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Hubert JN, Perret M, Riquet J, Demars J. Livestock species as emerging models for genomic imprinting. Front Cell Dev Biol 2024; 12:1348036. [PMID: 38500688 PMCID: PMC10945557 DOI: 10.3389/fcell.2024.1348036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 03/20/2024] Open
Abstract
Genomic imprinting is an epigenetically-regulated process of central importance in mammalian development and evolution. It involves multiple levels of regulation, with spatio-temporal heterogeneity, leading to the context-dependent and parent-of-origin specific expression of a small fraction of the genome. Genomic imprinting studies have therefore been essential to increase basic knowledge in functional genomics, evolution biology and developmental biology, as well as with regard to potential clinical and agrigenomic perspectives. Here we offer an overview on the contribution of livestock research, which features attractive resources in several respects, for better understanding genomic imprinting and its functional impacts. Given the related broad implications and complexity, we promote the use of such resources for studying genomic imprinting in a holistic and integrative view. We hope this mini-review will draw attention to the relevance of livestock genomic imprinting studies and stimulate research in this area.
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Affiliation(s)
| | | | | | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
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Verruma CG, Santos RS, Marchesi JAP, Sales SLA, Vila RA, Rios ÁFL, Furtado CLM, Ramos ES. Dynamic methylation pattern of H19DMR and KvDMR1 in bovine oocytes and preimplantation embryos. J Assist Reprod Genet 2024; 41:333-345. [PMID: 38231285 PMCID: PMC10894807 DOI: 10.1007/s10815-023-03011-7] [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: 08/09/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024] Open
Abstract
PURPOSE This study aimed to evaluate the epigenetic reprogramming of ICR1 (KvDMR1) and ICR2 (H19DMR) and expression of genes controlled by them as well as those involved in methylation, demethylation, and pluripotency. METHODS We collected germinal vesicle (GV) and metaphase II (MII) oocytes, and preimplantation embryos at five stages [zygote, 4-8 cells, 8-16 cells, morula, and expanded blastocysts (ExB)]. DNA methylation was assessed by BiSeq, and the gene expression was evaluated using qPCR. RESULTS H19DMR showed an increased DNA methylation from GV to MII oocytes (68.04% and 98.05%, respectively), decreasing in zygotes (85.83%) until morula (61.65%), and ExB (63.63%). H19 and IGF2 showed increased expression in zygotes, which decreased in further stages. KvDMR1 was hypermethylated in both GV (71.82%) and MII (69.43%) and in zygotes (73.70%) up to morula (77.84%), with a loss of methylation at the ExB (36.64%). The zygote had higher expression of most genes, except for CDKN1C and PHLDA2, which were highly expressed in MII and GV oocytes, respectively. DNMTs showed increased expression in oocytes, followed by a reduction in the earliest stages of embryo development. TET1 was downregulated until 4-8-cell and upregulated in 8-16-cell embryos. TET2 and TET3 showed higher expression in oocytes, and a downregulation in MII oocytes and 4-8-cell embryo. CONCLUSION We highlighted the heterogeneity in the DNA methylation of H19DMR and KvDMR1 and a dynamic expression pattern of genes controlled by them. The expression of DNMTs and TETs genes was also dynamic owing to epigenetic reprogramming.
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Affiliation(s)
- Carolina G Verruma
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Renan S Santos
- Postgraduate Program in Physiology and Pharmacology, Drug Research and Development Center (NPDM), Federal University of Ceara (UFC), Fortaleza, CE, 60430-275, Brazil
| | - Jorge A P Marchesi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Sarah L A Sales
- Postgraduate Program in Physiology and Pharmacology, Drug Research and Development Center (NPDM), Federal University of Ceara (UFC), Fortaleza, CE, 60430-275, Brazil
| | - Reginaldo A Vila
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Álvaro F L Rios
- Biotechnology Laboratory, Center of Bioscience and Biotechnology, State University of North Fluminense Darcy Ribeiro, Goitacazes Campus, Rio de Janeiro, Brazil
| | - Cristiana L M Furtado
- Experimental Biology Center, Graduate Program in Medical Sciences, University of Fortaleza - UNIFOR, Fortaleza, CE, 60811-905, Brazil
- Drug Research and Development Center (NPDM), Postgraduate Program in Translational Medicine, Federal University of Ceara (UFC), Fortaleza, CE, 60430-275, Brazil
| | - Ester S Ramos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil.
