterinary Medicine , Università degli Studi di Milano , Milano , Italy
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Perrini C, Strillacci MG, Bagnato A, Esposti P, Marini MG, Corradetti B, Bizzaro D, Idda A, Ledda S, Capra E, Pizzi F, Lange-Consiglio A, Cremonesi F. Microvesicles secreted from equine amniotic-derived cells and their potential role in reducing inflammation in endometrial cells in an in-vitro model. Stem Cell Res Ther 2016; 7:169. [PMID: 27863532 PMCID: PMC5114748 DOI: 10.1186/s13287-016-0429-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/22/2016] [Accepted: 10/21/2016] [Indexed: 12/24/2022] Open
Abstract
Background It is known that a paracrine mechanism exists between mesenchymal stem cells and target cells. This process may involve microvesicles (MVs) as an integral component of cell-to-cell communication. Methods In this context, this study aims to understand the efficacy of MVs in in-vitro endometrial stressed cells in view of potential healing in in-vivo studies. For this purpose, the presence and type of MVs secreted by amniotic mesenchymal stem cells (AMCs) were investigated and the response of endometrial cells to MVs was studied using a dose-response curve at different concentrations and times. Moreover, the ability of MVs to counteract the in vitro stress in endometrial cells induced by lipopolysaccharide was studied by measuring the rate of apoptosis and cell proliferation, the expression of some pro-inflammatory genes such as tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), interleukin 1β (IL-1β), and metalloproteinases (MMP) 1 and 13, and the release of some pro- or anti-inflammatory cytokines. Results MVs secreted by the AMCs ranged in size from 100 to 200 nm. The incorporation of MVs was gradual over time and peaked at 72 h. MVs reduced the apoptosis rate, increased cell proliferation values, downregulated pro-inflammatory gene expression, and decreased the secretion of pro-inflammatory cytokines. Conclusion Our data suggest that some microRNAs could contribute to counteracting in-vivo inflammation of endometrial tissue.
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Affiliation(s)
- Claudia Perrini
- Large Animal Hospital, Reproduction Unit, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy
| | | | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Milano, Italy
| | - Paola Esposti
- Large Animal Hospital, Reproduction Unit, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy
| | - Maria Giovanna Marini
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Bruna Corradetti
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Davide Bizzaro
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Antonella Idda
- Department of Veterinary Medicine, Università degli Studi di Sassari, Sassari, Italy
| | - Sergio Ledda
- Department of Veterinary Medicine, Università degli Studi di Sassari, Sassari, Italy
| | - Emanuele Capra
- Institute of Biology and Agricultural Biotechnology-CNR, Milano, Italy
| | - Flavia Pizzi
- Institute of Biology and Agricultural Biotechnology-CNR, Milano, Italy
| | - Anna Lange-Consiglio
- Large Animal Hospital, Reproduction Unit, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy.
| | - Fausto Cremonesi
- Large Animal Hospital, Reproduction Unit, Università degli Studi di Milano, Via dell'Università 6, 26900, Lodi, Italy.,Department of Veterinary Medicine, Università degli Studi di Milano, Milano, Italy
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Peletto S, Capucchio MT, Strillacci MG, Boin C, Biasibetti E, Modesto P, Schiavini F, Acutis PL, Bagnato A. P6008 Genomic basis of Lipomatous Myopathy in Piedmontese beef cattle. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4151a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Lipkin E, Strillacci MG, Eitam H, Yishay M, Schiavini F, Soller M, Bagnato A, Shabtay A. P6003 The use of Kosher phenotyping for mapping QTL affecting susceptibility to bovine respiratory disease. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4149x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Prinsen R, Strillacci M, Schiavini F, Santus E, Rossoni A, Maurer V, Bieber A, Gredler B, Dolezal M, Bagnato A. A genome-wide scan of copy number variants using high-density SNPs in Brown Swiss dairy cattle. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.08.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Durán Aguilar M, Román Ponce SI, Ruiz López FJ, González Padilla E, Vásquez Peláez CG, Bagnato A, Strillacci MG. Genome-wide association study for milk somatic cell score in holstein cattle using copy number variation as markers. J Anim Breed Genet 2016; 134:49-59. [PMID: 27578198 DOI: 10.1111/jbg.12238] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 08/03/2016] [Indexed: 12/21/2022]
