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Liu H, Xu X, Li J, Liu Z, Xiong Y, Yue M, Liu P. Overexpression of Plakophilin2 Mitigates Capillary Leak Syndrome in Severe Acute Pancreatitis by Activating the p38/MAPK Signaling Pathway. J Inflamm Res 2024; 17:4129-4149. [PMID: 38952564 PMCID: PMC11215460 DOI: 10.2147/jir.s459449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/18/2024] [Indexed: 07/03/2024] Open
Abstract
Purpose Capillary leak syndrome (CLS) is an intermediary phase between severe acute pancreatitis (SAP) and multiple organ failure. As a result, CLS is of clinical importance for enhancing the prognosis of SAP. Plakophilin2 (PKP2), an essential constituent of desmosomes, plays a critical role in promoting connections between epithelial cells. However, the function and mechanism of PKP2 in CLS in SAP are not clear at present. Methods We detected the expression of PKP2 in mice pancreatic tissue by transcriptome sequencing and bioinformatics analysis. PKP2 was overexpressed and knocked down to assess its influence on cell permeability, the cytoskeleton, tight junction molecules, cell adhesion junction molecules, and associated pathways. Results PKP2 expression was increased in the pancreatic tissues of SAP mice and human umbilical vein endothelial cells (HUVECs) after lipopolysaccharide (LPS) stimulation. PKP2 overexpression not only reduced endothelial cell permeability but also improved cytoskeleton relaxation in response to acute inflammatory stimulation. PKP2 overexpression increased levels of ZO-1, occludin, claudin1, β-catenin, and connexin43. The overexpression of PKP2 in LPS-induced HUVECs counteracted the inhibitory effect of SB203580 (a p38/MAPK signaling pathway inhibitor) on the p38/MAPK signaling pathway, thereby restoring the levels of ZO-1, β-catenin, and claudin1. Additionally, PKP2 suppression eliminated the enhanced levels of ZO-1, β-catenin, occludin, and claudin1 induced by dehydrocorydaline. We predicted that the upstream transcription factor PPARγregulates PKP2 expression, and our findings demonstrate that the PPARγactivator rosiglitazone significantly upregulates PKP2, whereas its antagonist GW9662 down-regulates PKP2. Administration of rosiglitazone significantly reduced the increase in HUVECs permeability stimulated by LPS. Conversely, PKP2 overexpression counteracted the GW9662-induced reduction in ZO-1, phosphorylated p38/p38, and claudin1. Conclusion The activation of the p38/MAPK signaling pathway by PKP2 mitigates CLS in SAP. PPARγactivator rosiglitazone can up-regulate PKP2. Overall, directing efforts toward PKP2 could prove to be a feasible treatment approach for effectively managing CLS in SAP.
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Affiliation(s)
- Hui Liu
- Department of Gastroenterology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, People’s Republic of China
- Gastroenterology Institute of Jiangxi Province, Nanchang, People’s Republic of China
| | - Xuan Xu
- Department of Gastroenterology, The People’s Hospital of Longhua, Shenzhen, People’s Republic of China
| | - Ji Li
- Department of Gastroenterology, The People’s Hospital of Longhua, Shenzhen, People’s Republic of China
| | - Zheyu Liu
- Department of Gastroenterology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, People’s Republic of China
| | - Yuwen Xiong
- Department of Gastroenterology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, People’s Republic of China
| | - Mengli Yue
- Affiliated Longhua People’s Hospital, The Third School of Clinical Medicine, Southern Medical University, Shenzhen, People’s Republic of China
| | - Pi Liu
- Department of Gastroenterology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, People’s Republic of China
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Lei Q, Zhang S, Wang J, Qi C, Liu J, Cao D, Li F, Han H, Liu W, Li D, Tang C, Zhou Y. Genome-wide association studies of egg production traits by whole genome sequencing of Laiwu Black chicken. Poult Sci 2024; 103:103705. [PMID: 38598913 DOI: 10.1016/j.psj.2024.103705] [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: 01/17/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
