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Alfattah MA, Correia CN, Browne JA, McGettigan PA, Pluta K, Carrington SD, MacHugh DE, Irwin JA. Transcriptomics analysis of the bovine endometrium during the perioestrus period. PLoS One 2024; 19:e0301005. [PMID: 38547106 PMCID: PMC10977793 DOI: 10.1371/journal.pone.0301005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/10/2024] [Indexed: 04/02/2024] Open
Abstract
During the oestrous cycle, the bovine endometrium undergoes morphological and functional changes, which are regulated by alterations in the levels of oestrogen and progesterone and consequent changes in gene expression. To clarify these changes before and after oestrus, RNA-seq was used to profile the transcriptome of oestrus-synchronized beef heifers. Endometrial samples were collected from 29 animals, which were slaughtered in six groups beginning 12 h after the withdrawal of intravaginal progesterone releasing devices until seven days post-oestrus onset (luteal phase). The groups represented proestrus, early oestrus, metoestrus and early dioestrus (luteal phase). Changes in gene expression were estimated relative to gene expression at oestrus. Ingenuity Pathway Analysis (IPA) was used to identify canonical pathways and functional processes of biological importance. A total of 5,845 differentially expressed genes (DEGs) were identified. The lowest number of DEGs was observed at the 12 h post-oestrus time point, whereas the greatest number was observed at Day 7 post-oestrus onset (luteal phase). A total of 2,748 DEGs at this time point did not overlap with any other time points. Prior to oestrus, Neurological disease and Organismal injury and abnormalities appeared among the top IPA diseases and functions categories, with upregulation of genes involved in neurogenesis. Lipid metabolism was upregulated before oestrus and downregulated at 48h post-oestrus, at which point an upregulation of immune-related pathways was observed. In contrast, in the luteal phase the Lipid metabolism and Small molecule biochemistry pathways were upregulated.
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Affiliation(s)
- Mohammed A. Alfattah
- UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, Ireland
- King Faisal University, Al-Ahsa, Saudi Arabia
| | - Carolina N. Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - John A. Browne
- UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - Paul A. McGettigan
- UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - Katarzyna Pluta
- UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - Stephen D. Carrington
- UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - David E. MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Jane A. Irwin
- UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, Ireland
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Cesarani A, Corte Pause F, Hidalgo J, Garcia A, Degano L, Vicario D, Macciota NPP, Stradaioli G. Genetic background of semen parameters in Italian Simmental bulls. ITALIAN JOURNAL OF ANIMAL SCIENCE 2023. [DOI: 10.1080/1828051x.2022.2160665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Francesca Corte Pause
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Jorge Hidalgo
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Andre Garcia
- Angus Genetics Inc. - American Angus Association, Saint Joseph, MO, USA
| | - Lorenzo Degano
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | - Daniele Vicario
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | | | - Giuseppe Stradaioli
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
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Chang C, He X, Di R, Wang X, Han M, Liang C, Chu M. Thyroid Transcriptomics Revealed the Reproductive Regulation of miRNA in the Follicular and Luteal Phases in Small-Tail Han Sheep with Different FecB Genotypes. Genes (Basel) 2023; 14:2024. [PMID: 38002966 PMCID: PMC10671830 DOI: 10.3390/genes14112024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
MicroRNA (miRNA) is a type of endogenous short-stranded ncRNA that influences many biological processes such as animal growth, development and metabolism. The thyroid gland is an important endocrine gland in sheep, and an increasing number of studies have shown that the thyroid gland plays an important role in animal reproduction, but the molecular mechanisms of the thyroid gland in sheep reproduction are poorly understood. In this study, RNA-seq was used to detect transcriptome expression patterns in the thyroid gland between the follicular phase (FP) and luteal phase (LP) in FecB BB (MM) and FecB ++ (ww) small-tail Han (STH) sheep, respectively, and to identify differentially expressed miRNAs (DEMs) associated with reproduction. Bioinformatic analysis of the target genes of these DEMs revealed that they can be enriched in multiple GO terms associated with the reproductive process in animals and in the KEGG signaling pathway. The miRNA-mRNA coexpression network revealed that oar-miR-133 and oar-miR-370-3p may play an important role in sheep reproduction. The results of the dual-luciferase reporter assay suggest a possible targeting relationship between novel-51 and TARBP2. These results provided a novel resource for elucidating regulatory mechanisms underlying STH sheep prolificacy.