Abstract
Mastitis, the most common and expensive disease in dairy cows, implies significant losses in the dairy industry worldwide. Many efforts have been made to improve genetic mastitis resistance in dairy populations, but low heritability of this trait made this process not as effective as desired. The purpose of this study was to identify genomic regions explaining genetic variation of somatic cell count using copy number variations (CNVs) as markers in the Holstein population, genotyped with the Illumina BovineHD BeadChip. We found 24 and 47 copy number variation regions significantly associated with estimated breeding values for somatic cell score (SCS_EBVs) using SVS 8.3.1 and PennCNV-CNVRuler software, respectively. The association analysis performed with these two software allowed the identification of 18 candidate genes (TERT, NOTCH1, SLC6A3, CLPTM1L, PPARα, BCL-2, ABO, VAV2, CACNA1S, TRAF2, RELA, ELF3, DBH, CDK5, NF2, FASN, EWSR1 and MAP3K11) that result classified in the same functional cluster. These genes are also part of two gene networks, whose genes share the 'stress', 'cell death', 'inflammation' and 'immune response' GO terms. Combining CNV detection/association analysis based on two different algorithms helps towards a more complete identification of genes linked to phenotypic variation of the somatic cell count.
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Affiliation(s)
- M Durán Aguilar
- Facultad de Estudios Superiores Cuautitlán, UNAM, Cuautitlán Izcalli, México
| | - S I Román Ponce
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, INIFAP, Auchitlán, Querétaro, México
| | - F J Ruiz López
- Centro Nacional de Investigación en Fisiología y Mejoramiento Animal, INIFAP, Auchitlán, Querétaro, México
| | - E González Padilla
- Departamento de Genética y Bioestadística, Facultad Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México DF, México
| | - C G Vásquez Peláez
- Departamento de Genética y Bioestadística, Facultad Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, México DF, México
| | - A Bagnato
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
| | - M G Strillacci
- Department of Veterinary Medicine (DiMeVet), University of Milan, Milan, Italy
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Ríos Utrera Á, Román Ponce SI, Vélez Izquierdo A, Cabrera Torre E, Cantú Covarrubias A, De la Cruz Colín L, Durán Aguilar M, Maldonado Jaquez JA, Martínez Silva FE, Martínez Velázquez G, De Jesús Ruiz López F, Bagnato A, Vega Murillo VE. Análisis de variables morfológicas de pavos de traspatio mexicanos (Meleagris gallopavo gallopavo). REV MEX CIENC PECU 2016. [DOI: 10.22319/rmcp.v7i3.4216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
El objetivo fue evaluar algunas características morfológicas de pavos de traspatio (n=248) provenientes de 126 unidades rurales de producción localizadas en 75 municipios de 24 estados de la República Mexicana. El modelo estadístico incluyó sexo, estado y municipio anidado en estado. Las tres variables explicativas afectaron a todas las variables de respuesta (P<0.01), excepto municipio, que no afectó circunferencia de la pechuga (P>0.05). Los machos tuvieron mayor (P<0.001) longitud corporal (10.4 cm más), envergadura (11.4 cm más), circunferencia de la pechuga (13.8 cm más), longitud de tarso (2.5 cm más), peso corporal (2.5 kg más), robustez (9.0 puntos porcentuales más) y solidez (2.8 puntos porcentuales más) que las hembras. Peso corporal mostró estar altamente correlacionado fenotípicamente (P<0.01) con circunferencia de la pechuga tanto en machos (r=0.74) como en hembras (r=0.71). En machos, longitud corporal mostró una correlación baja con longitud del tarso (r=0.25; P<0.01), pero en hembras no estuvo correlacionada (r=0.05; P>0.05). El peso corporal aumentó 143 g (P<0.01) en machos y 113 g en hembras (P<0.01) por cada centímetro que aumentó la circunferencia de la pechuga. Los colores predominantes en el plumaje, la piel y el tarso fueron negro, blanco y café, respectivamente. El pavo de traspatio mexicano presentó dimorfismo sexual significativo y alta correlación fenotípica entre circunferencia de la pechuga y peso corporal.