Compared to high-yield commercial laying hens, Chinese indigenous chicken breeds have poor egg laying capacity due to the lack of intensive selection. However, as these breeds have not undergone systematic selection, it is possible that there is a greater abundance of genetic variations related to egg laying traits. In this study, we assessed 5 egg number (EN) traits at different stages of the egg-laying period: EN1 (from the first egg to 23 wk), EN2 (from 23 to 35 wk), EN3 (from 35 to 48 wk), EN4 (from the first egg to 35 wk), and EN5 (from the first egg to 48 wk). To investigate the molecular mechanisms underlying egg number traits in a Chinese local chicken breed, we conducted a genome-wide association study (GWAS) using data from whole-genome sequencing (WGS) of 399 Laiwu Black chickens. We obtained a total of 3.01 Tb of raw data with an average depth of 7.07 × per individual. A total of 86 genome-wide suggestive or significant single-nucleotide polymorphisms (SNP) contained within a set of 45 corresponding candidate genes were identified and found to be associated with stages EN1-EN5. The genes vitellogenin 2 (VTG2), lipase maturation factor 1 (LMF1), calcium voltage-gated channel auxiliary subunit alpha2delta 3 (CACNA2D3), poly(A) binding protein cytoplasmic 1 (PABPC1), programmed cell death 11 (PDCD11) and family with sequence similarity 213 member A (FAM213A) can be considered as the candidate genes associated with egg number traits, due to their reported association with animal reproduction traits. Noteworthy, results suggests that VTG2 and PDCD11 are not only involved in the regulation of EN3, but also in the regulation of EN5, implies that VTG2 and PDCD11 have a significant influence on egg production traits. Our study offers valuable genomic insights into the molecular genetic mechanisms that govern egg number traits in a Chinese indigenous egg-laying chicken breed. These findings have the potential to enhance the egg-laying performance of chickens.
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Affiliation(s)
- Qiuxia Lei
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, 250023, Ji'nan, China
| | - Jie Wang
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Chao Qi
- Shandong Animal Husbandry General Station, 250023, Ji'nan, China
| | - Jie Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Dingguo Cao
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Fuwei Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Haixia Han
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Wei Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Dapeng Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Cunwei Tang
- Fujian Sunnzer Biological Technology Development Co. Ltd., 354100, Guang'ze, China
| | - Yan Zhou
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China..
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Berteli TS, Wang F, McKerrow W, Navarro PA, Fenyo D, Boeke JD, Kohlrausch FB, Keefe DL. Transposon insertion profiling by sequencing (TIPseq) identifies novel LINE-1 insertions in human sperm. J Assist Reprod Genet 2023; 40:1835-1843. [PMID: 37310664 PMCID: PMC10371950 DOI: 10.1007/s10815-023-02852-6] [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: 03/27/2023] [Accepted: 06/01/2023] [Indexed: 06/14/2023] Open
Abstract
PURPOSE Long interspersed nuclear element-1 (LINE-1 or L1) comprises 17% of the human genome. Retrotransposons may perturb gene integrity or alter gene expression by altering regulatory regions in the genome. The germline employs a number of mechanisms, including cytosine methylation, to repress retrotransposon transcription throughout most of life. Demethylation during germ cell and early embryo development de-represses retrotransposons. Intriguingly, de novo genetic variation appearing in sperm has been implicated in a number of disorders in offspring, including autism spectrum disorder, schizophrenia, and bipolar disorder. We hypothesize that human sperm exhibit de novo retrotransposition and employ a new sequencing method, single cell transposon insertion profiling by sequencing (scTIPseq) to map them in small amounts of human sperm. METHODS Cross-sectional case-control study of sperm samples (n=10 men; ages 32-55 years old) from consenting men undergoing IVF at NYU Langone Fertility Center. scTIPseq identified novel LINE-1 insertions in individual sperm and TIPseqHunter, a custom bioinformatics pipeline, compared the architecture of sperm LINE-1 to known LINE-1 insertions from the European database of Human specific LINE-1 (L1Hs) retrotransposon insertions (euL1db). RESULTS scTIPseq identified 17 novel insertions in sperm. New insertions were mainly intergenic or intronic. Only one sample did not exhibit new insertions. The location or number of novel insertions did not differ by paternal age. CONCLUSION This study for the first time reports novel LINE-1 insertions in human sperm, demonstrating the feasibility of scTIPseq, and identifies new contributors to genetic diversity in the human germ line.
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Affiliation(s)
- Thalita S Berteli
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY, USA.
