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Wang X, Li W, Feng X, Li J, Liu GE, Fang L, Yu Y. Harnessing male germline epigenomics for the genetic improvement in cattle. J Anim Sci Biotechnol 2023; 14:76. [PMID: 37277852 PMCID: PMC10242889 DOI: 10.1186/s40104-023-00874-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/02/2023] [Indexed: 06/07/2023] Open
Abstract
Sperm is essential for successful artificial insemination in dairy cattle, and its quality can be influenced by both epigenetic modification and epigenetic inheritance. The bovine germline differentiation is characterized by epigenetic reprogramming, while intergenerational and transgenerational epigenetic inheritance can influence the offspring's development through the transmission of epigenetic features to the offspring via the germline. Therefore, the selection of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers. We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.
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Affiliation(s)
- Xiao Wang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Konge Larsen ApS, Kongens Lyngby, 2800, Denmark
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Wenlong Li
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xia Feng
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianbing Li
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, USDA, Beltsville, MD, 20705, USA
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Ying Yu
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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2
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Capra E, Turri F, Lazzari B, Biffani S, Lange Consiglio A, Ajmone Marsan P, Stella A, Pizzi F. CpG DNA methylation changes during epididymal sperm maturation in bulls. Epigenetics Chromatin 2023; 16:20. [PMID: 37254160 DOI: 10.1186/s13072-023-00495-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/19/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND During epididymal transit spermatozoa acquire specific morphological features which enhance their ability to swim in a progressive manner and interact with the oocytes. At the same time, sperm cells undergo specific molecular rearrangements essential for the fertilizing sperm to drive a correct embryo development. To assess epigenetic sperm changes during epididymal maturation, the caput, corpus and cauda epididymis sperm tracts were isolated from eight bulls and characterized for different sperm quality parameters and for CpG DNA methylation using Reduced Representation Bisulfite Sequencing (RRBS) able to identify differentially methylated regions (DMRs) in higher CpG density regions. RESULTS Caput sperm showed significant variation in motility and sperm kinetics variables, whereas spermatozoa collected from the corpus presented morphology variation and significant alterations in variables related to acrosome integrity. A total of 57,583 methylated regions were identified across the eight bulls, showing a significantly diverse distribution for sperm collected in the three epididymal regions. Differential methylation was observed between caput vs corpus (n = 11,434), corpus vs cauda (n = 12,372) and caput vs cauda (n = 2790). During epididymal transit a high proportion of the epigenome was remodeled, showing several regions in which methylation decreases from caput to corpus and increases from corpus to cauda. CONCLUSIONS Specific CpG DNA methylation changes in sperm isolated from the caput, corpus, and cauda epididymis tracts are likely to refine the sperm epigenome during sperm maturation, potentially impacting sperm fertilization ability and spatial organization of the genome during early embryo development.
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Affiliation(s)
- Emanuele Capra
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 26900, Lodi, Italy.
| | - F Turri
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 26900, Lodi, Italy
| | - B Lazzari
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 26900, Lodi, Italy
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 20133, Milano, Italy
| | - S Biffani
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 20133, Milano, Italy
| | - A Lange Consiglio
- Department of Veterinary Medicine and Animal Sciences (DIVAS), Università degli Studi di Milano, 26900, Lodi, Italy
| | - P Ajmone Marsan
- Department of Animal Science, Food and Technology-DIANA, and Romeo and Enrica Invernizzi Research Center on Sustainable Dairy Production-CREI, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
| | - A Stella
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 20133, Milano, Italy
| | - F Pizzi
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, 26900, Lodi, Italy
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3
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Costes V, Chaulot-Talmon A, Sellem E, Perrier JP, Aubert-Frambourg A, Jouneau L, Pontlevoy C, Hozé C, Fritz S, Boussaha M, Le Danvic C, Sanchez MP, Boichard D, Schibler L, Jammes H, Jaffrézic F, Kiefer H. Predicting male fertility from the sperm methylome: application to 120 bulls with hundreds of artificial insemination records. Clin Epigenetics 2022; 14:54. [PMID: 35477426 PMCID: PMC9047354 DOI: 10.1186/s13148-022-01275-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/08/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Conflicting results regarding alterations to sperm DNA methylation in cases of spermatogenesis defects, male infertility and poor developmental outcomes have been reported in humans. Bulls used for artificial insemination represent a relevant model in this field, as the broad dissemination of bull semen considerably