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Colombi D, Rovelli G, Luigi-Sierra MG, Ceccobelli S, Guan D, Perini F, Sbarra F, Quaglia A, Sarti FM, Pasquini M, Amills M, Lasagna E. Population structure and identification of genomic regions associated with productive traits in five Italian beef cattle breeds. Sci Rep 2024; 14:8529. [PMID: 38609445 PMCID: PMC11014930 DOI: 10.1038/s41598-024-59269-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/09/2024] [Indexed: 04/14/2024] Open
Abstract
Italy has a long history in beef production, with local breeds such as Marchigiana, Chianina, Romagnola, Maremmana, and Podolica which produce high-quality meat. Selection has improved meat production, precocity, growth ability and muscle development, but the genetic determinism of such traits is mostly unknown. Using 33K SNPs-data from young bulls (N = 4064) belonging to these five Italian breeds, we demonstrated that the Maremmana and Podolica rustic breeds are closely related, while the specialised Marchigiana, Chianina, and Romagnola breeds are more differentiated. A genome-wide association study for growth and muscle development traits (average daily gain during the performance test, weight at 1 year old, muscularity) was conducted in the five Italian breeds. Results indicated a region on chromosome 2, containing the myostatin gene (MSTN), which displayed significant genome-wide associations with muscularity in Marchigiana cattle, a breed in which the muscle hypertrophy phenotype is segregating. Moreover, a significant SNP on chromosome 14 was associated, in the Chianina breed, to muscularity. The identification of diverse genomic regions associated with conformation traits might increase our knowledge about the genomic basis of such traits in Italian beef cattle and, eventually, such information could be used to implement marker-assisted selection of young bulls tested in the performance test.
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Affiliation(s)
- Daniele Colombi
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Giacomo Rovelli
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonòma de Barcelona, Carrer de la Vall Moronta, 08193, Bellaterra de Cerdanyola del Vallés, Spain
| | - Maria Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonòma de Barcelona, Carrer de la Vall Moronta, 08193, Bellaterra de Cerdanyola del Vallés, Spain
| | - Simone Ceccobelli
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonòma de Barcelona, Carrer de la Vall Moronta, 08193, Bellaterra de Cerdanyola del Vallés, Spain
- Department of Animal Science, University of California, Davis, CA, 2251, USA
| | - Francesco Perini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020, Legnaro, Italy
| | - Fiorella Sbarra
- National Association of Italian Beef-Cattle Breeders (ANABIC), 06132, San Martino in Colle, Perugia, Italy
| | - Andrea Quaglia
- National Association of Italian Beef-Cattle Breeders (ANABIC), 06132, San Martino in Colle, Perugia, Italy
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Marina Pasquini
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autonòma de Barcelona, Carrer de la Vall Moronta, 08193, Bellaterra de Cerdanyola del Vallés, Spain.
- Department of Animal and Food Science, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
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Karatosidi D, Ligda C, Colonna MA, Avgeris E, Tarricone S. Meat Quality in Katerini and Podolian Young Bulls Raised on Pasture: A Comparison between Organic Production Systems in Greek and Italian Environments. Animals (Basel) 2023; 13:3102. [PMID: 37835708 PMCID: PMC10571818 DOI: 10.3390/ani13193102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Local and typical agri-food products (TAP) are receiving increasing interest from consumers, since they are perceived as genuine, healthy and tasty because they are produced under environmentally friendly farming systems. This has aroused a renewed interest among breeders from the inner regions of Italy and Greece toward autochthonous animal populations, such as Greek Katerini and Italian Podolian cattle. Twenty animals were used, divided into two homogeneous groups of ten subjects per each genotype. Animals were fed only on natural pasture and were slaughtered at 18 months of age. Meat from the Katerini young bulls showed a lower a* value, higher moisture and was leaner, and its fat was richer in n-3 fatty acids and had a better n-6/n-3 ratio. Meat from Podolian young bulls was more tender and showed a higher redness value and a significantly greater MUFA concentration. This preliminary study provides a contribution to the local actors and relevant authorities to develop a conservation program for the endangered Katerini breed based on the nutritional and sensorial characterization of its products.