- Human Reproduction Division, Department of Gynecology and Obstetrics, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, SP, Brazil.
| | - Fang Wang
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Paula A Navarro
- Human Reproduction Division, Department of Gynecology and Obstetrics, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - David Fenyo
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Fabiana B Kohlrausch
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY, USA
- Biology Institute, Department of General Biology, Fluminense Federal University (UFF), Niteroi, RJ, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY, USA
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Dan Y, Radic N, Gay M, Fernández-Torras A, Arauz G, Vilaseca M, Aloy P, Canovas B, Nebreda A. Characterization of p38α signaling networks in cancer cells using quantitative proteomics and phosphoproteomics. Mol Cell Proteomics 2023; 22:100527. [PMID: 36894123 PMCID: PMC10105487 DOI: 10.1016/j.mcpro.2023.100527] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
p38α (encoded by MAPK14) is a protein kinase that regulates cellular responses to almost all types of environmental and intracellular stresses. Upon activation, p38α phosphorylates many substrates both in the cytoplasm and nucleus, allowing this pathway to regulate a wide variety of cellular processes. While the role of p38α in the stress response has been widely investigated, its implication in cell homeostasis is less understood. To investigate the signaling networks regulated by p38α in proliferating cancer cells, we performed quantitative proteomic and phosphoproteomic analyses in breast cancer cells in which this pathway had been either genetically targeted or chemically inhibited. Our study identified with high confidence 35 proteins and 82 phosphoproteins (114 phosphosites) that are modulated by p38α, and highlighted the implication of various protein kinases, including MK2 and mTOR, in the p38α-regulated signaling networks. Moreover, functional analyses revealed an important contribution of p38α to the regulation of cell adhesion, DNA replication and RNA metabolism. Indeed, we provide experimental evidence supporting that p38α facilitates cancer cell adhesion, and showed that this p38α function is likely mediated by the modulation of the adaptor protein ArgBP2. Collectively, our results illustrate the complexity of the p38α regulated signaling networks, provide valuable information on p38α-dependent phosphorylation events in cancer cells, and document a mechanism by which p38α can regulate cell adhesion.
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Affiliation(s)
- Yuzhen Dan
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Nevenka Radic
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Adrià Fernández-Torras
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Gianluca Arauz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Begoña Canovas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - AngelR Nebreda
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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Sammad A, Zhang H, Shi R, Dong Y, Luo H, Chen Z, Liu L, Guo G, Liu A, Wang Y. A Post-GWAS Functional Analysis Confirming Effects of Three BTA13 Genes CACNB2, SLC39A12, and ZEB1 on Dairy Cattle Reproduction. Front Genet 2022; 13:882951. [PMID: 35754833 PMCID: PMC9216173 DOI: 10.3389/fgene.2022.882951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/18/2022] [Indexed: 11/26/2022] Open
Abstract
In our previous GWAS of Chinese and Nordic dairy cattle, genes CACNB2, SLC39A12, and ZEB1 locating on BTA 13 were suggested as candidate genes for reproduction. In this study, validation of these associations was performed in an independent population with records of nine reproductive traits. More importantly, functions of these genes in the reproductive process were verified by employing the expression data of ovarian follicles. The potential variants within the three genes were firstly detected in 68 Chinese Holstein bulls, and then screened in 1,588 Chinese Holstein cows using the KASP (Kompetitive allele-specific PCR) method. There were nine variants with polymorphisms in CACNB2, five in SLC39A12, and four in ZEB1, respectively, of which one SNP was in the upstream regulatory region, two in exon region, four in downstream regulatory region, and 11 SNPs in intronic regions. Amongst the 18 variants, g.33267056T/G in CACNB2 explained the largest phenotypic variance for age at first calving (0.011%), interval from first to last insemination (0.004%), and calving ease (0.002%), while g.32751518G/A in SLC39A12 contributed the most to stillbirth in heifers (0.038%). Two haplotype blocks were constructed for CACNB2 while one each for SLC39A12 and ZEB1, which were significantly associated with five reproductive traits, including age at the first service, age at the first calving, calving ease in heifers and cows, and the interval from calving to the first insemination. We then studied the profile of gene expression in granulosa cells isolated from four developmental stages of ovarian follicles from eight dairy cows. All three genes were differentially expressed between ovarian follicles with different sizes (p < 0.05), indicating their potential roles in the reproductive process of dairy cows. This study successfully demonstrated the associations of three BTA 13 genes CACNB2, SLC39A12, and ZEB1 with reproduction and further examined their expression levels in ovarian follicles directly. These findings can be beneficial for the ongoing genomic selection program for reproductive traits which have long been considered as traits that are difficult to achieve genetic improvement due to the lack of efficient genetic markers.