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Affiliation(s)
- Cheng Chang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Xiaoyun He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Ran Di
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Xiangyu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Miaoceng Han
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Chen Liang
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
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de Souza Fonseca PA, Suárez-Vega A, Cánovas A. Unrevealing functional candidate genes for bovine fertility through RNA sequencing meta-analysis and regulatory elements networks of co-expressed genes and lncRNAs. Funct Integr Genomics 2022; 22:1361-1376. [PMID: 36001276 DOI: 10.1007/s10142-022-00893-1] [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: 03/29/2022] [Revised: 07/16/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022]
Abstract
The high genetic heterogeneity and environmental effects of subfertility in livestock species make the elucidation of the genetic mechanisms associated with reproductive efficiency a difficult task. Network and co-expression network meta-analyses were applied alongside genetic variant calling and long non-coding RNA (lncRNA) characterization to identify functionally relevant target genes and regulatory subnetworks associated with fertility in dairy cattle. In total, 505 lncRNAs (441 previously annotated in the bovine reference genome ARS-UCD 1.2 and 64 novel lncRNAs) were identified. Seven differentially expressed genes between high-fertile (HF) and sub-fertile (SF) Holstein cows were identified in the network meta-analysis (CA5A, ENSBTAG00000051149, ENSBTAG00000003272, DEFB7, DIO2, TRPV3, and COL4A4). Additionally, seven functional candidate differentially co-expressed (DcoExp) modules with a differential regulatory pattern (|z-score|>2) were identified between HF and SF cows. The functional candidate genes and DcoExp modules identified were associated with fertility relevant processes such as the regulation of embryonic implantation and proliferation, interaction and molecule transfer between the fetus and the cow, and the immune system. These results help to better understand the genetic mechanisms associated with reproductive efficiency in dairy cattle through the identification of potential biomarkers and genetic variants associated with differentially expressed regulatory gene and lncRNAs regulatory element networks.
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Affiliation(s)
- Pablo Augusto de Souza Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Aroa Suárez-Vega
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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Elshalofy A, Wagener K, Weber K, Blanco M, Bauersachs S, Bollwein H. Identification of genes associated with susceptibility to persistent breeding-induced endometritis by RNA-sequencing of uterine cytobrush samples. Reprod Biol 2021; 22:100577. [PMID: 34883452 DOI: 10.1016/j.repbio.2021.100577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022]
Abstract
This study aimed to investigate the susceptibility to persistent breeding-induced endometritis (PBIE). Cytobrush samples were collected from 81 broodmares 1-3 days before artificial insemination (AI). Susceptibility to PBIE was evaluated by the presence of ≥ 2 cm of intrauterine fluid 24 h after AI, besides the fertility was determined by a sonographic pregnancy diagnosis 2 weeks after ovulation. RNA expressions were compared between susceptible non-pregnant (SNP) mares (n=9) and resistant pregnant (RP) mares (n=9) as well as between susceptible pregnant (SP) mares (n=9) and susceptible non-pregnant (SNP) mares. 66 differentially expressed genes (DEGs) were identified between SNP and RP mares and 60 DEGs between SP and SNP mares. In SNP compared to RP mares, transcript levels of genes regulating steroid hormone metabolism and neutrophil chemotaxis were lower, while higher for genes participating in uterine inflammation.Transcripts of genes related to extracellular matrix degradation, tissue adhesions, and fibrosis were lower in SP mares than in SNP mares, while higher for genes related to uterine cell proliferation, differentiation, and angiogenesis in SP mares than SNP mares. In conclusion, increased transcript levels of apolipoprotein E (APOE) and roundabout 2 (ROBO2), cluster domain 44 (CD44), integrin beta 3 (ITGB3), and epidermal growth factor (EGF) are possible biomarkers for susceptibility to PBIE. While higher expression of fibroblast growth factor 9 (FGF9), kinase domain receptor (KDR), and C-X-C motif chemokine ligand (CXCL) 16, collagen type V alpha 2 (COL5A2) and fibronectin (FN1) are suggested indicators of fertility in susceptible mares if they receive proper breeding management.