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Lipkin E, Strillacci MG, Eitam H, Yishay M, Schiavini F, Soller M, Bagnato A, Shabtay A. The Use of Kosher Phenotyping for Mapping QTL Affecting Susceptibility to Bovine Respiratory Disease. PLoS One 2016; 11:e0153423. [PMID: 27077383 PMCID: PMC4831767 DOI: 10.1371/journal.pone.0153423] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/29/2016] [Indexed: 02/06/2023] Open
Abstract
Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in feedlot cattle, caused by multiple pathogens that become more virulent in response to stress. As clinical signs often go undetected and various preventive strategies failed, identification of genes affecting BRD is essential for selection for resistance. Selective DNA pooling (SDP) was applied in a genome wide association study (GWAS) to map BRD QTLs in Israeli Holstein male calves. Kosher scoring of lung adhesions was used to allocate 122 and 62 animals to High (Glatt Kosher) and Low (Non-Kosher) resistant groups, respectively. Genotyping was performed using the Illumina BovineHD BeadChip according to the Infinium protocol. Moving average of -logP was used to map QTLs and Log drop was used to define their boundaries (QTLRs). The combined procedure was efficient for high resolution mapping. Nineteen QTLRs distributed over 13 autosomes were found, some overlapping previous studies. The QTLRs contain polymorphic functional and expression candidate genes to affect kosher status, with putative immunological and wound healing activities. Kosher phenotyping was shown to be a reliable means to map QTLs affecting BRD morbidity.
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Affiliation(s)
- Ehud Lipkin
- Department of Genetics, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Harel Eitam
- Department of Ruminant Sciences, Agricultural Research Organization (ARO), Bet-Dagan, Israel
| | - Moran Yishay
- Department of Ruminant Sciences, Agricultural Research Organization (ARO), Bet-Dagan, Israel
| | | | - Morris Soller
- Department of Genetics, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Ariel Shabtay
- Department of Ruminant Sciences, Agricultural Research Organization (ARO), Bet-Dagan, Israel
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Samoré AB, Romani C, Rossoni A, Frigo E, Pedron O, Bagnato A. Genetic parameters for casein and urea contentin the Italian Brown Swiss dairy cattle. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2007.1s.201] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- A. B. Samoré
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare, Università di Milano, Italy
| | - C. Romani
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare, Università di Milano, Italy
| | - A. Rossoni
- AAssociazione Nazionale Allevatori di Razza Bruna, Verona, Italy
| | - E. Frigo
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare, Università di Milano, Italy
| | - O. Pedron
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare, Università di Milano, Italy
| | - A. Bagnato
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare, Università di Milano, Italy
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Bagnato A, Schiavini F, Dolezal M, Dubini S, Rossoni A, Maltecca C, Santus E, Medugorac I, Sölkner J, Fontanesi L, Friedman A, Lipkin E, Soller M. The BovMAS Consortium: identification of QTL for milk yield and milk protein percent on chromosome 14 in the Brown Swiss breed. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2005.2s.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Frigo E, Samorè AB, Vicario D, Bagnato A, Pedron O. Heritabilities and Genetic Correlations of Body Condition Score and Muscularity with Productive Traits and their Trend Functions in Italian Simmental Cattle. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2013.e40] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Colombo E, Strillacci MG, Cozzi MC, Madeddu M, Mangiagalli MG, Mosca F, Zaniboni L, Bagnato A, Cerolini S. Feasibility Study on the FAO Chicken Microsatellite Panel to Assess Genetic Variability in the Turkey (Meleagris Gallopavo). Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2014.3334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tullo E, Frigo E, Rossoni A, Finocchiaro R, Serra M, Rizzi N, Samorè AB, Canavesi F, Strillacci MG, Prinsen RTMM, Bagnato A. Genetic Parameters of Fatty Acids in Italian Brown Swiss and Holstein Cows. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2014.3208] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bagnato A, Strillacci MG, Pellegrino L, Schiavini F, Frigo E, Rossoni A, Fontanesi L, Maltecca C, Prinsen RT, Dolezal MA. Identification and Validation of Copy Number Variants in Italian Brown Swiss Dairy Cattle Using Illumina Bovine SNP50 Beadchip®. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2015.3900] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alessandro Bagnato
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, University of Bologna, Italy
| | - Maria G. Strillacci
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Laura Pellegrino