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Worku D, Hussen J, De Matteis G, Schusser B, Alhussien MN. Candidate genes associated with heat stress and breeding strategies to relieve its effects in dairy cattle: a deeper insight into the genetic architecture and immune response to heat stress. Front Vet Sci 2023; 10:1151241. [PMID: 37771947 PMCID: PMC10527375 DOI: 10.3389/fvets.2023.1151241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 08/31/2023] [Indexed: 09/30/2023] Open
Abstract
The need for food products of animal origin is increasing worldwide. Satisfying these needs in a way that has minimal impact on the environment requires cutting-edge technologies and techniques to enhance the genetic quality of cattle. Heat stress (HS), in particular, is affecting dairy cattle with increasing frequency and severity. As future climatic challenges become more evident, identifying dairy cows that are more tolerant to HS will be important for breeding dairy herds that are better adapted to future environmental conditions and for supporting the sustainability of dairy farming. While research into the genetics of HS in the context of the effect of global warming on dairy cattle is gaining momentum, the specific genomic regions involved in heat tolerance are still not well documented. Advances in omics information, QTL mapping, transcriptome profiling and genome-wide association studies (GWAS) have identified genomic regions and variants associated with tolerance to HS. Such studies could provide deeper insights into the genetic basis for response to HS and make an important contribution to future breeding for heat tolerance, which will help to offset the adverse effects of HS in dairy cattle. Overall, there is a great interest in identifying candidate genes and the proportion of genetic variation associated with heat tolerance in dairy cattle, and this area of research is currently very active worldwide. This review provides comprehensive information pertaining to some of the notable recent studies on the genetic architecture of HS in dairy cattle, with particular emphasis on the identified candidate genes associated with heat tolerance in dairy cattle. Since effective breeding programs require optimal knowledge of the impaired immunity and associated health complications caused by HS, the underlying mechanisms by which HS modulates the immune response and renders animals susceptible to various health disorders are explained. In addition, future breeding strategies to relieve HS in dairy cattle and improve their welfare while maintaining milk production are discussed.
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Affiliation(s)
- Destaw Worku
- Department of Animal Science, College of Agriculture, Food and Climate Sciences, Injibara University, Injibara, Ethiopia
| | - Jamal Hussen
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Giovanna De Matteis
- Council for Agricultural Research and Economics, CREA Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Benjamin Schusser
- Reproductive Biotechnology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mohanned Naif Alhussien
- Reproductive Biotechnology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Bina M. Defining Candidate Imprinted loci in Bos taurus. Genes (Basel) 2023; 14:1036. [PMID: 37239396 PMCID: PMC10217866 DOI: 10.3390/genes14051036] [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: 03/31/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
Using a whole-genome assembly of Bos taurus, I applied my bioinformatics strategy to locate candidate imprinting control regions (ICRs) genome-wide. In mammals, genomic imprinting plays essential roles in embryogenesis. In my strategy, peaks in plots mark the locations of known, inferred, and candidate ICRs. Genes in the vicinity of candidate ICRs correspond to potential imprinted genes. By displaying my datasets on the UCSC genome browser, one could view peak positions with respect to genomic landmarks. I give two examples of candidate ICRs in loci that influence spermatogenesis in bulls: CNNM1 and CNR1. I also give examples of candidate ICRs in loci that influence muscle development: SIX1 and BCL6. By examining the ENCODE data reported for mice, I deduced regulatory clues about cattle. I focused on DNase I hypersensitive sites (DHSs). Such sites reveal accessibility of chromatin to regulators of gene expression. For inspection, I chose DHSs in chromatin from mouse embryonic stem cells (ESCs) ES-E14, mesoderm, brain, heart, and skeletal muscle. The ENCODE data revealed that the SIX1 promoter was accessible to the transcription initiation apparatus in mouse ESCs, mesoderm, and skeletal muscles. The data also revealed accessibility of BCL6 locus to regulatory proteins in mouse ESCs and examined tissues.