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Affiliation(s)
- Abdul Sammad
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hailiang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Rui Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yixin Dong
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hanpeng Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ziwei Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lin Liu
- Beijing Dairy Cattle Center, Beijing, China
| | - Gang Guo
- Beijing Sunlon Livestock Development Co. Ltd., Beijing, China
| | - Aoxing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Roberts JF, Jeff Huang CC. Bovine models for human ovarian diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 189:101-154. [PMID: 35595347 DOI: 10.1016/bs.pmbts.2022.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
During early embryonic development, late fetal growth, puberty, adult reproductive years, and advanced aging, bovine and human ovaries closely share molecular pathways and hormonal signaling mechanisms. Other similarities between these species include the size of ovaries, length of gestation, ovarian follicular and luteal dynamics, and pathophysiology of ovarian diseases. As an economically important agriculture species, cattle are a foundational species in fertility research with decades of groundwork using physiologic, genetic, and therapeutic experimental techniques. Many technologies used in modern reproductive medicine, such as ovulation induction using hormonal therapy, were first used in cows before human trials. Human ovarian diseases with naturally occurring bovine correlates include premature ovary insufficiency (POI), polycystic ovarian syndrome (PCOS), and sex-cord stromal tumors (SCSTs). This article presents an overview of bovine ovary research related to causes of infertility, ovarian diseases, diagnostics, and therapeutics, emphasizing where the bovine model can offer advantages over other lab animals for translational applications.
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Affiliation(s)
- John F Roberts
- Department of Comparative, Diagnostic & Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States.
| | - Chen-Che Jeff Huang
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
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A Large-Scale Genome-Wide Association Study of Epistasis Effects of Production Traits and Daughter Pregnancy Rate in U.S. Holstein Cattle. Genes (Basel) 2021; 12:genes12071089. [PMID: 34356105 PMCID: PMC8304971 DOI: 10.3390/genes12071089] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 11/22/2022] Open
Abstract
Epistasis is widely considered important, but epistasis studies lag those of SNP effects. Genome-wide association study (GWAS) using 76,109 SNPs and 294,079 first-lactation Holstein cows was conducted for testing pairwise epistasis effects of five production traits and three fertility traits: milk yield (MY), fat yield (FY), protein yield (PY), fat percentage (FPC), protein percentage (PPC), and daughter pregnancy rate (DPR). Among the top 50,000 pairwise epistasis effects of each trait, the five production traits had large chromosome regions with intra-chromosome epistasis. The percentage of inter-chromosome epistasis effects was 1.9% for FPC, 1.6% for PPC, 10.6% for MY, 29.9% for FY, 39.3% for PY, and 84.2% for DPR. Of the 50,000 epistasis effects, the number of significant effects with log10(1/p) ≥ 12 was 50,000 for FPC and PPC, and 10,508, 4763, 4637 and 1 for MY, FY, PY and DPR, respectively, and A × A effects were the most frequent epistasis effects for all traits. Majority of the inter-chromosome epistasis effects of FPC across all chromosomes involved a Chr14 region containing DGAT1, indicating a potential regulatory role of this Chr14 region affecting all chromosomes for FPC. The epistasis results provided new understanding about the genetic mechanism underlying quantitative traits in Holstein cattle.