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Fausta Schiavini
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Erika Frigo
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Attilio Rossoni
- Associazione Nazionale Allevatori Razza Bruna, Bussolengo (VR), Italy
| | - Luca Fontanesi
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, University of Bologna, Italy
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Raphaelle T.M.M. Prinsen
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Marlies A. Dolezal
- Institut für Populationsgenetik Veterinärmedizinische, University of Wien, Austria
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44
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Bellagamba F, Velayutham D, Cozzi MC, Caprino F, Vasconi M, Busetto ML, Bagnato A, Moretti VM. Cytochrome Oxidase-I Sequence Based Studies of Commercially Available Pangasius Hypophthalmus in Italy. Italian Journal of Animal Science 2016. [DOI: 10.4081/ijas.2015.3928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Dinesh Velayutham
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Maria Cristina Cozzi
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Fabio Caprino
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Mauro Vasconi
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Maria Letizia Busetto
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Alessandro Bagnato
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Vittorio Maria Moretti
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
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Bocchi V, Strillacci MG, Zecconi A, Galli C, Stadaioli G, Brevini TAL, Bagnato A, Gandolfi F. 191 SEARCHING FOR THE IN VIVO TRANSCRIPTOME BLUEPRINT OF COMPETENT BOVINE OOCYTES. Reprod Fertil Dev 2016. [DOI: 10.1071/rdv28n2ab191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Gene expression in early stage embryos relies mostly on post-transcriptional control of maternal transcripts accumulated during oocyte maturation. However, while the building process to obtain a competent oocyte is now better understood, it is still not clear what transcriptome blueprint composes a competent oocyte. The aim of the study was to compare the mRNA expression pattern between oocytes collected from fertile heifers and repeat breeders by using RNAseq. Oocytes were collected by ovum pickup from 3 heifers that were 11–15 months of age and became pregnant at the following oestrus and from 4 adult cows with an age of 4 to 7 years, classified as repeat breeders after they failed to become pregnant for a minimum of 3 consecutive AI. To obtain oocytes from follicles with the same degree of development, at time 0 all follicles visible through transrectal ultrasound examination were removed by transvaginal aspiration. Five days later oocytes were collected by ovum pick up from the newly formed follicles with diameters >5 mm. Oocytes from each animal were pooled and sequenced as a single sample. Total RNA was extracted by RNeasy Micro Kit (Qiagen, Valencia, CA, USA). Amplified cDNA, was prepared starting from total RNA using the Ovation RNA-Seq System V2 (Nugen Technologies, San Carlos, CA, USA). After library preparation with TruSeq DNA Sample Prep kit (Illumina, Madison, WI, USA), sequencing was performed on an Illumina HiSEqn 2000. Galaxy and Chipster open web-based platforms were used to analyse the data. We identified 49 differentially expressed genes. Heifers’ oocytes mRNA pattern indicated greater potential to sustain cell division. In particular, oocytes expressed more Keratin 14 (a gene involved in cell proliferation) and kinesin family member 20B (a protein involved in cytokinesis). More competent oocytes also have a greater ability to repair single-strand breaks due to the high levels of endo/exonuclease (5′-3′), endonuclease G-like. This may reflect greater capacity to neutralise DNA damage and, therefore, greater ability to preserve and transmit high-quality DNA. Repeat breeders portray a different landscape; their greater expression of Jun oncogene, Heat shock protein 1, Stimulated by retinoic acid gene6, arylhydrocarbon receptor nuclear translocator, fibromodulin, and aryl-hydrocarbon receptor repressor suggest that these oocytes have been subjected to environmental stress during oocyte maturation. Their greater expressions of inhibin α, stearoyl-CoA desaturase, junctional adhesion molecule 2 have been previously shown to correlate with a reduced oocyte developmental potential. Furthermore, the Cannabinoid receptor protein 1 expression suggests a compromised ion function that can lead to a failed activation of the development program. Finally, the greater expression of Ubiquilin3 and Heat shock protein 1 led to high protein and mRNA degradation, respectively, suggesting that these oocytes are deprived of essential components to sustain embryo growth. In conclusion our data provide the first detailed snapshot of the mRNA pattern defining the differences between a competent oocyte and an incompetent oocyte in vivo.