alleviates confounding factors and enables the precise assessment of male fertility. This study was therefore designed to assess the potential for sperm DNA methylation to predict bull fertility. RESULTS A unique collection of 100 sperm samples was constituted by pooling 2-5 ejaculates per bull from 100 Montbéliarde bulls of comparable ages, assessed as fertile (n = 57) or subfertile (n = 43) based on non-return rates 56 days after insemination. The DNA methylation profiles of these samples were obtained using reduced representation bisulfite sequencing. After excluding putative sequence polymorphisms, 490 fertility-related differentially methylated cytosines (DMCs) were identified, most of which were hypermethylated in subfertile bulls. Interestingly, 46 genes targeted by DMCs are involved in embryonic and fetal development, sperm function and maturation, or have been related to fertility in genome-wide association studies; five of these were further analyzed by pyrosequencing. In order to evaluate the prognostic value of fertility-related DMCs, the sperm samples were split between training (n = 67) and testing (n = 33) sets. Using a Random Forest approach, a predictive model was built from the methylation values obtained on the training set. The predictive accuracy of this model was 72% on the testing set and 72% on individual ejaculates collected from an independent cohort of 20 bulls. CONCLUSION This study, conducted on the largest set of bull sperm samples so far examined in epigenetic analyses, demonstrated that the sperm methylome is a valuable source of male fertility biomarkers. The next challenge is to combine these results with other data on the same sperm samples in order to improve the quality of the model and better understand the interplay between DNA methylation and other molecular features in the regulation of fertility. This research may have potential applications in human medicine, where infertility affects the interaction between a male and a female, thus making it difficult to isolate the male factor.
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Affiliation(s)
- Valentin Costes
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France.,R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France.,Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | - Aurélie Chaulot-Talmon
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Eli Sellem
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France.,R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France
| | - Jean-Philippe Perrier
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Anne Aubert-Frambourg
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Luc Jouneau
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Charline Pontlevoy
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Chris Hozé
- R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France.,Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | - Sébastien Fritz
- R&D Department, ALLICE, 149 rue de Bercy, 75012, Paris, France.,Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | - Mekki Boussaha
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | | | - Marie-Pierre Sanchez
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | - Didier Boichard
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | | | - Hélène Jammes
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Florence Jaffrézic
- Université Paris-Saclay, AgroParisTech, INRAE, GABI, 78350, Jouy-en-Josas, France
| | - Hélène Kiefer
- INRAE, BREED, Université Paris-Saclay, UVSQ, 78350, Jouy-en-Josas, France. .,Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France.
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Özbek M, Hitit M, Kaya A, Jousan FD, Memili E. Sperm Functional Genome Associated With Bull Fertility. Front Vet Sci 2021; 8:610888. [PMID: 34250055 PMCID: PMC8262648 DOI: 10.3389/fvets.2021.610888] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 05/05/2021] [Indexed: 01/08/2023] Open
Abstract
Bull fertility is an important economic trait in sustainable cattle production, as infertile or subfertile bulls give rise to large economic losses. Current methods to assess bull fertility are tedious and not totally accurate. The massive collection of functional data analyses, including genomics, proteomics, metabolomics, transcriptomics, and epigenomics, helps researchers generate extensive knowledge to better understand the unraveling physiological mechanisms underlying subpar male fertility. This review focuses on the sperm phenomes of the functional genome and epigenome that are associated with bull fertility. Findings from multiple sources were integrated to generate new knowledge that is transferable to applied andrology. Diverse methods encompassing analyses of molecular and cellular dynamics in the fertility-associated molecules and conventional sperm parameters can be considered an effective approach to determine bull fertility for efficient and sustainable cattle production. In addition to gene expression information, we also provide methodological information, which is important for the rigor and reliability of the studies. Fertility is a complex trait influenced by several factors and has low heritability, although heritability of scrotal circumference is high and that it is a known fertility maker. There is a need for new knowledge on the expression levels and functions of sperm RNA, proteins, and metabolites. The new knowledge can shed light on additional fertility markers that can be used in combination with scrotal circumference to predict the fertility of breeding bulls. This review provides a comprehensive review of sperm functional characteristics or phenotypes associated with bull fertility.