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Affiliation(s)
- Despoina Karatosidi
- Research Institute of Animal Science, Hellenic Agricultural Organization-DIMITRA, 58100 Giannitsa, Greece
| | - Christina Ligda
- Veterinary Research Institute, Hellenic Agricultural Organization-DIMITRA, 60458 Thessaloniki, Greece;
| | - Maria Antonietta Colonna
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, 70125 Bari, Italy;
| | - Efthymios Avgeris
- Panellinia Enosi Ektropheon Autochthonon Fylon Agrotikon Zoon-PEEAFAZ, S. Sarafi 30, 42100 Trikala, Greece;
| | - Simona Tarricone
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, 70125 Bari, Italy;
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Sawicka-Zugaj W, Chabuz W, Kasprzak-Filipek K. The Role of Reproduction and Genetic Variation in Polish White-Backed Cows in the Breed Restoration Process. Animals (Basel) 2023; 13:2790. [PMID: 37685054 PMCID: PMC10486713 DOI: 10.3390/ani13172790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Local breeds are the main reservoir of biodiversity of farm animals. According to FAO, they account for 87% of all described breeds in the world. To ensure that they are adequately protected, they should be continually monitored for genetic variation. Another crucial factor is reproduction, which is the most important guarantee of population growth. In the present study, genetic variation in 372 Polish White-Backed cows was determined using DNA microsatellite sequences, taking into account their parentage. Reproductive parameters were analysed as well, based on data from 3658 lactations of 1128 Polish White-Backed cows. The results indicate that despite the small initial population and the implementation of a moderate selection of animals, the existing population of Polish White-Backed cattle has a high level of genetic variation, reflected in the degree of heterozygosity (0.761). Regarding reproductive traits, despite their late age at first calving, Polish White-Backed cows were shown to be distinguished by very good fertility parameters in comparison to other breeds raised in Poland. These findings not only confirm the value of protecting local cattle breeds around the world but may also be of importance in developing selection indices for highly productive breeds, in which reproductive functioning should be one of the most important factors considered.
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Affiliation(s)
| | - Witold Chabuz
- Department of Cattle Breeding and Genetic Resources Conservation, University of Life Sciences in Lublin, 20-950 Lublin, Poland; (W.S.-Z.); (K.K.-F.)
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Solodneva E, Svishcheva G, Smolnikov R, Bazhenov S, Konorov E, Mukhina V, Stolpovsky Y. Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle ( Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers. Int J Mol Sci 2023; 24:5061. [PMID: 36902492 PMCID: PMC10003406 DOI: 10.3390/ijms24055061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/09/2023] Open
Abstract
Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research.