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Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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Wyss P, Song C, Bina M. Along the Bos taurus genome, uncover candidate imprinting control regions. BMC Genomics 2022; 23:478. [PMID: 35764919 PMCID: PMC9241299 DOI: 10.1186/s12864-022-08694-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
Background In mammals, Imprinting Control Regions (ICRs) regulate a subset of genes in a parent-of-origin-specific manner. In both human and mouse, previous studies identified a set of CpG-rich motifs occurring as clusters in ICRs and germline Differentially Methylated Regions (gDMRs). These motifs consist of the ZFP57 binding site (ZFBS) overlapping a subset of MLL binding units known as MLL morphemes. MLL or MLL1 (Mixed Lineage Leukemia 1) is a relatively large multidomain protein that plays a central role in the regulation of transcription. The structures of both MLL1 and MLL2 include a domain (MT) that binds CpG-rich DNA and a conserved domain (SET) that methylates lysine 4 in histone H3 producing H3K4me3 marks in chromatin. Results Since genomic imprinting impacts many developmental and key physiological processes, we followed a previous bioinformatics strategy to pinpoint ICR positions in the Bos taurus genome. Initial genome-wide analyses involved finding the positions of ZFP57 binding sites, and the CpG-rich motifs (ZFBS-morph overlaps) along cattle chromosomal DNA. By creating plots displaying the density of ZFBS-morph overlaps, we removed background noise and thus improved signal detection. With the density-plots, we could view the positions of peaks locating known and candidate ICRs in cattle DNA. Our evaluations revealed the correspondence of peaks in plots to reported known and inferred ICRs/DMRs in cattle. Beside peaks pinpointing such ICRs, the density-plots also revealed additional peaks. Since evaluations validated the robustness of our approach, we inferred that the additional peaks may correspond to candidate ICRs for imprinted gene expression. Conclusion Our bioinformatics strategy offers the first genome-wide approach for systematically localizing candidate ICRs. Furthermore, we have tailored our datasets for upload onto the UCSC genome browser so that researchers could find known and candidate ICRs with respect to a wide variety of annotations at all scales: from the positions of Single Nucleotide Polymorphisms (SNPs), to positions of genes, transcripts, and repeated DNA elements. Furthermore, the UCSC genome browser offers tools to produce enlarged views: to uncover the genes in the vicinity of candidate ICRs and thus discover potential imprinted genes for experimental validations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08694-3.
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Affiliation(s)
- Phillip Wyss
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Carol Song
- Information Technology, Purdue University, West Lafayette, IN, 47907, USA
| | - Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
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Mangiavacchi PM, Caldas-Bussiere MC, Mendonça MDS, Dias AJB, Rios ÁFL. Multi-locus imprinting disturbances of Beckwith-Wiedemann and Large offspring syndrome/Abnormal offspring syndrome: A brief review. Theriogenology 2021; 173:193-201. [PMID: 34399383 DOI: 10.1016/j.theriogenology.2021.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/30/2021] [Accepted: 08/05/2021] [Indexed: 12/30/2022]
Abstract
In vitro fertilization and somatic cell nuclear transfer are assisted reproduction technologies commonly used in humans and cattle, respectively. Despite advances in these technologies, molecular failures can occur, increasing the chance of the onset of imprinting disorders in the offspring. Large offspring syndrome/abnormal offspring syndrome (LOS/AOS) has been described in cattle and has features such as hypergrowth, malformation of organs, and skeletal and placental defects. In humans, Beckwith-Wiedemann syndrome (BWS) has phenotypic characteristics similar to those found in LOS/AOS. In both syndromes, disruption of genomic imprinting associated with loss of parental-specific expression and parental-specific epigenetic marks is involved in the molecular etiology. Changes in the imprinting pattern of these genes lead to loss of imprinting (LOI) due to gain or loss of methylation, inducing the emergence of these syndromes. Several studies have reported locus-specific alterations in these syndromes, such as hypomethylation in imprinting control region 2 (KvDMR1) in BWS and LOS/AOS. These LOI events can occur at multiple imprinted loci in the same affected individual, which are called multi-locus methylation defect (MLMD) events. Although the bovine species has been proposed as a developmental model for human imprinting disorders, there is little information on bovine imprinted genes in the literature, even the correlation of epimutation data with clinical characteristics. In this study, we performed a systematic review of all the multi-locus LOI events described in human BWS and LOS/AOS, in order to determine in which imprinted genes the largest changes in the pattern of DNA methylation and expression occur, helping to fill gaps for a better understanding of the etiology of both syndromes.