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Affiliation(s)
- Memmet Özbek
- Department of Histology and Embryology, Faculty of Veterinary Medicine, Burdur Mehmet Akif Ersoy University, Burdur, Turkey
| | - Mustafa Hitit
- Department of Genetics, Faculty of Veterinary Medicine, Kastamonu University, Kastamonu, Turkey
| | - Abdullah Kaya
- Department of Artificial Insemination and Reproduction, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | - Frank Dean Jousan
- Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS, United States
| | - Erdogan Memili
- Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS, United States
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Takeda K, Kobayashi E, Ogata K, Imai A, Sato S, Adachi H, Hoshino Y, Nishino K, Inoue M, Kaneda M, Watanabe S. Differentially methylated CpG sites related to fertility in Japanese Black bull spermatozoa: epigenetic biomarker candidates to predict sire conception rate. J Reprod Dev 2021; 67:99-107. [PMID: 33441501 PMCID: PMC8075730 DOI: 10.1262/jrd.2020-137] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For semen suppliers, predicting the low fertility of service bull candidates before artificial insemination would help prevent economic loss; however,
predicting bull fertility through in vitro assessment of semen is yet to be established. In the present study, we focused on the methylated CpG
sites of sperm nuclear DNA and examined methylation levels to screen new biomarkers for predicting bull fertility. In frozen-thawed semen samples collected from
Japanese Black bulls, for which the sire conception rate (SCR) was recorded, the methylation level of each CpG site was analyzed using human methylation
microarray. According to regression analysis, 143 CpG sites related to SCR were significantly differentially methylated. Whole genome bisulfite sequence data
were obtained from three semen samples and the differentially methylated regions (DMRs) that included the target CpG sites selected by human methylation
microarray were confirmed. Using combined bisulfite restriction analysis, fertility-related methylation changes were detected in 10 DMRs. With the exception of
one DMR, the methylation levels of these DMRs were significantly different between groups with high fertility (> 50%) and low fertility (< 40%). From
multiple regression analysis of methylation levels and SCR, three DMRs were selected that could effectively predict bull fertility. We suggest that these
fertility-related differences in spermatozoal methylation levels could be new epigenetic biomarkers for predicting bull fertility.
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Affiliation(s)
- Kumiko Takeda
- Institute of Livestock and Grassland Science, NARO, Ibaraki 305-0901, Japan
| | - Eiji Kobayashi
- Institute of Livestock and Grassland Science, NARO, Ibaraki 305-0901, Japan
| | - Kazuko Ogata
- Institute of Livestock and Grassland Science, NARO, Ibaraki 305-0901, Japan
| | - Akira Imai
- Hiroshima Prefectural Livestock Technology Research Center, Hiroshima 739-0151, Japan
| | - Shinya Sato
- Hiroshima Prefectural Livestock Technology Research Center, Hiroshima 739-0151, Japan
| | - Hiromichi Adachi
- Hida Beef Cattle Research, Gifu Prefectural Livestock Research Institute, Gifu 506-0101, Japan
| | | | - Kagetomo Nishino
- Beef Cattle Institute, Ibaraki Prefectural Livestock Research Center, Ibaraki 319-2224, Japan
| | - Masahiro Inoue
- Tottori Prefectural Livestock Research Institute, Tottori 689-2503, Japan
| | - Masahiro Kaneda
- Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Shinya Watanabe
- Institute of Livestock and Grassland Science, NARO, Ibaraki 305-0901, Japan.,Western Region Agricultural Research Center, NARO, Shimane 694-0013, Japan
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Roque-Jiménez JA, Rosa-Velázquez M, Pinos-Rodríguez JM, Vicente-Martínez JG, Mendoza-Cervantes G, Flores-Primo A, Lee-Rangel HA, Relling AE. Role of Long Chain Fatty Acids in Developmental Programming in Ruminants. Animals (Basel) 2021; 11:ani11030762. [PMID: 33801880 PMCID: PMC8001802 DOI: 10.3390/ani11030762] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary The objective of the current review is to provide a broad perspective on developmental program aspects of dietary n-3 FA supplementation in ruminants during pre-conception, conception, pregnancy, early life, including its effects on production, lipid metabolism, and health of the offspring. Offspring growth and metabolism could change depending on the FA profile and the stage of gestation when the dam is supplemented. Despite this extended review we are highlighting areas that we consider that there is a lack of information. Abstract Nutrition plays a critical role in developmental programs. These effects can be during gametogenesis, gestation, or early life. Omega-3 polyunsaturated fatty acids (PUFA) are essential for normal physiological functioning and for the health of humans and all domestic species. Recent studies have demonstrated the importance of n-3 PUFA in ruminant diets during gestation and its effects on pre-and postnatal offspring growth and health indices. In addition, different types of fatty acids have different metabolic functions, which affects the developmental program differently depending on when they are supplemented. This review provides a broad perspective of the effect of fatty acid supplementation on the developmental program in ruminants, highlighting the areas of a developmental program that are better known and the areas that more research may be needed.
