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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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Ceccobelli S, Perini F, Trombetta MF, Tavoletti S, Lasagna E, Pasquini M. Effect of Myostatin Gene Mutation on Slaughtering Performance and Meat Quality in Marchigiana Bulls. Animals (Basel) 2022; 12:ani12040518. [PMID: 35203227 PMCID: PMC8868461 DOI: 10.3390/ani12040518] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/10/2022] [Accepted: 02/17/2022] [Indexed: 02/07/2023] Open
Abstract
Simple Summary The aim of this work was the evaluation of slaughtering performance in a sample of 78 Marchigiana bulls with different allelic situation at the myostatin locus; in addition, the qualitative composition of meat samples collected from Longissimus thoracis muscle was evaluated. At the myostatin gene, 67 homozygotes normal, 11 heterozygotes, and no double-muscled homozygote bulls were detected. Heterozygote bulls showed high values in final live weight and dressing yield; moreover, they were characterized by a low incidence of fat at steak dissection, as well as in meat chemical composition. A better muscular conformation in heterozygote bulls’ carcasses was highlighted, with a higher incidence of their carcasses in class E and evident convexity of round, back, and shoulder muscular masses compared to the carcasses of Marchigiana bulls which were normal at the myostatin gene. Abstract The myostatin gene also called Growth Differentiation Factor 8 gene (GDF8) is one of the most investigated loci that can be responsible for several quantitative and qualitative carcass and meat traits in double-muscled beef cattle. The objective of the study was to bring to light the effect of the myostatin polymorphism on slaughtering performance and meat quality in Marchigiana beef cattle. The experiment was carried out on 78 bulls reared according to the “cow-calf” extensive managing system. At the end of the fattening period, in vivo and carcass data were recorded. From each carcass, a steak of Longissimus thoracis was taken and used to determine the meat’s analytical composition and colorimetric properties. Finally, from each steak a sample of Longissimus thoracis was collected, then used for DNA extraction and genotyping at the myostatin locus. The heterozygous bulls showed slight superiority in the carcass data (e.g., hot carcass weight: 426.09 kg—heterozygotes vs. 405.32 kg—normal) and meat quality parameters, although not always with statistical significance. Only fat and ashes content were significantly affected by the myostatin genotype (heterozygotes: 2.01%, 1.26%; normal: 3.04%, 1.15%). The greater muscularity of heterozygous animals compared to normal ones could be a starting point to improving productive efficiency in Marchigiana beef cattle.
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Affiliation(s)
- Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (M.F.T.); (S.T.); (M.P.)
- Correspondence:
| | - Francesco Perini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, 06121 Perugia, Italy; (F.P.); (E.L.)
| | - Maria Federica Trombetta
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (M.F.T.); (S.T.); (M.P.)
| | - Stefano Tavoletti
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (M.F.T.); (S.T.); (M.P.)
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, 06121 Perugia, Italy; (F.P.); (E.L.)
| | - Marina Pasquini
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (M.F.T.); (S.T.); (M.P.)
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Rovelli G, Luigi-Sierra MG, Guan D, Sbarra F, Quaglia A, Sarti FM, Amills M, Lasagna E. Evolution of inbreeding: a gaze into five Italian beef cattle breeds history. PeerJ 2021; 9:e12049. [PMID: 34692245 PMCID: PMC8483007 DOI: 10.7717/peerj.12049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/03/2021] [Indexed: 01/25/2023] Open
Abstract
In the last decades, intensive selection programs have led to sustained increases of inbreeding in dairy cattle, a feature that might have adverse consequences on the viability and phenotypic performance of their offspring. This study aimed to determine the evolution of inbreeding of five Italian beef cattle breeds (Marchigiana, Chianina, Romagnola, Maremmana, and Podolica) during a period of almost 20 years (2002–2019). The estimates of Ho, He, Fhat2, and Fped averaged across years (2002–2019) in the studied breeds fluctuated between 0.340–0.401, 0.348–0.392, –0.121–0.072, and 0.000–0.068, respectively. Moreover, annual rates of increase of the estimated inbreeding coefficients have been very low (Fhat2 = 0.01–0.02%; Fped = 0.003–0.004%). The use of a high number of bulls combined with strategies implemented by the Association of Italian Beef Cattle Breeders ANABIC to minimize inbreeding might explain these results. Despite the fact that diversity and inbreeding have remained quite stable during the last two decades, we have detected a sustained decrease of the population effective size of these five breeds. Such results should be interpreted with caution due to the inherent difficulty of estimating Ne from SNPs data in a reliable manner.