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Affiliation(s)
- Paula Magnelli Mangiavacchi
- Laboratory of Reproduction and Animal Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602, Campos dos Goytacazes, RJ, Brazil
| | - Maria Clara Caldas-Bussiere
- Laboratory of Reproduction and Animal Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602, Campos dos Goytacazes, RJ, Brazil
| | - Mariana da Silva Mendonça
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602, Campos dos Goytacazes, RJ, Brazil
| | - Angelo José Burla Dias
- Laboratory of Reproduction and Animal Breeding, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602, Campos dos Goytacazes, RJ, Brazil
| | - Álvaro Fabrício Lopes Rios
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, 28013-602, Campos dos Goytacazes, RJ, Brazil.
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Hao D, Wang X, Wang X, Thomsen B, Qu K, Lan X, Huang Y, Lei C, Huang B, Chen H. Resveratrol stimulates microRNA expression during differentiation of bovine primary myoblasts. Food Nutr Res 2021. [DOI: 10.29219/fnr.v65.5453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Genetic and Epigenetic Regulation of Immune Response and Resistance to Infectious Diseases in Domestic Ruminants. Vet Clin North Am Food Anim Pract 2019; 35:405-429. [PMID: 31590895 DOI: 10.1016/j.cvfa.2019.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Infectious diseases are the outcome of complex interactions between the host, pathogen, and environment. After exposure to a pathogen, the host immune system uses various mechanisms to remove the pathogen. However, environmental factors and characteristics of pathogens can compromise the host immune responses and subsequently alter the outcome of infection. In this article, genetic and epigenetic factors that shape the individual variation in mounting protective responses are reviewed. Different approaches that have been used by researchers to investigate the genetic regulation of immunity in ruminants and various sources of genetic information are discussed.
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Lim KS, Chang SS, Choi BH, Lee SH, Lee KT, Chai HH, Park JE, Park W, Lim D. Genome-Wide Analysis of Allele-Specific Expression Patterns in Seventeen Tissues of Korean Cattle (Hanwoo). Animals (Basel) 2019; 9:ani9100727. [PMID: 31561539 PMCID: PMC6826869 DOI: 10.3390/ani9100727] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 12/20/2022] Open
Abstract
The functional hemizygosity could be caused by the MAE of a given gene and it can be one of the sources to affect the phenotypic variation in cattle. We aimed to identify MAE genes across the transcriptome in Korean cattle (Hanwoo). For three Hanwoo family trios, the transcriptome data of 17 tissues were generated in three offspring. Sixty-two MAE genes had a monoallelic expression in at least one tissue. Comparing genotypes among each family trio, the preferred alleles of 18 genes were identified (maternal expression, n = 9; paternal expression, n = 9). The MAE genes are involved in gene regulation, metabolic processes, and immune responses, and in particular, six genes encode transcription factors (FOXD2, FOXM1, HTATSF1, SCRT1, NKX6-2, and UBN1) with tissue-specific expression. In this study, we report genome-wide MAE genes in seventeen tissues of adult cattle. These results could help to elucidate epigenetic effects on phenotypic variation in Hanwoo.
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Affiliation(s)
- Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
| | - Sun-Sik Chang
- Hanwoo Research Institute, National Institute of Animal Science, Rural Development Administration, Pyeongchang 25340, Korea.
| | - Bong-Hwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.
| | - Seung-Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea.
| | - Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju 55365, Korea.