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Affiliation(s)
- José Alejandro Roque-Jiménez
- Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78321, Mexico; (J.A.R.-J.); (H.A.L.-R.)
| | - Milca Rosa-Velázquez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Veracruz 91710, Mexico; (M.R.-V.); (J.M.P.-R.); (J.G.V.-M.); (A.F.-P.)
| | - Juan Manuel Pinos-Rodríguez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Veracruz 91710, Mexico; (M.R.-V.); (J.M.P.-R.); (J.G.V.-M.); (A.F.-P.)
| | - Jorge Genaro Vicente-Martínez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Veracruz 91710, Mexico; (M.R.-V.); (J.M.P.-R.); (J.G.V.-M.); (A.F.-P.)
| | | | - Argel Flores-Primo
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Veracruz 91710, Mexico; (M.R.-V.); (J.M.P.-R.); (J.G.V.-M.); (A.F.-P.)
| | - Héctor Aarón Lee-Rangel
- Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78321, Mexico; (J.A.R.-J.); (H.A.L.-R.)
| | - Alejandro E. Relling
- Department of Animal Sciences, The Ohio State University, Wooster, OH 44691, USA
- Correspondence: ; Tel.: +1-330-263-3900
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Perrier JP, Kenny DA, Chaulot-Talmon A, Byrne CJ, Sellem E, Jouneau L, Aubert-Frambourg A, Schibler L, Jammes H, Lonergan P, Fair S, Kiefer H. Accelerating Onset of Puberty Through Modification of Early Life Nutrition Induces Modest but Persistent Changes in Bull Sperm DNA Methylation Profiles Post-puberty. Front Genet 2020; 11:945. [PMID: 33005172 PMCID: PMC7479244 DOI: 10.3389/fgene.2020.00945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 07/28/2020] [Indexed: 12/11/2022] Open
Abstract
In humans and model species, alterations of sperm DNA methylation patterns have been reported in cases of spermatogenesis defects, male infertility and exposure to toxins or nutritional challenges, suggesting that a memory of environmental or physiological changes is recorded in the sperm methylome. The objective of this study was to ascertain if early life plane of nutrition could have a latent effect on DNA methylation patterns in sperm produced post-puberty. Holstein-Friesian calves were assigned to either a high (H) or moderate (M) plane of nutrition for the first 24 weeks of age, then reassigned to the M diet until puberty, resulting in HM and MM groups. Sperm DNA methylation patterns from contrasted subgroups of bulls in the HM (ejaculates recovered at 15 months of age; n = 9) and in the MM (15 and 16 months of age; n = 7 and 9, respectively) were obtained using Reduced Representation Bisulfite Sequencing. Both 15 and 16 months were selected in the MM treatment as these bulls reached puberty approximately 1 month after the HM bulls. Hierarchical clustering demonstrated that inter-individual variability unrelated to diet or age dominated DNA methylation profiles. While the comparison between 15 and 16 months of age revealed almost no change, 580 differentially methylated CpGs (DMCs) were identified between the HM and MM groups. Differentially methylated CpGs were mostly hypermethylated in the HM group, and enriched in endogenous retrotransposons, introns, intergenic regions, and shores and shelves of CpG islands. Furthermore, genes involved in spermatogenesis, Sertoli cell function, and the hypothalamic-pituitary-gonadal axis were targeted by differential methylation when HM and MM groups were compared at 15 months of age, reflecting the earlier timing of puberty onset in the HM bulls. In contrast, the genes still differentially methylated in MM bulls at 16 months of age were enriched for ATP-binding molecular function, suggesting that changes to the sperm methylome could persist even after the HM and MM bulls reached a similar level of sexual maturity. Together, results demonstrate that enhanced plane of nutrition in pre-pubertal calves associated with advanced puberty induced modest but persistent changes in sperm DNA methylation profiles after puberty.