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Affiliation(s)
- Evgenia Solodneva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Gulnara Svishcheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Rodion Smolnikov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Sergey Bazhenov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Evgenii Konorov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Gorbatov Federal Research Center for Food Systems, Russian Academy of Sciences, 109316 Moscow, Russia
| | - Vera Mukhina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Yurii Stolpovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
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González ARM, Navas González FJ, Crudeli GÁ, Delgado Bermejo JV, Camacho Vallejo ME, Quirino CR. Process of Introduction of Australian Braford Cattle to South America: Configuration of Population Structure and Genetic Diversity Evolution. Animals (Basel) 2022; 12:ani12030275. [PMID: 35158599 PMCID: PMC8833419 DOI: 10.3390/ani12030275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/05/2022] [Accepted: 01/20/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary The Braford breed originated in the USA and Australia from a cross between the Brahman and Hereford breeds to obtain animals suitable for the subtropical climate and resistant to hoof diseases, eye cancer, and ectoparasites, mainly ticks. This resistance to ticks was what attracted the attention of South American breeders, who acquired animals from Australia. The first breeder to do so was Uruguay around 1970. From then on, the breed was distributed across Argentina, Paraguay, and Brazil. Each country has its own association of breeders, and each one keeps the herdbook of the breed where the animals are registered. Selective breeding was conducted, thereby shaping genetic diversity over the years. The analysis of the pedigree database allowed us to evaluate these changes and the evolution of diversity over time. The objective of the present work was to analyze the population structure of the Braford breed in four countries, the repercussions of founders and ancestors, and the parameters of genetic diversity to suggest effective strategies for Braford breeders. Abstract This study analyzes the evolution of the population structure and genetic diversity of Braford cattle in South America from 1949 to 2019 to suggest effective strategies for breeding in the future. The percentage of bulls historically increased. The average generational interval decreased to 11.78 years for the current population. Average inbreeding (F) and coancestry (C) are low and show a historically increasing trend (0.001% to 0.002%, respectively). The degree of nonrandom mating (α) increased from −0.0001 to 0.0001 denoting a change in the trend to mate similar individuals. The average relatedness coefficient (ΔR) increased in the current period from 0.002% to 0.004%. A single ancestor explained 4.55% to 7.22% of the population’s gene pool. While the effective population size based on the individual inbreeding rate (NeFi) was 462.963, when based on the individual coancestry rate (NeCi), it was 420.168. Genetic diversity loss is small and mainly ascribed to bottlenecks (0.12%) and to unequal contributions of the founders (0.02%). Even if adequate levels of diversity can be found, practices that consider the overuse of individual bulls (conditioned by nature or not), could lead to a long-term reduction in diversity. The present results permit tailoring genetic management strategies that are perfectly adapted to the needs that the population demands internationally.
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Affiliation(s)
- Araceli Rocío Marisel González
- Laboratory of Animal Reproduction and Genetic Improvement, Northern Rio de Janeiro State University (Universidade Estadual do Norte Fluminense/UENF), Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil; (A.R.M.G.); (C.R.Q.)
| | - Francisco Javier Navas González
- Institute of Agricultural Research and Training (IFAPA), Alameda del Obispo, 14014 Córdoba, Spain;
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain;
- Correspondence: ; Tel.: +34-638-535-046 (ext. 621262)
| | - Gustavo Ángel Crudeli
- Theriogenology Area, Faculty of Veterinary Sciences, National University of the Chaco Austral (Universidad Nacional del Chaco Austral/UNCAus), Chaco 3700, Argentina;
| | | | | | - Celia Raquel Quirino
- Laboratory of Animal Reproduction and Genetic Improvement, Northern Rio de Janeiro State University (Universidade Estadual do Norte Fluminense/UENF), Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil; (A.R.M.G.); (C.R.Q.)
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Senczuk G, Mastrangelo S, Ajmone-Marsan P, Becskei Z, Colangelo P, Colli L, Ferretti L, Karsli T, Lancioni H, Lasagna E, Marletta D, Persichilli C, Portolano B, Sarti FM, Ciani E, Pilla F. On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data. Genet Sel Evol 2021; 53:48. [PMID: 34078254 PMCID: PMC8173809 DOI: 10.1186/s12711-021-00639-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022] Open
Abstract
Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00639-w.
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Affiliation(s)
- Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy.
