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Braz CU, Passamonti MM, Khatib H. Characterization of genomic regions escaping epigenetic reprogramming in sheep. Environ Epigenet 2023; 10:dvad010. [PMID: 38496251 PMCID: PMC10944287 DOI: 10.1093/eep/dvad010] [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] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 03/19/2024]
Abstract
The mammalian genome undergoes two global epigenetic reprogramming events during the establishment of primordial germ cells and in the pre-implantation embryo after fertilization. These events involve the erasure and re-establishment of DNA methylation marks. However, imprinted genes and transposable elements (TEs) maintain their DNA methylation signatures to ensure normal embryonic development and genome stability. Despite extensive research in mice and humans, there is limited knowledge regarding environmentally induced epigenetic marks that escape epigenetic reprogramming in other species. Therefore, the objective of this study was to examine the characteristics and locations of genomic regions that evade epigenetic reprogramming in sheep, as well as to explore the biological functions of the genes within these regions. In a previous study, we identified 107 transgenerationally inherited differentially methylated cytosines (DMCs) in the F1 and F2 generations in response to a paternal methionine-supplemented diet. These DMCs were found in TEs, non-repetitive regions, and imprinted and non-imprinted genes. Our findings suggest that genomic regions, rather than TEs and imprinted genes, have the propensity to escape reprogramming and serve as potential candidates for transgenerational epigenetic inheritance. Notably, 34 transgenerational methylated genes influenced by paternal nutrition escaped reprogramming, impacting growth, development, male fertility, cardiac disorders, and neurodevelopment. Intriguingly, among these genes, 21 have been associated with neural development and brain disorders, such as autism, schizophrenia, bipolar disease, and intellectual disability. This suggests a potential genetic overlap between brain and infertility disorders. Overall, our study supports the concept of transgenerational epigenetic inheritance of environmentally induced marks in mammals.
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Affiliation(s)
- Camila U Braz
- Department of Animal Sciences, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition, Universit’a Cattolica del Sacro Cuore, Piacenza, 29122, Italy
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI 53706, USA
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Ramirez-Diaz J, Cenadelli S, Bornaghi V, Bongioni G, Montedoro SM, Achilli A, Capelli C, Rincon JC, Milanesi M, Passamonti MM, Colli L, Barbato M, Williams JL, Marsan PA. Identification of genomic regions associated with total and progressive sperm motility in Italian Holstein bulls. J Dairy Sci 2023; 106:407-420. [PMID: 36400619 DOI: 10.3168/jds.2021-21700] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 12/13/2021] [Accepted: 08/10/2022] [Indexed: 11/17/2022]
Abstract
Sperm motility is directly related to the ability of sperm to move through the female reproductive tract to reach the ovum. Sperm motility is a complex trait that is influenced by environmental and genetic factors and is associated with male fertility, oocyte penetration rate, and reproductive success of cattle. In this study we carried out a GWAS in Italian Holstein bulls to identify candidate regions and genes associated with variations in progressive and total motility (PM and TM, respectively). After quality control, the final data set consisted of 5,960 records from 949 bulls having semen collected in 10 artificial insemination stations and genotyped at 412,737 SNPs (call rate >95%; minor allele frequency >5%). (Co)variance components were estimated using single trait mixed models, and associations between SNPs and phenotypes were assessed using a genomic BLUP approach. Ten windows that explained the greatest percentage of genetic variance were located on Bos taurus autosomes 1, 2, 4, 6, 7, 23, and 26 for TM and Bos taurus autosomes 1, 2, 4, 6, 8, 16, 23, and 26 for PM. A total of 150 genes for TM and 72 genes for PM were identified within these genomic regions. Gene Ontology enrichment analyses identified significant Gene Ontology terms involved with energy homeostasis, membrane functions, sperm-egg interactions, protection against oxidative stress, olfactory receptors, and immune system. There was significant enrichment of quantitative trait loci for fertility, calving ease, immune response, feed intake, and carcass weight within the candidate windows. These results contribute to understanding the architecture of the genetic control of sperm motility and may aid in the development of strategies to identify subfertile bulls and improve reproductive success.
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Affiliation(s)
- J Ramirez-Diaz
- Department of Animal Sciences, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy 29122; Institute of Agricultural Biology and Biotechnology (IBBA), Consiglio Nazionale di Ricerca, Milano, Italy.