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Yang Y, Liu C, Adeola AC, Sulaiman X, Xie HB, Zhang YP. Artificial selection drives differential gene expression during pig domestication. J Genet Genomics 2019; 46:97-100. [PMID: 30850275 DOI: 10.1016/j.jgg.2018.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/08/2018] [Accepted: 09/04/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Yang Yang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Chaorui Liu
- National Pilot School of Software, Yunnan University, Kunming, 650500, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | | | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.
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Cao Y, Dong Z, Zhang D, Zhou H. Stillbirth risk on fat-1 transgenic foetus of sheep caused by deregulated DNA methylation of imprinted genes. JOURNAL OF APPLIED ANIMAL RESEARCH 2019. [DOI: 10.1080/09712119.2019.1575224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Yu Cao
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Zhicheng Dong
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Dong Zhang
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Huanmin Zhou
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
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Sequence variation of necdin gene in Bovidae. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2018; 60:32. [PMID: 30598832 PMCID: PMC6302488 DOI: 10.1186/s40781-018-0191-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 12/10/2018] [Indexed: 11/28/2022]
Abstract
Background Necdin (NDN), a member of the melanoma antigen family showing imprinted pattern of expression, has been implicated as causing Prader-Willi symptoms, and known to participate in cellular growth, cellular migration and differentiation. The region where NDN is located has been associated to QTLs affecting reproduction and early growth in cattle, but location and functional analysis of the molecular mechanisms have not been established. Methods Here we report the sequence variation of the entire coding sequence from 72 samples of cattle, yak, buffalo, goat and sheep, and discuss its variation in Bovidae. Median-joining network analysis was used to analyze the variation found in the species. Synonymous and non-synonymous substitution rates were determined for the analysis of all the polymorphic sites. Phylogenetic analysis were carried out among the species of Bovidae to reconstruct their relationships. Results From the phylogenetic analysis with the consensus sequences of the studied Bovidae species, we found that only 11 of the 26 nucleotide changes that differentiate them produced amino acid changes. All the SNPs found in the cattle breeds were novel and showed similar percentages of nucleotides with non-synonymous substitutions at the N-terminal, MHD and C-terminal (12.3, 12.8 and 12.5%, respectively), and were much higher than the percentage of synonymous substitutions (2.5, 2.6 and 4.9%, respectively). Three mutations in cattle and one in sheep, detected in heterozygous individuals were predicted to be deleterious. Additionally, the analysis of the biochemical characteristics in the most common form of the proteins in each species show very little difference in molecular weight, pI, net charge, instability index, aliphatic index and GRAVY (Table 4) in the Bovidae species, except for sheep, which had a higher molecular weight, instability index and GRAVY. Conclusions There is sufficient variation in this gene within and among the studied species, and because NDN carry key functions in the organism, it can have effects in economically important traits in the production of these species. NDN sequence is phylogenetically informative in this group, thus we propose this gene as a phylogenetic marker to study the evolution and conservation in Bovidae.
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Siqueira LG, Tribulo P, Chen Z, Denicol AC, Ortega MS, Negrón-Pérez VM, Kannampuzha-Francis J, Pohler KG, Rivera RM, Hansen PJ. Colony-stimulating factor 2 acts from days 5 to 7 of development to modify programming of the bovine conceptus at day 86 of gestation†. Biol Reprod 2018; 96:743-757. [PMID: 28379294 DOI: 10.1093/biolre/iox018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/27/2017] [Indexed: 11/13/2022] Open
Abstract
Colony-stimulating factor 2 (CSF2) is an embryokine that improves competence of the embryo to establish pregnancy and which may participate in developmental programming. We tested whether culture of bovine embryos with CSF2 alters fetal development and alleviates abnormalities associated with in vitro production (IVP) of embryos. Pregnancies were established by artificial insemination (AI), transfer of an IVP embryo (IVP), or transfer of an IVP embryo treated with 10 ng/ml CSF2 from day 5 to 7 of development (CSF2). Pregnancies were produced using X-sorted semen. Female singleton conceptuses were collected on day 86 of gestation. There were few morphological differences between groups, although IVP and CSF2 fetuses were heavier than AI fetuses. Bicarbonate concentration in allantoic fluid was lower for IVP than for AI or CSF2. Expression of 92 genes in liver, placenta, and muscle was determined. The general pattern for liver and placenta was for IVP to alter expression and for CSF2 to sometimes reverse this effect. For muscle, CSF2 affected gene expression but did not generally reverse effects of IVP. Levels of methylation for each of the three tissues at 12 loci in the promoter of insulin-like growth factor 2 (IGF2) and five in the promoter of growth factor receptor bound protein 10 were unaffected by treatment except for CSF2 effects on two CpG for IGF2 in placenta and muscle. In conclusion, CSF2 can act as a developmental programming agent but alone is not able to abolish the adverse effects of IVP on fetal characteristics.