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Paolo Ajmone-Marsan
- Department of Animal Science Food and Nutrition, DIANA, Nutrigenomics and Proteomics Research Centre, PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre, BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Zsolt Becskei
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine, Bulevar Oslobodjenja street 18, 11000, Belgrade, Serbia
| | - Paolo Colangelo
- National Council of Research (CNR), Research Institute On Terrestrial Ecosystems (IRET), Via Salaria km 29.300, Montelibretti, 00015, Rome, Italy
| | - Licia Colli
- Department of Animal Science Food and Nutrition, DIANA, Nutrigenomics and Proteomics Research Centre, PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre, BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Luca Ferretti
- Department of Biology and Biotechnology, University of Pavia, Italy, Pavia
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di sotto, 06123, Perugia, Italy
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Donata Marletta
- Department of Agriculture, Food and Environment, University of Catania, 95125, Catania, Italy
| | - Christian Persichilli
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Baldassare Portolano
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | - Francesca M Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Elena Ciani
- Department of Bioscience, Biotechnology and Biopharmaceuticals, University of Bari, 70124, Bari, Italy
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
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Ben-Jemaa S, Senczuk G, Ciani E, Ciampolini R, Catillo G, Boussaha M, Pilla F, Portolano B, Mastrangelo S. Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle. Front Genet 2021; 12:675569. [PMID: 33995500 PMCID: PMC8113768 DOI: 10.3389/fgene.2021.675569] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/07/2021] [Indexed: 12/31/2022] Open
Abstract
The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses revealed selection signatures distributed over 19 genomic regions. Of these, six relevant candidate regions were identified by at least two approaches. We found genomic signatures of selective sweeps spanning genes related to mitochondrial function, muscle development, growth, and meat traits (SCIN, THSD7A, ETV1, UCHL1, and MYOD1), which reflects the different breeding schemes between Maremmana (semi-wild conditions) and the other Podolian-derived Italian breeds (semi-extensive). We also identified several genes linked to Maremmana adaptation to the environment of the western-central part of Italy, known to be hyperendemic for malaria and other tick-borne diseases. These include several chemokine (C-C motif) ligand genes crucially involved in both innate and adaptive immune responses to intracellular parasite infections and other genes playing key roles in pulmonary disease (HEATR9, MMP28, and ASIC2) or strongly associated with malaria resistance/susceptibility (AP2B1). Our results provide a glimpse into diverse selection signatures in Maremmana cattle and can be used to enhance our understanding of the genomic basis of environmental adaptation in cattle.
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Affiliation(s)
- Slim Ben-Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, University of Carthage, Ariana, Tunisia
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro”, Bari, Italy
| | | | - Gennaro Catillo
- Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), Centro di Ricerca Zootecnia e Acquacoltura, Lodi, Italy
| | - Mekki Boussaha
- INRAE, AgroParisTech, University of Paris Saclay, Saint Aubin, France
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
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Biscarini F, Mastrangelo S, Catillo G, Senczuk G, Ciampolini R. Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data. Animals (Basel) 2020; 10:E2285. [PMID: 33287320 PMCID: PMC7761732 DOI: 10.3390/ani10122285] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches (FIS and FROH), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (HE=0.261, HO=0.274). Pedigree-based average inbreeding (F) was estimated at 4.9%. The correlation was low between F and genomic-based approaches (r=0.03 with FIS, r=0.21 with FROH), while it was higher between FIS and FROH (r=0.78). The low correlation between F and FROH coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like FROH may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals' pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity.
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Affiliation(s)
- Filippo Biscarini
- CNR-IBBA (National Research Council, Institute of Agricultural Biology and Biotechnology), 20133 Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy;
| | - Gennaro Catillo
- CREA Research Centre for Animal Production and Acquaculture, CREA, 00015 Monterotondo, Italy;
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy;
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie—Università di Pisa, 56124 Pisa, Italy;
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Dar AH, Kumar S, Mukesh M, Ahmad SF, Singh DV, Sharma RK, Ghosh AK, Singh B, Rahman JU, Sodhi M. Genetic characterization and population structure of different coat colour variants of Badri cattle. Mol Biol Rep 2020; 47:8485-8497. [PMID: 33063149 DOI: 10.1007/s11033-020-05890-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 10/03/2020] [Indexed: 11/25/2022]
Abstract
The present study aimed to genetically characterize the Badri cattle and its three colour variants and assess their population structure using 24 microsatellite markers. Out of 96 animals analyzed, 32 each were collected from grey (GVBC), brown (BrVBC) and black (BVBC) colour variants of Badri cattle (BC). The genetic diversity parameters including allele frequencies, observed and effective number of alleles, observed and expected heterozygosity, PIC, Shannon's indices and F-statistics were estimated using POPGENE software. Bottleneck analysis was performed using both qualitative and quantitative approaches. A total of 274 alleles (50 private and 224 shared) were scored for BC, GVBC, BrVBC and BVBC with mean number of 11.417, 9.083, 9.125 and 9.083 alleles, respectively. All populations exhibited average heterozygosity estimate > 0.5 indicating existence of substantial genetic variability, concurrent with revelations from Shannon's indices. Observed mean PIC estimates (> 0.74) were indicative of optimum informativeness of used microsatellite markers. The mean inbreeding estimates (F) in GVBC, BrVBC and BVBC were 0.041, - 0.024 and 0.016, respectively. The pair wise genetic (> 0.91) pointed towards similarity between different colour variant populations. STRUCTURE analysis also revealed clear admixture for the three Badri colour variants indicating absence of genetic differentiation. The present study revealed first-hand information that populations of Badri cattle with different phenotypes with respect to coat colour are genetically related and can be considered as a single breed. The comprehensive knowledge generated for Badri cattle will help in designing breeding plan for its genetic improvement and deciding the conservation priorities.