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Davis DN, Strong MD, Chambers E, Hart MD, Bettaieb A, Clarke SL, Smith BJ, Stoecker BJ, Lucas EA, Lin D, Chowanadisai W. A role for zinc transporter gene SLC39A12 in the nervous system and beyond. Gene 2021; 799:145824. [PMID: 34252531 DOI: 10.1016/j.gene.2021.145824] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/28/2021] [Accepted: 05/19/2021] [Indexed: 12/21/2022]
Abstract
The SLC39A12 gene encodes the zinc transporter protein ZIP12, which is expressed across many tissues and is highly abundant in the vertebrate nervous system. As a zinc transporter, ZIP12 functions to transport zinc across cellular membranes, including cellular zinc influx across the plasma membrane. Genome-wide association and exome sequencing studies have shown that brain susceptibility-weighted magnetic resonance imaging (MRI) intensity is associated with ZIP12 polymorphisms and rare mutations. ZIP12 is required for neural tube closure and embryonic development in Xenopus tropicalis. Frog embryos depleted of ZIP12 by antisense morpholinos develop an anterior neural tube defect and lack viability. ZIP12 is also necessary for neurite outgrowth and mitochondrial function in mouse neural cells. ZIP12 mRNA is increased in brain regions of schizophrenic patients. Outside of the nervous system, hypoxia induces ZIP12 expression in multiple mammalian species, including humans, which leads to endothelial and smooth muscle thickening in the lung and contributes towards pulmonary hypertension. Other studies have associated ZIP12 with other diseases such as cancer. Given that ZIP12 is highly expressed in the brain and that susceptibility-weighted MRI is associated with brain metal content, ZIP12 may affect neurological diseases and psychiatric illnesses such as Parkinson's disease, Alzheimer's disease, and schizophrenia. Furthermore, the induction of ZIP12 and resultant zinc uptake under pathophysiological conditions may be a critical component of disease pathology, such as in pulmonary hypertension. Drug compounds that bind metals like zinc may be able to treat diseases associated with impaired zinc homeostasis and altered ZIP12 function.
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Affiliation(s)
- Danielle N Davis
- Oklahoma State University, Department of Nutritional Sciences, Stillwater, OK 74078, USA
| | - Morgan D Strong
- Oklahoma State University, Department of Nutritional Sciences, Stillwater, OK 74078, USA
| | - Emily Chambers
- Oklahoma State University, Department of Nutritional Sciences, Stillwater, OK 74078, USA
| | - Matthew D Hart
- Oklahoma State University, Department of Nutritional Sciences, Stillwater, OK 74078, USA
| | - Ahmed Bettaieb
- University of Tennessee, Department of Nutrition, Knoxville, TN 37996, USA
| | - Stephen L Clarke
- Oklahoma State University, Department of Nutritional Sciences, Stillwater, OK 74078, USA
| | - Brenda J Smith
- Oklahoma State University, Department of Nutritional Sciences, Stillwater, OK 74078, USA
| | - Barbara J Stoecker
- Oklahoma State University, Department of Nutritional Sciences, Stillwater, OK 74078, USA
| | - Edralin A Lucas
- Oklahoma State University, Department of Nutritional Sciences, Stillwater, OK 74078, USA
| | - Dingbo Lin
- Oklahoma State University, Department of Nutritional Sciences, Stillwater, OK 74078, USA
| | - Winyoo Chowanadisai
- Oklahoma State University, Department of Nutritional Sciences, Stillwater, OK 74078, USA.
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Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
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Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Melo-Baez B, Wong YS, Aguilera CJ, Cabezas J, Mançanares ACF, Riadi G, Castro FO, Rodriguez-Alvarez L. MicroRNAs from Extracellular Vesicles Secreted by Bovine Embryos as Early Biomarkers of Developmental Competence. Int J Mol Sci 2020; 21:ijms21238888. [PMID: 33255183 PMCID: PMC7727673 DOI: 10.3390/ijms21238888] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022] Open
Abstract
During early development, embryos secrete extracellular vesicles (EVs) that participate in embryo–maternal communication. Among other molecules, EVs carry microRNAs (miRNAs) that interfere with gene expression in target cells; miRNAs participate in embryo–maternal communication. Embryo selection based on secreted miRNAs may have an impact on bovine breeding programs. This research aimed to evaluate the size, concentration, and miRNA content of EVs secreted by bovine embryos with different developmental potential, during the compaction period (days 3.5–5). Individual culture media from in vitro–produced embryos were collected at day 5, while embryos were further cultured and classified at day 7, as G1 (conditioned-culture media by embryos arrested in the 8–16-cells stage) and G2 (conditioned-culture media by embryos that reached blastocyst stages at day 7). Collected nanoparticles from embryo conditioned culture media were cataloged as EVs by their morphology and the presence of classical molecular markers. Size and concentration of EVs from G1 were higher than EVs secreted by G2. We identified 95 miRNAs; bta-miR-103, bta-miR-502a, bta-miR-100, and bta-miR-1 were upregulated in G1, whereas bta-miR-92a, bta-miR-140, bta-miR-2285a, and bta-miR-222 were downregulated. The most significant upregulated pathways were fatty acid biosynthesis and metabolism, lysine degradation, gap junction, and signaling pathways regulating pluripotency of stem cells. The characteristics of EVs secreted by bovine embryos during the compaction period vary according to embryo competence. Embryos that reach the blastocyst stage secrete fewer and smaller vesicles. Furthermore, the loading of specific miRNAs into the EVs depends on embryo developmental competence.