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Affiliation(s)
- Luiz G Siqueira
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA.,Embrapa Gado de Leite, Juiz de Fora, Minas Gerais, Brazil
| | - Paula Tribulo
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Zhiyuan Chen
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Anna C Denicol
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - M Sofia Ortega
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Veronica M Negrón-Pérez
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Jasmine Kannampuzha-Francis
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Ky G Pohler
- Department of Animal Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Rocio M Rivera
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Peter J Hansen
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
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Bruford MW, Ginja C, Hoffmann I, Joost S, Orozco-terWengel P, Alberto FJ, Amaral AJ, Barbato M, Biscarini F, Colli L, Costa M, Curik I, Duruz S, Ferenčaković M, Fischer D, Fitak R, Groeneveld LF, Hall SJG, Hanotte O, Hassan FU, Helsen P, Iacolina L, Kantanen J, Leempoel K, Lenstra JA, Ajmone-Marsan P, Masembe C, Megens HJ, Miele M, Neuditschko M, Nicolazzi EL, Pompanon F, Roosen J, Sevane N, Smetko A, Štambuk A, Streeter I, Stucki S, Supakorn C, Telo Da Gama L, Tixier-Boichard M, Wegmann D, Zhan X. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025. Front Genet 2015; 6:314. [PMID: 26539210 PMCID: PMC4612686 DOI: 10.3389/fgene.2015.00314] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/05/2015] [Indexed: 12/20/2022] Open
Abstract
Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.
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Affiliation(s)
- Michael W Bruford
- School of Biosciences, Cardiff University Cardiff, UK ; Sustainable Places Research Institute, Cardiff University Cardiff, UK
| | - Catarina Ginja
- Faculdade de Ciências, Centro de Ecologia, Evolução e Alterações Ambientais (CE3C), Universidade de Lisboa Lisboa, Portugal ; Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão Portugal
| | - Irene Hoffmann
- Food and Agriculture Organization of the United Nations, Animal Genetic Resources Branch, Animal Production and Health Division Rome, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Florian J Alberto
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Andreia J Amaral
- Faculty of Sciences, BioISI- Biosystems and Integrative Sciences Institute, University of Lisbon Campo Grande, Portugal
| | - Mario Barbato
- School of Biosciences, Cardiff University Cardiff, UK
| | | | - Licia Colli
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Mafalda Costa
- School of Biosciences, Cardiff University Cardiff, UK
| | - Ino Curik
- Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - Solange Duruz
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Daniel Fischer
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland
| | - Robert Fitak
- Institut für Populationsgenetik Vetmeduni, Vienna, Austria
| | | | | | - Olivier Hanotte
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Faiz-Ul Hassan
- School of Life Sciences, University of Nottingham Nottingham, UK ; Department of Animal Breeding and Genetics, University of Agriculture Faisalabad, Pakistan
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp Antwerp, Belgium
| | - Laura Iacolina
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland ; Department of Biology, University of Eastern Finland Kuopio, Finland
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Paolo Ajmone-Marsan
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Charles Masembe
- Institute of the Environment and Natural Resources, Makerere University Kampala, Uganda
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands
| | - Mara Miele
- School of Planning and Geography, Cardiff University Cardiff, UK
| | | | | | - François Pompanon
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Jutta Roosen
- TUM School of Management, Technische Universität München Munich, Germany
| | - Natalia Sevane
- Department of Animal Production, Veterinary Faculty, Universidad Complutense de Madrid Madrid, Spain
| | | | - Anamaria Štambuk
- Department of Biology, Faculty of Science, University of Zagreb Zagreb, Croatia
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, UK
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - China Supakorn
- School of Life Sciences, University of Nottingham Nottingham, UK ; School of Agricultural Technology, Walailak University Tha Sala, Thailand
| | - Luis Telo Da Gama
- Centre of Research in Animal Health (CIISA) - Faculty of Veterinary Medicine, University of Lisbon Lisbon, Portugal
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg Fribourg, Switzerland
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Beijing, China ; Cardiff University - Institute of Zoology, Joint Laboratory for Biocomplexity Research Beijing, China
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15