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Affiliation(s)
- Aashaq Hussain Dar
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Sanjay Kumar
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Manishi Mukesh
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, 132001, India
| | - Sheikh Firdous Ahmad
- ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Dev Vrat Singh
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Rabendra Kumar Sharma
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Ashis Kumar Ghosh
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Balwinder Singh
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Javid Ur Rahman
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Monika Sodhi
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, 132001, India.
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10
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Patel N, Bergamaschi M, Cagnin M, Bittante G. Exploration of the effect of farm, breed, sex and animal on detailed mineral profile of beef and their latent explanatory factors. Int J Food Sci Technol 2019. [DOI: 10.1111/ijfs.14455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Nageshvar Patel
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE) University of Padova viale dell’Università 16 35020 Legnaro Italy
| | - Matteo Bergamaschi
- Department of Animal Science North Carolina State University 27695 Raleigh NC USA
| | - Massimo Cagnin
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE) University of Padova viale dell’Università 16 35020 Legnaro Italy
| | - Giovanni Bittante
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE) University of Padova viale dell’Università 16 35020 Legnaro Italy
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11
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Patel N, Bergamaschi M, Magro L, Petrini A, Bittante G. Relationships of a Detailed Mineral Profile of Meat with Animal Performance and Beef Quality. Animals (Basel) 2019; 9:ani9121073. [PMID: 31816888 PMCID: PMC6940732 DOI: 10.3390/ani9121073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 11/18/2022] Open
Abstract
Simply Summary Minerals play direct or indirect role in different biological process of animals. These biological processes finally affect the meat quality. Therefore, analysis of minerals in cattle’s diet is important for assessing potential effects on beef quality. However, minerals profile and concentration in beef are affected by several factors such as animals rearing practices, age, environment, breed etc. Hence, we analyzed 20 minerals in 192 beef samples and studied the different sources of variation which affect the minerals profile in beef. In order to understand the complex and intriguing relations of beef qualities and minerals, we utilized correlation and factor analysis with 16 traits related to animal performance and beef quality. Our analysis shows many significant associations of minerals in beef with animal performance and beef qualities. Five groups of minerals (latent factors) were associated with almost all quality traits of beef. The knowledge about the mineral contents in beef is important to understand the complex interrelationships of animal rearing, farm management, environmental conditions with regard to animal performance and beef quality. Abstract The mineral profile of beef is a subject of human health interest, but also animal performance and meat quality. This study analyzes the relationships of 20 minerals in beef inductively coupled plasma-optical emission spectrometry (ICP-OES) with three animal performance and 13 beef quality traits analyzed on 182 samples of Longissimus thoracis. Animals’ breed and sex showed limited effects. The major sources of variation (farm/date of slaughter, individual animal within group and side/sample within animal) differed greatly from trait to trait. Mineral contents were correlated to animal performance and beef quality being significant 52 out of the 320 correlations at the farm/date level, and 101 out of the 320 at the individual animal level. Five latent factors explained 69% of mineral co-variation. The most important, “Mineral quantity” factor correlated with age at slaughter and with the beef color traits. Two latent factors (“Na + Fe + Cu” and “Fe + Mn”) correlated with performance and beef color traits. Two other (“K-B-Pb” and “Zn”) correlated with beef chemical composition and the latter also with carcass weight and daily gain, and beef color traits. Beef cooking losses correlated with “K-B-Pb”. Latent factor analysis appears be a useful means of disentangling the very complex relationships that the minerals in beef have with animal performance and beef quality traits.