| | - S Cenadelli
- Institute Lazzaro Spallanzani, Rivolta d'Adda (CR), Cremona, Italy
| | - V Bornaghi
- Institute Lazzaro Spallanzani, Rivolta d'Adda (CR), Cremona, Italy
| | - G Bongioni
- Institute Lazzaro Spallanzani, Rivolta d'Adda (CR), Cremona, Italy
| | - S M Montedoro
- Institute Lazzaro Spallanzani, Rivolta d'Adda (CR), Cremona, Italy
| | - A Achilli
- Department of Biology and Biotechnology, Università degli Studi di Pavia, Pavia, Italy
| | - C Capelli
- Department of Chemical, Life and Environmental Sustainability Sciences, Università degli Studi di Parma, Parma, Italy
| | - J C Rincon
- Department of Animal Science, Universidad Nacional de Colombia, Palmira, Valle del Cauca, Colombia
| | - M Milanesi
- Department for Innovation in Biological, Agri-food and Forestry Systems (DIBAF), Università degli Studi della Tuscia, Viterbo, Italy
| | - M M Passamonti
- Department of Animal Sciences, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy 29122
| | - L Colli
- Department of Animal Sciences, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy 29122
| | - M Barbato
- Department of Animal Sciences, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy 29122
| | - J L Williams
- Department of Animal Sciences, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy 29122
| | - P Ajmone Marsan
- Department of Animal Sciences, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy 29122
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Passamonti MM, Somenzi E, Barbato M, Chillemi G, Colli L, Joost S, Milanesi M, Negrini R, Santini M, Vajana E, Williams JL, Ajmone-Marsan P. The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock. Animals (Basel) 2021; 11:2833. [PMID: 34679854 PMCID: PMC8532622 DOI: 10.3390/ani11102833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/14/2022] Open
Abstract
Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.
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Affiliation(s)
- Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Elisa Somenzi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Mario Barbato
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Licia Colli
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Research Center on Biodiversity and Ancient DNA—BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - Marco Milanesi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Riccardo Negrini
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Monia Santini
- Impacts on Agriculture, Forests and Ecosystem Services (IAFES) Division, Fondazione Centro Euro-Mediterraneo Sui Cambiamenti Climatici (CMCC), Viale Trieste 127, 01100 Viterbo, Italy;
| | - Elia Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - John Lewis Williams
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Nutrigenomics and Proteomics Research Center—PRONUTRIGEN, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
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Milanesi M, Passamonti MM, Cappelli K, Minuti A, Palombo V, Sgorlon S, Capomaccio S, D’Andrea M, Trevisi E, Stefanon B, Williams JL, Ajmone-Marsan P. Genetic Regulation of Biomarkers as Stress Proxies in Dairy Cows. Genes (Basel) 2021; 12:genes12040534. [PMID: 33917627 PMCID: PMC8067459 DOI: 10.3390/genes12040534] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 01/02/2023] Open
Abstract
Stress in livestock reduces productivity and is a welfare concern. At a physiological level, stress is associated with the activation of inflammatory responses and increased levels of harmful reactive oxygen species. Biomarkers that are indicative of stress could facilitate the identification of more stress-resilient animals. We examined twenty-one metabolic, immune response, and liver function biomarkers that have been associated with stress in 416 Italian Simmental and 436 Italian Holstein cows which were genotyped for 150K SNPs. Single-SNP and haplotype-based genome-wide association studies were carried out to assess whether the variation in the levels in these biomarkers is under genetic control and to identify the genomic loci involved. Significant associations were found for the plasma levels of ceruloplasmin (Bos taurus chromosome 1-BTA1), paraoxonase (BTA4) and γ-glutamyl transferase (BTA17) in the individual breed analysis that coincided with the position of the genes coding for these proteins, suggesting that their expression is under cis-regulation. A meta-analysis of both breeds identified additional significant associations with paraoxonase on BTA 16 and 26. Finding genetic associations with variations in the levels of these biomarkers suggests that the selection for high or low levels of expression could be achieved rapidly. Whether the level of expression of the biomarkers correlates with the response to stressful situations has yet to be determined.
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Affiliation(s)
- Marco Milanesi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.M.); (M.M.P.); (A.M.); (E.T.); (J.L.W.)
- Department for Innovation in Biological, Agro-Food and Forest Systems—DIBAF, Università della Tuscia, 01100 Viterbo, Italy
| | - Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.M.); (M.M.P.); (A.M.); (E.T.); (J.L.W.)
| | - Katia Cappelli
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, 06126 Perugia, Italy; (K.C.); (S.C.)
| | - Andrea Minuti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.M.); (M.M.P.); (A.M.); (E.T.); (J.L.W.)
| | - Valentino Palombo
- Dipartimento Agricoltura Ambiente e Alimenti, Università del Molise, 86100 Campobasso, Italy; (V.P.); (M.D.)
| | - Sandy Sgorlon
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali. Università degli Studi di Udine, 33100 Udine, Italy; (S.S.); (B.S.)
| | - Stefano Capomaccio
- Dipartimento di Medicina Veterinaria, Università degli Studi di Perugia, 06126 Perugia, Italy; (K.C.); (S.C.)
| | - Mariasilvia D’Andrea
- Dipartimento Agricoltura Ambiente e Alimenti, Università del Molise, 86100 Campobasso, Italy; (V.P.); (M.D.)
| | - Erminio Trevisi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.M.); (M.M.P.); (A.M.); (E.T.); (J.L.W.)
| | - Bruno Stefanon
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali. Università degli Studi di Udine, 33100 Udine, Italy; (S.S.); (B.S.)
| | - John Lewis Williams
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.M.); (M.M.P.); (A.M.); (E.T.); (J.L.W.)
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5371, Australia
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (M.M.); (M.M.P.); (A.M.); (E.T.); (J.L.W.)
- Nutrigenomics and Proteomics Research Center-PRONUTRIGEN, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
- Correspondence:
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