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Ibeagha-Awemu EM, Zhao X. Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs. Front Genet 2015; 6:302. [PMID: 26442116 PMCID: PMC4585011 DOI: 10.3389/fgene.2015.00302] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 09/11/2015] [Indexed: 12/30/2022] Open
Abstract
Improvement in animal productivity has been achieved over the years through careful breeding and selection programs. Today, variations in the genome are gaining increasing importance in livestock improvement strategies. Genomic information alone, however, explains only a part of the phenotypic variance in traits. It is likely that a portion of the unaccounted variance is embedded in the epigenome. The epigenome encompasses epigenetic marks such as DNA methylation, histone tail modifications, chromatin remodeling, and other molecules that can transmit epigenetic information such as non-coding RNA species. Epigenetic factors respond to external or internal environmental cues such as nutrition, pathogens, and climate, and have the ability to change gene expression leading to emergence of specific phenotypes. Accumulating evidence shows that epigenetic marks influence gene expression and phenotypic outcome in livestock species. This review examines available evidence of the influence of epigenetic marks on livestock (cattle, sheep, goat, and pig) traits and discusses the potential for consideration of epigenetic markers in livestock improvement programs. However, epigenetic research activities on farm animal species are currently limited partly due to lack of recognition, funding and a global network of researchers. Therefore, considerable less attention has been given to epigenetic research in livestock species in comparison to extensive work in humans and model organisms. Elucidating therefore the epigenetic determinants of animal diseases and complex traits may represent one of the principal challenges to use epigenetic markers for further improvement of animal productivity.
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Affiliation(s)
- Eveline M. Ibeagha-Awemu
- Dairy and Swine Research and Development Centre, Agriculture and Agri-Food CanadaSherbrooke, QC, Canada
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-De-BellevueQC, Canada
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16
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Consequences of paternally inherited effects on the genetic evaluation of maternal effects. Genet Sel Evol 2015; 47:63. [PMID: 26268933 PMCID: PMC4534045 DOI: 10.1186/s12711-015-0141-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 07/17/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mixed models are commonly used for the estimation of variance components and genetic evaluation of livestock populations. Some evaluation models include two types of additive genetic effects, direct and maternal. Estimates of variance components obtained with models that account for maternal effects have been the subject of a long-standing controversy about strong negative estimates of the covariance between direct and maternal effects. Genomic imprinting is known to be in some cases statistically confounded with maternal effects. In this study, we analysed the consequences of ignoring paternally inherited effects on the partitioning of genetic variance. RESULTS We showed that the existence of paternal parent-of-origin effects can bias the estimation of variance components when maternal effects are included in the evaluation model. Specifically, we demonstrated that adding a constraint on the genetic parameters of a maternal model resulted in correlations between relatives that were the same as those obtained with a model that fits only paternally inherited effects for most pairs of individuals, as in livestock pedigrees. The main consequence is an upward bias in the estimates of the direct and maternal additive genetic variances and a downward bias in the direct-maternal genetic covariance. This was confirmed by a simulation study that investigated five scenarios, with the trait affected by (1) only additive genetic effects, (2) only paternally inherited effects, (3) additive genetic and paternally inherited effects, (4) direct and maternal additive genetic effects and (5) direct and maternal additive genetic plus paternally inherited effects. For each scenario, the existence of a paternally inherited effect not accounted for by the estimation model resulted in a partitioning of the genetic variance according to the predicted pattern. In addition, a model comparison test confirmed that direct and maternal additive models and paternally inherited models provided an equivalent fit. CONCLUSIONS Ignoring paternally inherited effects in the maternal models for genetic evaluation can lead to a specific pattern of bias in variance component estimates, which may account for the unexpectedly strong negative direct-maternal genetic correlations that are typically reported in the literature.