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Affiliation(s)
- Nageshvar Patel
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell’Università 16, 35020 Legnaro (PD), Italy; (L.M.); (G.B.)
- Correspondence:
| | - Matteo Bergamaschi
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, USA;
| | - Luciano Magro
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell’Università 16, 35020 Legnaro (PD), Italy; (L.M.); (G.B.)
| | - Andrea Petrini
- Consorzio Tutela del Vitellone Bianco dell’Appennino Centrale, via delle Fascine 4, San Martino in Campo, 06132 Perugia, Italy;
| | - Giovanni Bittante
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, viale dell’Università 16, 35020 Legnaro (PD), Italy; (L.M.); (G.B.)
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12
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Identification of genomic regions harboring diversity between Holstein and two local endangered breeds, Modenese and Maremmana. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Di Lorenzo P, Lancioni H, Ceccobelli S, Colli L, Cardinali I, Karsli T, Capodiferro MR, Sahin E, Ferretti L, Ajmone Marsan P, Sarti FM, Lasagna E, Panella F, Achilli A. Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin. PLoS One 2018; 13:e0192567. [PMID: 29462170 PMCID: PMC5819780 DOI: 10.1371/journal.pone.0192567] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/25/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Over the past 15 years, 300 out of 6000 breeds of all farm animal species identified by the Food and Agriculture Organization of the United Nations (FAO) have gone extinct. Among cattle, many Podolian breeds are seriously endangered in various European areas. Podolian cattle include a group of very ancient European breeds, phenotypically close to the aurochs ancestors (Bos primigenius). The aim of the present study was to assess the genetic diversity of Podolian breeds and to reconstruct their origin. METHODOLOGY The mitochondrial DNA (mtDNA) control-regions of 18 Podolian breeds have been phylogenetically assessed. Nine non-Podolian breeds have been also included for comparison. CONCLUSION The overall analysis clearly highlights some peculiarities in the mtDNA gene pool of some Podolian breeds. In particular, a principal component analysis point to a genetic proximity between five breeds (Chianina, Marchigiana, Maremmana, Podolica Italiana and Romagnola) reared in Central Italy and the Turkish Grey. We here propose the suggestive hypothesis of a dual ancestral contribution to the present gene pool of Podolian breeds, one deriving from Eastern European cattle; the other arising from the arrival of Middle Eastern cattle into Central Italy through a different route, perhaps by sea, ferried by Etruscan boats. The historical migration of Podolian cattle from North Eastern Europe towards Italy has not cancelled the mtDNA footprints of this previous ancient migration.