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Affiliation(s)
- Giacomo Rovelli
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Perugia, Italy.,Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autónoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Maria Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autónoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autónoma de Barcelona, Bellaterra, Barcelona, Spain.,Department of Animal Science, University of California, Davis, Davis, CA, United States of America
| | - Fiorella Sbarra
- National Association of Italian Beef-Cattle Breeders (ANABIC), San Martino in Colle, Perugia, Italy
| | - Andrea Quaglia
- National Association of Italian Beef-Cattle Breeders (ANABIC), San Martino in Colle, Perugia, Italy
| | - Francesca Maria Sarti
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Perugia, Italy
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autónoma de Barcelona, Bellaterra, Barcelona, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autónoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences (DSA3), University of Perugia, Perugia, Italy
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Zalewska M, Puppel K, Sakowski T. Associations between gene polymorphisms and selected meat traits in cattle - A review. Anim Biosci 2021; 34:1425-1438. [PMID: 33561332 PMCID: PMC8495340 DOI: 10.5713/ab.20.0672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
Maintaining a high level of beef consumption requires paying attention not only to quantitative traits but also to the quality and dietary properties of meat. Growing consumer demands do not leave producers many options for how animals are selected for breeding and animal keeping. Meat and carcass fatness quality traits, which are influenced by multiple genes, are economically important in beef cattle breeding programs. The recent availability of genome sequencing methods and many previously identified molecular markers offer new opportunities for animal breeding, including the use of molecular information in selection programs. Many gene polymorphisms have thus far been analyzed and evaluated as potential candidates for molecular markers of meat quality traits. Knowledge of these markers can be further applied to breeding programs through marker-assisted selection. In this literature review, we discuss the most promising and well-described candidates and their associations with selected beef production traits.
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Affiliation(s)
- Magdalena Zalewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland
| | - Kamila Puppel
- Institute of Animal Science, Warsaw University of Life Sciences, Warsaw 02-786, Poland
| | - Tomasz Sakowski
- Department of Biotechnology and Nutrigenomics, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences (PAS), Magdalenka 05-552, Poland
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Ramzan F, Gültas M, Bertram H, Cavero D, Schmitt AO. Combining Random Forests and a Signal Detection Method Leads to the Robust Detection of Genotype-Phenotype Associations. Genes (Basel) 2020; 11:E892. [PMID: 32764260 PMCID: PMC7465705 DOI: 10.3390/genes11080892] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022] Open
Abstract
Genome wide association studies (GWAS) are a well established methodology to identify genomic variants and genes that are responsible for traits of interest in all branches of the life sciences. Despite the long time this methodology has had to mature the reliable detection of genotype-phenotype associations is still a challenge for many quantitative traits mainly because of the large number of genomic loci with weak individual effects on the trait under investigation. Thus, it can be hypothesized that many genomic variants that have a small, however real, effect remain unnoticed in many GWAS approaches. Here, we propose a two-step procedure to address this problem. In a first step, cubic splines are fitted to the test statistic values and genomic regions with spline-peaks that are higher than expected by chance are considered as quantitative trait loci (QTL). Then the SNPs in these QTLs are prioritized with respect to the strength of their association with the phenotype using a Random Forests approach. As a case study, we apply our procedure to real data sets and find trustworthy numbers of, partially novel, genomic variants and genes involved in various egg quality traits.
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Affiliation(s)
- Faisal Ramzan
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.R.); (M.G.); (H.B.)
- Department of Animal Breeding and Genetics, University of Agriculture Faisalabad, 38000 Faisalabad, Pakistan
| | - Mehmet Gültas
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.R.); (M.G.); (H.B.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Hendrik Bertram
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.R.); (M.G.); (H.B.)
| | | | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.R.); (M.G.); (H.B.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
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