Study supported by PRIN 2008, 2009 and EU-Quantomics.
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Semprucci E, Tocci P, Cianfrocca R, Sestito R, Caprara V, Veglione M, Castro VD, Spadaro F, Ferrandina G, Bagnato A, Rosanò L. Endothelin A receptor drives invadopodia function and cell motility through the β-arrestin/PDZ-RhoGEF pathway in ovarian carcinoma. Oncogene 2015; 35:3432-42. [PMID: 26522724 DOI: 10.1038/onc.2015.403] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 09/16/2015] [Accepted: 09/18/2015] [Indexed: 02/07/2023]
Abstract
The endothelin-1 (ET-1)/ET A receptor (ETAR) signalling pathway is a well-established driver of epithelial ovarian cancer (EOC) progression. One key process promoted by ET-1 is tumor cell invasion, which requires the scaffolding functions of β-arrestin-1 (β-arr1) downstream of the receptor; however, the potential role of ET-1 in inducing invadopodia, which are crucial for cellular invasion and tumor metastasis, is completely unknown. We describe here that ET-1/ETAR, through β-arr1, activates RhoA and RhoC GTPase and downstream ROCK (Rho-associated coiled coil-forming kinase) kinase activity, promoting actin-based dynamic remodelling and enhanced cell invasion. This is accomplished by the direct interaction of β-arr1 with PDZ-RhoGEF (postsynaptic density protein 95/disc-large/zonula occludens-RhoGEF). Interestingly, ETAR-mediated invasive properties are related to the regulation of invadopodia, as evaluated by colocalization of actin with cortactin, as well as with TKS5 and MT1-MMP (membrane type 1-matrix metalloproteinase) with areas of matrix degradation, and activation of cofilin pathway, which is crucial for regulating invadopodia activity. Depletion of PDZ-RhoGEF, or β-arr1, or RhoC, as well as the treatment with the dual ET-1 receptor antagonist macitentan, significantly impairs invadopodia function, MMP activity and invasion, demonstrating that β-arr1/PDZ-RhoGEF interaction mediates ETAR-driven ROCK-LIMK-cofilin pathway through the control of RhoC activity. In vivo, macitentan is able to inhibit metastatic dissemination and cofilin phosphorylation. Collectively, our data unveil a noncanonical activation of the RhoC/ROCK pathway through the β-arr1/PDZ-RhoGEF complex as a regulator of ETAR-induced motility and metastasis, establishing ET-1 axis as a novel regulator of invadopodia protrusions through the RhoC/ROCK/LIMK/cofilin pathway during the initial steps of EOC invasion.