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Affiliation(s)
- Piera Di Lorenzo
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
- * E-mail: (HL); (AA)
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Licia Colli
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy
- Biodiversity and Ancient DNA Research Center–BioDNA, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, University of Akdeniz, Antalya, Turkey
| | | | - Emine Sahin
- Korkuteli Vocational School, University of Akdeniz, Antalya, Turkey
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
| | - Paolo Ajmone Marsan
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy
- Biodiversity and Ancient DNA Research Center–BioDNA, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Francesca Maria Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Francesco Panella
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
- * E-mail: (HL); (AA)
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14
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Zhao J, Li T, Zhu C, Jiang X, Zhao Y, Xu Z, Yang S, Chen A. Selection and use of microsatellite markers for individual identification and meat traceability of six swine breeds in the Chinese market. FOOD SCI TECHNOL INT 2017; 24:292-300. [PMID: 29277102 DOI: 10.1177/1082013217748457] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Meat traceability based on molecular markers is exerting a great influence on food safety and will enhance its key role in the future. This study aimed to investigate and verify the polymorphism of 23 microsatellite markers and select the most suitable markers for individual identification and meat traceability of six swine breeds in the Chinese market. The mean polymorphism information content value of these 23 loci was 0.7851, and each locus exhibited high polymorphism in the pooled population. There were 10 loci showing good polymorphism in each breed, namely, Sw632, S0155, Sw2406, Sw830, Sw2525, Sw72, Sw2448, Sw911, Sw122 and CGA. When six highly polymorphic loci were combined, the match probability value for two random individual genotypes among the pig breeds (Beijing Black, Sanyuan and Taihu) was lower than 1.151 E-06. An increasing number of loci indicated a gradually decreasing match probability value and therefore enhanced traceability accuracy. The validation results of tracing 18 blood and corresponding meat samples based on five highly polymorphic loci (Sw2525, S0005, Sw0107, Sw911 and Sw857) were successful, with 100% conformation probability, which provided a foundation for establishing a traceability system for pork in the Chinese market.
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Affiliation(s)
- Jie Zhao
- 1 Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,2 Key Laboratory of Agro-product Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Tingting Li
- 1 Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,2 Key Laboratory of Agro-product Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Chao Zhu
- 1 Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,2 Key Laboratory of Agro-product Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Xiaoling Jiang
- 1 Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,2 Key Laboratory of Agro-product Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Yan Zhao
- 1 Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,2 Key Laboratory of Agro-product Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Zhenzhen Xu
- 1 Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,2 Key Laboratory of Agro-product Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Shuming Yang
- 1 Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,2 Key Laboratory of Agro-product Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Ailiang Chen
- 1 Institute of Quality Standard & Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.,2 Key Laboratory of Agro-product Quality and Safety, Ministry of Agriculture, Beijing, China
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15
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Maretto F, Cassandro M. Temporal Variation in Genetic Diversity and Population Structure of Burlina Cattle Breed. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2014.3091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Agung PP, Saputra F, Septian WA, Lusiana, Zein MSA, Sulandari S, Anwar S, Wulandari AS, Said S, Tappa B. Study of Genetic Diversity among Simmental Cross Cattle in West Sumatra Based on Microsatellite Markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:176-83. [PMID: 26732442 PMCID: PMC4698697 DOI: 10.5713/ajas.15.0155] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/11/2015] [Accepted: 07/17/2015] [Indexed: 11/27/2022]
Abstract
A study was conducted to assess the genetic diversity among Simmental Cross cattle in West Sumatra using microsatellite DNA markers. A total of 176 individual cattle blood samples was used for obtaining DNA samples. Twelve primers of microsatellite loci as recommended by FAO were used to identify the genetic diversity of the Simmental Cross cattle population. Multiplex DNA fragment analysis method was used for allele identification. All the microsatellite loci in this study were highly polymorphic and all of the identified alleles were able to classify the cattle population into several groups based on their genetic distance. The heterozygosity values of microsatellite loci in this study ranged from 0.556 to 0.782. The polymorphism information content (PIC) value of the 12 observed loci is high (PIC>0.5). The highest PIC value in the Simmental cattle population was 0.893 (locus TGLA53), while the lowest value was 0.529 (locus BM1818). Based on the genetic distance value, the subpopulation of the Simmental Cross-Agam and the Simmental Cross-Limapuluh Kota was exceptionally close to the Simmental Purebred thus indicating that a grading-up process has taken place with the Simmental Purebred. In view of the advantages possessed by the Simmental Cross cattle and the evaluation of the genetic diversity results, a number of subpopulations in this study can be considered as the initial (base) population for the Simmental Cross cattle breeding programs in West Sumatra, Indonesia.