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Affiliation(s)
- Amr Elshalofy
- Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zurich, Switzerland; Department of Theriogenology, Faculty of Veterinary Medicine, Cairo University, Egypt.
| | - Karen Wagener
- Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Katharina Weber
- Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zurich, Switzerland
| | | | - Stefan Bauersachs
- Institute of Veterinary Anatomy, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Heinrich Bollwein
- Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zurich, Switzerland.
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Quirke LD, Maclean PH, Haack NA, Edwards SJ, Heiser A, Juengel JL. Characterization of local and peripheral immune system in pregnant and nonpregnant ewes. J Anim Sci 2021; 99:6317661. [PMID: 34240172 PMCID: PMC8363041 DOI: 10.1093/jas/skab208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/07/2021] [Indexed: 12/16/2022] Open
Abstract
Modulation of the immune system is known to be important for successful pregnancy but how immune function might differ between the lymph nodes draining the reproductive tract and peripheral lymph nodes is not well understood. Additionally, if immune system changes in response to the presence of an embryo during early pregnancy, and if this response differs in local versus peripheral immune tissue, has not been well characterized. To address these questions, we examined expression of genes important for immune function using NanoString technology in the ampulla and isthmus of the oviduct, endometrium, lymph nodes draining the reproductive tract (lumbo-aortic and medial iliac) as well as a peripheral lymph node (axillary), the spleen, and circulating immune cells from ewes on day 5 of the estrous cycle or pregnancy. Concentrations of estradiol and progesterone in plasma were also determined. Principal component analysis revealed separation of the local from the peripheral lymph nodes (MANOVA P = 3.245e-08, R2 = 0.3) as well as separation of tissues from pregnant and nonpregnant animals [lymph nodes (MANOVA P = 2.337e-09, R2 = 0.5), reproductive tissues (MANOVA P = 2.417e-14, R2 = 0.47)]. Nine genes were differentially (FDR < 0.10) expressed between lymph node types, with clear difference in expression of these genes between the lumbo-aortic and axillary lymph nodes. Expression of these genes in the medial iliac lymph node was not consistently different to either the axillary or the lumbo-aortic lymph node. Expression of IL10RB was increased (FDR < 0.05) by 24% in the reproductive tissue of the pregnant animals compared to nonpregnant animals. Analysis of gene categories revealed that expression of genes of the T-cell receptor pathway in reproductive tract tissues was associated (P < 0.05) with pregnancy status. In conclusion, assessment of gene expression of reproductive and immune tissue provides evidence for a specialization of the local immune system around the reproductive tract potentially important for successful establishment of pregnancy. Additionally, differences in gene expression patterns in reproductive tissue from pregnant and nonpregnant animals could be discerned as early as day 5 of pregnancy. This was found to be associated with expression of genes important for T-cell function and thus highlights the important role of these cells in early pregnancy.