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Affiliation(s)
- Jean-Philippe Perrier
- Laboratory of Animal Reproduction, Department of Biological Sciences, Biomaterials Research Cluster, Bernal Institute, University of Limerick, Limerick, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland
| | - Aurélie Chaulot-Talmon
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Colin J Byrne
- Laboratory of Animal Reproduction, Department of Biological Sciences, Biomaterials Research Cluster, Bernal Institute, University of Limerick, Limerick, Ireland.,Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland
| | | | - Luc Jouneau
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Anne Aubert-Frambourg
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | | | - Hélène Jammes
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Patrick Lonergan
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Sean Fair
- Laboratory of Animal Reproduction, Department of Biological Sciences, Biomaterials Research Cluster, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Hélène Kiefer
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
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8
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Khezri A, Narud B, Stenseth EB, Zeremichael TT, Myromslien FD, Wilson RC, Ahmad R, Kommisrud E. Sperm DNA Hypomethylation Proximal to Reproduction Pathway Genes in Maturing Elite Norwegian Red Bulls. Front Genet 2020; 11:922. [PMID: 32849856 PMCID: PMC7431628 DOI: 10.3389/fgene.2020.00922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/24/2020] [Indexed: 01/08/2023] Open
Abstract
Genomic selection in modern farming demands sufficient semen production in young bulls. Factors affecting semen quality and production capacity in young bulls are not well understood; DNA methylation, a complicated phenomenon in sperm cells, is one such factors. In this study, fresh and frozen-thawed semen samples from the same Norwegian Red (NR) bulls at both 14 and 17 months of age were examined for sperm chromatin integrity parameters, ATP content, viability, and motility. Furthermore, reduced representation bisulfite libraries constructed according to two protocols, the Ovation® RRBS Methyl-Seq System (Ovation method) and a previously optimized gel-free method and were sequenced to study the sperm DNA methylome in frozen-thawed semen samples. Sperm quality analyses indicated that sperm concentration, total motility and progressivity in fresh semen from 17 months old NR bulls were significantly higher compared to individuals at 14 months of age. The percentage of DNA fragmented sperm cells significantly decreased in both fresh and frozen-thawed semen samples in bulls with increasing age. Libraries from the Ovation method exhibited a greater percentage of read loss and shorter read size following trimming. Downstream analyses for reads obtained from the gel-free method revealed similar global sperm DNA methylation but differentially methylated regions (DMRs) between 14- and 17 months old NR bulls. The majority of identified DMRs were hypomethylated in 14 months old bulls. Most of the identified DMRs (69%) exhibited a less than 10% methylation difference while only 1.5% of DMRs exceeded a 25% methylation difference. Pathway analysis showed that genes annotated with DMRs having low methylation differences (less than 10%) and DMRs having between 10 and 25% methylation differences, could be associated with important hormonal signaling and sperm function relevant pathways, respectively. The current research shows that RRBS in parallel with routine sperm quality analyses could be informative in reproductive capacity of young NR bulls. Although global sperm DNA methylation levels in 14 and 17 months old NR bulls were similar, regions with low and varying levels of DNA methylation differences can be identified and linked with important sperm function and hormonal pathways.
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Affiliation(s)
- Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Birgitte Narud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Else-Berit Stenseth
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | | | | | - Robert C Wilson
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Elisabeth Kommisrud
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
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