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Affiliation(s)
- Paskah Partogi Agung
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Ferdy Saputra
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Wike Andre Septian
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Lusiana
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Moch Syamsul Arifin Zein
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Sri Sulandari
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Saiful Anwar
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Ari Sulistyo Wulandari
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Syahruddin Said
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
| | - Baharuddin Tappa
- Research Center for Biology-Indonesian Institute of Sciences, Cibinong 16911, West Java, Indonesia
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17
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Mastrangelo S, Saura M, Tolone M, Salces-Ortiz J, Di Gerlando R, Bertolini F, Fontanesi L, Sardina MT, Serrano M, Portolano B. The genome-wide structure of two economically important indigenous Sicilian cattle breeds. J Anim Sci 2014; 92:4833-42. [PMID: 25253807 DOI: 10.2527/jas.2014-7898] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genomic technologies, such as high-throughput genotyping based on SNP arrays, provided background information concerning genome structure in domestic animals. The aim of this work was to investigate the genetic structure, the genome-wide estimates of inbreeding, coancestry, effective population size (Ne), and the patterns of linkage disequilibrium (LD) in 2 economically important Sicilian local cattle breeds, Cinisara (CIN) and Modicana (MOD), using the Illumina Bovine SNP50K v2 BeadChip. To understand the genetic relationship and to place both Sicilian breeds in a global context, genotypes from 134 other domesticated bovid breeds were used. Principal component analysis showed that the Sicilian cattle breeds were closer to individuals of Bos taurus taurus from Eurasia and formed nonoverlapping clusters with other breeds. Between the Sicilian cattle breeds, MOD was the most differentiated, whereas the animals belonging to the CIN breed showed a lower value of assignment, the presence of substructure, and genetic links with the MOD breed. The average molecular inbreeding and coancestry coefficients were moderately high, and the current estimates of Ne were low in both breeds. These values indicated a low genetic variability. Considering levels of LD between adjacent markers, the average r(2) in the MOD breed was comparable to those reported for others cattle breeds, whereas CIN showed a lower value. Therefore, these results support the need of more dense SNP arrays for a high-power association mapping and genomic selection efficiency, particularly for the CIN cattle breed. Controlling molecular inbreeding and coancestry would restrict inbreeding depression, the probability of losing beneficial rare alleles, and therefore the risk of extinction. The results generated from this study have important implications for the development of conservation and/or selection breeding programs in these 2 local cattle breeds.
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Affiliation(s)
- S Mastrangelo
- Dipartimento di Scienze Agrarie e Forestali, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - M Saura
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña Km 7.5, 28040 Madrid, Spain
| | - M Tolone
- Dipartimento di Scienze Agrarie e Forestali, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - J Salces-Ortiz
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña Km 7.5, 28040 Madrid, Spain
| | - R Di Gerlando
- Dipartimento di Scienze Agrarie e Forestali, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - F Bertolini
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - L Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - M T Sardina
- Dipartimento di Scienze Agrarie e Forestali, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - M Serrano
- Departamento de Mejora Genética Animal, INIA, Carretera de la Coruña Km 7.5, 28040 Madrid, Spain
| | - B Portolano
- Dipartimento di Scienze Agrarie e Forestali, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
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Sbarra F, Mantovani R, Quaglia A, Bittante G. Genetics of slaughter precocity, carcass weight, and carcass weight gain in Chianina, Marchigiana, and Romagnola young bulls under protected geographical indication1. J Anim Sci 2013; 91:2596-604. [DOI: 10.2527/jas.2013-6235] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- F. Sbarra
- National Breeders Association of Italian Beef Breeds, Via Visciolosa 06132 S. Martino in Colle, Italy
| | - R. Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of Padova, Agripolis 35020 Legnaro, Italy
| | - A. Quaglia
- National Breeders Association of Italian Beef Breeds, Via Visciolosa 06132 S. Martino in Colle, Italy
| | - G. Bittante
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of Padova, Agripolis 35020 Legnaro, Italy
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