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Affiliation(s)
- Laurel D Quirke
- Reproduction, Animal Science, Invermay Agricultural Centre, AgResearch Ltd, Mosgiel, 9092, New Zealand
| | - Paul H Maclean
- Bioinformatics and Statistics, AgResearch Ltd, Grasslands Research Centre, Private Bag 11008, Palmerston North, New Zealand
| | - Neville A Haack
- Infectious Diseases, Hopkirk Research Institute, AgResearch Ltd, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Sara J Edwards
- Reproduction, Animal Science, Invermay Agricultural Centre, AgResearch Ltd, Mosgiel, 9092, New Zealand
| | - Axel Heiser
- Infectious Diseases, Hopkirk Research Institute, AgResearch Ltd, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Jennifer L Juengel
- Reproduction, Animal Science, Invermay Agricultural Centre, AgResearch Ltd, Mosgiel, 9092, New Zealand.,Infectious Diseases, Hopkirk Research Institute, AgResearch Ltd, Private Bag 11008, Palmerston North, 4442, New Zealand
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Chankeaw W, Lignier S, Richard C, Ntallaris T, Raliou M, Guo Y, Plassard D, Bevilacqua C, Sandra O, Andersson G, Humblot P, Charpigny G. Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (2): impacts of post-partum negative energy balance on stromal, glandular and luminal epithelial cells. BMC Genomics 2021; 22:450. [PMID: 34139988 PMCID: PMC8212477 DOI: 10.1186/s12864-021-07713-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/13/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND In post-partum dairy cows, the energy needs to satisfy high milk production induces a status of more or less pronounced Negative Energy Balance (NEB). NEB associated with fat mobilization impairs reproductive function. In a companion paper, we described constitutive gene expression in the three main endometrial cell types (stromal, glandular and luminal epithelial cells) isolated by laser capture micro-dissection (LCM) showing the specificities of their transcriptomic profiles. This study investigates the specific impact of NEB on gene expression in these cells around 80 days after parturition at day 15 of the oestrus cycle and describes their specific response to NEB. RESULTS Following the description of their constitutive expression, the transcriptome profiles obtained by RNA sequencing of the three cells types revealed that differences related to the severity of NEB altered mainly specific patterns of expression related to individual cell types. Number of differentially expressed genes between severe NEB (SNEB) and mild NEB (MNEB) cows was higher in ST than in LE and GE, respectively. SNEB was associated with differential expression of genes coding for proteins involved in metabolic processes and embryo-maternal interactions in ST. Under-expression of genes encoding proteins with functions related to cell structure was found in GE whereas genes encoding proteins participating in pro-inflammatory pathways were over-expressed. Genes associated to adaptive immunity were under-expressed in LE. CONCLUSION The severity of NEB after calving is associated with changes in gene expression around 80 days after parturition corresponding to the time of breeding. Specific alterations in GEs are associated with activation of pro-inflammatory mechanisms. Concomitantly, changes in the expression of genes encoding proteins involved in cell interactions and maternal recognition of pregnancy takes place in ST. The combination of these effects possibly altering the uterine environment and embryo maternal interactions may negatively influence the establishment of pregnancy.
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Affiliation(s)
- Wiruntita Chankeaw
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, SLU, PO Box 7054, 750 07, Uppsala, Sweden
- Faculty of Veterinary Science, Rajamangala University of Technolgy Srivijaya (RUTS), Thungyai, Nakhon si thammarat, 80240, Thailand
| | - Sandra Lignier
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
| | - Christophe Richard
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
| | - Theodoros Ntallaris
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, SLU, PO Box 7054, 750 07, Uppsala, Sweden
| | - Mariam Raliou
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
| | - Yongzhi Guo
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, SLU, PO Box 7054, 750 07, Uppsala, Sweden
| | - Damien Plassard
- GenomEast Platform CERBM GIE, IGBMC, 67404, Illkirch Cedex, France
| | - Claudia Bevilacqua
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy en Josas, France
| | - Olivier Sandra
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SLU, PO Box 7023, 750 07, Uppsala, Sweden
| | - Patrice Humblot
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, SLU, PO Box 7054, 750 07, Uppsala, Sweden
| | - Gilles Charpigny
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France.
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Uterine Insulin Sensitivity Defects Induced Embryo Implantation Loss Associated with Mitochondrial Dysfunction-Triggered Oxidative Stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6655685. [PMID: 33953835 PMCID: PMC8057892 DOI: 10.1155/2021/6655685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/18/2021] [Accepted: 02/27/2021] [Indexed: 11/18/2022]
Abstract
Methods and Results Herein, a comprehensive proteomic analysis was conducted on proliferative endometria from sows with low and normal reproductive performance (LRP and NRP, respectively). Enrichment analysis of differentially expressed proteins revealed alterations in endometrial remodeling, substance metabolism (mainly lipid, nitrogen, and retinol metabolism), immunological modulation, and insulin signaling in LRP sows. Importantly, aberrant lipid metabolite accumulation and dysregulation of insulin signaling were coincidently confirmed in endometria of LPR sows, proving an impaired insulin sensitivity. Furthermore, established high-fat diet- (HFD-) induced insulin-resistant mouse models revealed that uterine insulin resistance beginning before pregnancy deteriorated uterine receptivity and decreased implantation sites and fetal numbers. Mitochondrial biogenesis and fusion were decreased, and reactive oxygen species was overproduced in uteri from the HFD group during the implantation period. Ishikawa and JAR cells directly demonstrated that oxidative stress compromised implantation in vitro. Conclusions This study demonstrated that uterine insulin sensitivity impairment beginning before pregnancy resulted in implantation and fetal loss associated with oxidative stress induced by mitochondrial dysfunction.