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Affiliation(s)
- E Semprucci
- Regina Elena National Cancer Institute Rome, Rome, Italy
| | - P Tocci
- Regina Elena National Cancer Institute Rome, Rome, Italy
| | - R Cianfrocca
- Regina Elena National Cancer Institute Rome, Rome, Italy
| | - R Sestito
- Regina Elena National Cancer Institute Rome, Rome, Italy
| | - V Caprara
- Regina Elena National Cancer Institute Rome, Rome, Italy
| | - M Veglione
- Regina Elena National Cancer Institute Rome, Rome, Italy
| | - V Di Castro
- Regina Elena National Cancer Institute Rome, Rome, Italy
| | - F Spadaro
- Section of Experimental Immunotherapy, Department of Haematology, Oncology and Molecular Medicine, Istituto Superiore di Sanita', Rome, Italy
| | - G Ferrandina
- Gynecologic Oncology Unit, Catholic University of Rome, Rome, Italy
| | - A Bagnato
- Regina Elena National Cancer Institute Rome, Rome, Italy
| | - L Rosanò
- Regina Elena National Cancer Institute Rome, Rome, Italy
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Fontanesi L, Scotti E, Samorè A, Bagnato A, Russo V. Association of 20 candidate gene markers with milk production and composition traits in sires of Reggiana breed, a local dairy cattle population. Livest Sci 2015. [DOI: 10.1016/j.livsci.2015.03.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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48
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Strillacci MG, Frigo E, Schiavini F, Samoré AB, Canavesi F, Vevey M, Cozzi MC, Soller M, Lipkin E, Bagnato A. Genome-wide association study for somatic cell score in Valdostana Red Pied cattle breed using pooled DNA. BMC Genet 2014; 15:106. [PMID: 25288516 PMCID: PMC4198737 DOI: 10.1186/s12863-014-0106-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/25/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Mastitis is a major disease of dairy cattle occurring in response to environmental exposure to infective agents with a great economic impact on dairy industry. Somatic cell count (SCC) and its log transformation in somatic cell score (SCS) are traits that have been used as indirect measures of resistance to mastitis for decades in selective breeding. A selective DNA pooling (SDP) approach was applied to identify Quantitative Trait Loci (QTL) for SCS in Valdostana Red Pied cattle using the Illumina Bovine HD BeadChip. RESULTS A total of 171 SNPs reached the genome-wide significance for association with SCS. Fifty-two SNPs were annotated within genes, some of those involved in the immune response to mastitis. On BTAs 1, 2, 3, 4, 9, 13, 15, 17, 21 and 22 the largest number of markers in association to the trait was found. These regions identified novel genomic regions related to mastitis (1-Mb SNP windows) and confirmed those already mapped. The largest number of significant SNPs exceeding the threshold for genome-wide significant signal was found on BTA 15, located at 50.43-51.63 Mb. CONCLUSIONS The genomic regions identified in this study contribute to a better understanding of the genetic control of the mastitis immune response in cattle and may allow the inclusion of more detailed QTL information in selection programs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Alessandro Bagnato
- Department of Health, Animal Science and Food Safety (VESPA), University of Milan, Via Celoria 10, Milan, 20133, Italy.
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Abstract
Background Genomic prediction is based on the accurate estimation of the genomic relationships among and between training animals and selection candidates in order to obtain accurate estimates of the genomic estimated breeding values (GEBV). Various methods have been used to predict GEBV based on population-wide linkage disequilibrium relationships (GIBS) or sometimes on linkage analysis relationships (GLA). Here, we propose a novel method to predict GEBV based on a genomic relationship matrix using runs of homozygosity (GROH). Runs of homozygosity were used to derive probabilities of multi-locus identity by descent chromosome segments. The accuracy and bias of the prediction of GEBV using GROH were compared to those using GIBS and GLA. Comparisons were performed using simulated datasets derived from a random pedigree and a real pedigree of Italian Brown Swiss bulls. The comparison of accuracies of GEBV was also performed on data from 1086 Italian Brown Swiss dairy cattle. Results Simulations with various thresholds of minor allele frequency for markers and quantitative trait loci showed that GROH achieved consistently more accurate GEBV (0 to 4% points higher) than GIBS and GLA. The bias of GEBV prediction for simulated data was higher based on the real pedigree than based on a random pedigree. In the analyses with real data, GROH and GLA had similar accuracies. However, GLA achieved a higher accuracy when the prediction was done on the youngest animals. The GIBS matrices calculated with and without standardized marker genotypes resulted in similar accuracies. Conclusions The present study proposes GROH as a novel method to estimate genomic relationship matrices and predict GEBV based on runs of homozygosity and shows that it can result in higher or similar accuracies of GEBV prediction than GLA, except for the real data analysis with validation of young animals. Compared to GIBS, GROH resulted in more accurate GEBV predictions.
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Affiliation(s)
- Tu Luan
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, N-1432, Norway.
| | - Xijiang Yu
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, N-1432, Norway.
| | - Marlies Dolezal
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare, Università degli Studi di Milano, Via Celoria 10, 20133, Milano, Italy.
| | - Alessandro Bagnato
- Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare, Università degli Studi di Milano, Via Celoria 10, 20133, Milano, Italy.
| | - Theo He Meuwissen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, N-1432, Norway.
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50
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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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