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Smith LC, Therrien J, Filion F, Bressan F, Meirelles FV. Epigenetic consequences of artificial reproductive technologies to the bovine imprinted genes SNRPN, H19/IGF2, and IGF2R. Front Genet 2015; 6:58. [PMID: 25763013 PMCID: PMC4340261 DOI: 10.3389/fgene.2015.00058] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 02/07/2015] [Indexed: 12/28/2022] Open
Abstract
Animal breeders have made widespread use of assisted reproductive technologies to accelerate genetic improvement programs aimed at obtaining more, better and cheaper food products. Selection approaches have traditionally focused on Mendel’s laws of inheritance using parental phenotypic characteristics and quantitative genetics approaches to choose the best parents for the next generation, regardless of their gender. However, apart from contributing DNA sequence variants, male and female gametes carry parental-specific epigenetic marks that play key roles during pre- and post-natal development and growth of the offspring. We herein review the epigenetic anomalies that are associated with artificial reproductive technologies in current use in animal breeding programs. For instance, we demonstrate that bovine embryos and fetuses derived by in vitro culture and somatic cell nuclear transfer show epigenetic anomalies in the differentially methylated regions controlling the expression of some imprinted genes. Although these genomic imprinting errors are undetected in the somatic tissues after birth, further research is warranted to examine potential germ cell transmission of epimutations and the potential risks of reproducing cattle using artificial reproductive technologies.
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Affiliation(s)
- Lawrence C Smith
- Department of Veterinary Biomedicine, Centre de Recherche en Reproduction Animale, Faculty of Veterinary Medicine, University of Montreal , Saint-Hyacinthe, QC, Canada
| | - Jacinthe Therrien
- Department of Veterinary Biomedicine, Centre de Recherche en Reproduction Animale, Faculty of Veterinary Medicine, University of Montreal , Saint-Hyacinthe, QC, Canada
| | - France Filion
- Department of Veterinary Biomedicine, Centre de Recherche en Reproduction Animale, Faculty of Veterinary Medicine, University of Montreal , Saint-Hyacinthe, QC, Canada
| | - Fabiana Bressan
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga , Brazil
| | - Flávio V Meirelles
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga , Brazil
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O'Doherty AM, McGettigan PA. Epigenetic processes in the male germline. Reprod Fertil Dev 2015; 27:725-38. [DOI: 10.1071/rd14167] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/01/2014] [Indexed: 12/12/2022] Open
Abstract
Sperm undergo some of the most extensive chromatin modifications seen in mammalian biology. During male germline development, paternal DNA methylation marks are erased and established on a global scale through waves of demethylation and de novo methylation. As spermatogenesis progresses, the majority of the histones are removed and replaced by protamines, enabling a tighter packaging of the DNA and transcriptional shutdown. Following fertilisation, the paternal genome is rapidly reactivated, actively demethylated, the protamines are replaced with histones and the embryonic genome is activated. The development of new assays, made possible by high-throughput sequencing technology, has resulted in the revisiting of what was considered settled science regarding the state of DNA packaging in mammalian spermatozoa. Researchers have discovered that not all histones are replaced by protamines and, in certain experiments, various species of RNA have been detected in what was previously considered transcriptionally quiescent spermatozoa. Most controversially, several groups have suggested that environmental modifications of the epigenetic state of spermatozoa may operate as a non-DNA-based form of inheritance, a process known as ‘transgenerational epigenetic inheritance’. Other developments in the field include the increased focus on the involvement of short RNAs, such as microRNAs, long non-coding RNAs and piwi-interacting RNAs. There has also been an accumulation of evidence illustrating associations between defects in sperm DNA packaging and disease and fertility. In this paper we review the literature, recent findings and areas of controversy associated with epigenetic processes in the male germline, focusing on DNA methylation dynamics, non-coding RNAs, the biology of sperm chromatin packaging and transgenerational inheritance.
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