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Campanile G, Baruselli PS, Limone A, D'Occhio MJ. Local action of cytokines and immune cells in communication between the conceptus and uterus during the critical period of early embryo development, attachment and implantation - Implications for embryo survival in cattle: A review. Theriogenology 2021; 167:1-12. [PMID: 33743503 DOI: 10.1016/j.theriogenology.2021.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/15/2021] [Accepted: 02/24/2021] [Indexed: 12/16/2022]
Abstract
Early embryo development, implantation and pregnancy involve a complex dialogue between the embryo and mother. In cattle this dialogue starts as early as days 3-4 when the embryo is still in the oviduct, and it continues to implantation. Immunological processes involving cytokines, mast cells and macrophages form an important part of this dialogue. Amongst the cytokines, interleukin-6 (Il-6) and leukemia inhibitory factor (LIF) are secreted by both the embryo and uterine endometrium and form part of an ongoing and reciprocating dialogue. Mast cells and macrophages populate the uterine endometrium during embryo development and are involved in achieving the correct balance between inflammatory and anti-inflammatory reactions at the uterus that are associated with embryo attachment and implantation. Embryo loss is the major cause of reproductive wastage in cattle, and livestock generally. A deeper understanding of immunological processes during early embryo development will help to achieve the next step change in the efficiency of natural and assisted breeding.
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Affiliation(s)
- Giuseppe Campanile
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy.
| | - Pietro S Baruselli
- Department of Animal Reproduction, Faculty of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, Brazil.
| | - Antonio Limone
- Instituto Zooprofilattico Sperimentale Del Mezzogiorno, Portici, Naples, Italy
| | - Michael J D'Occhio
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, New South Wales, 2006, Australia
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Li Y, Li B, Yang M, Han H, Chen T, Wei Q, Miao Z, Yin L, Wang R, Shen J, Li X, Xu X, Fang M, Zhao S. Genome-Wide Association Study and Fine Mapping Reveals Candidate Genes for Birth Weight of Yorkshire and Landrace Pigs. Front Genet 2020; 11:183. [PMID: 32292414 PMCID: PMC7118202 DOI: 10.3389/fgene.2020.00183] [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: 09/30/2019] [Accepted: 02/14/2020] [Indexed: 12/19/2022] Open
Abstract
Birth weight of pigs is an important economic factor in the livestock industry. The identification of the genes and variants that underlie birth weight is of great importance. In this study, we integrated two genotyping methods, single nucleotide polymorphism (SNP) chip analysis and restriction site associated DNA sequencing (RAD-seq) to genotype genome-wide SNPs. In total, 45,175 and 139,634 SNPs were detected with the SNP chip and RAD-seq, respectively. The genome-wide association study (GWAS) of the combined SNP panels identified two significant loci located at chr1: 97,745,041 and chr4: 112,031,589, that explained 6.36% and 4.25% of the phenotypic variance respectively. To reduce interval containing causal variants, we imputed sequence-level SNPs in the GWAS identified regions and fine-mapped the causative variants into two narrower genomic intervals: a ∼100 kb interval containing 71 SNPs and a broader ∼870 kb interval with 432 SNPs. This fine-mapping highlighted four promising candidate genes, SKOR2, SMAD2, VAV3, and NTNG1. Additionally, the functional genes, SLC25A24, PRMT6 and STXBP3, are also located near the fine-mapping region. These results suggest that these candidate genes may have contribute substantially to the birth weight of pigs.
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Affiliation(s)
- Yong Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Bin Li
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Manman Yang
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Hu Han
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Tao Chen
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Qiang Wei
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Zepu Miao
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Lilin Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Ran Wang
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Junran Shen
- Shenzhen Engineering Laboratory for Genomics - Assisted Animal Breeding, BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Ming Fang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Education, Huazhong Agricultural University, Wuhan, China
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