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Affiliation(s)
- Bárbara Melo-Baez
- Laboratory of Animal Biotechnology, Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Av. Vicente Mendez 595, Chillan 3780000, Chile; (B.M.-B.); (Y.S.W.); (C.J.A.); (J.C.); (A.C.F.M.); (F.O.C.)
| | - Yat S. Wong
- Laboratory of Animal Biotechnology, Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Av. Vicente Mendez 595, Chillan 3780000, Chile; (B.M.-B.); (Y.S.W.); (C.J.A.); (J.C.); (A.C.F.M.); (F.O.C.)
| | - Constanza J. Aguilera
- Laboratory of Animal Biotechnology, Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Av. Vicente Mendez 595, Chillan 3780000, Chile; (B.M.-B.); (Y.S.W.); (C.J.A.); (J.C.); (A.C.F.M.); (F.O.C.)
| | - Joel Cabezas
- Laboratory of Animal Biotechnology, Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Av. Vicente Mendez 595, Chillan 3780000, Chile; (B.M.-B.); (Y.S.W.); (C.J.A.); (J.C.); (A.C.F.M.); (F.O.C.)
| | - Ana C. F. Mançanares
- Laboratory of Animal Biotechnology, Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Av. Vicente Mendez 595, Chillan 3780000, Chile; (B.M.-B.); (Y.S.W.); (C.J.A.); (J.C.); (A.C.F.M.); (F.O.C.)
| | - Gonzalo Riadi
- ANID-Millennium Science Initiative Program Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Center for Bioinformatics, Simulation and Modeling, CBSM, Department of Bioinformatics, Faculty of Engineering, Campus Talca, University of Talca, Talca 3460000, Chile;
| | - Fidel O. Castro
- Laboratory of Animal Biotechnology, Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Av. Vicente Mendez 595, Chillan 3780000, Chile; (B.M.-B.); (Y.S.W.); (C.J.A.); (J.C.); (A.C.F.M.); (F.O.C.)
| | - Lleretny Rodriguez-Alvarez
- Laboratory of Animal Biotechnology, Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Av. Vicente Mendez 595, Chillan 3780000, Chile; (B.M.-B.); (Y.S.W.); (C.J.A.); (J.C.); (A.C.F.M.); (F.O.C.)
- Correspondence: ; Tel.: +56-242208835
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11
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Gross N, Strillacci MG, Peñagaricano F, Khatib H. Characterization and functional roles of paternal RNAs in 2-4 cell bovine embryos. Sci Rep 2019; 9:20347. [PMID: 31889064 PMCID: PMC6937301 DOI: 10.1038/s41598-019-55868-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/03/2019] [Indexed: 12/26/2022] Open
Abstract
Embryos utilize oocyte-donated RNAs until they become capable of producing RNAs through embryonic genome activation (EGA). The sperm's influence over pre-EGA RNA content of embryos remains unknown. Recent studies have revealed that sperm donate non-genomic components upon fertilization. Thus, sperm may also contribute to RNA presence in pre-EGA embryos. The first objective of this study was to investigate whether male fertility status is associated with the RNAs present in the bovine embryo prior to EGA. A total of 65 RNAs were found to be differentially expressed between 2-4 cell bovine embryos derived from high and low fertility sires. Expression patterns were confirmed for protein phosphatase 1 regulatory subunit 36 (PPP1R36) and ataxin 2 like (ATXN2L) in three new biological replicates. The knockdown of ATXN2L led to a 22.9% increase in blastocyst development. The second objective of this study was to characterize the parental origin of RNAs present in pre-EGA embryos. Results revealed 472 sperm-derived RNAs, 2575 oocyte-derived RNAs, 2675 RNAs derived from both sperm and oocytes, and 663 embryo-exclusive RNAs. This study uncovers an association of male fertility with developmentally impactful RNAs in 2-4 cell embryos. This study also provides an initial characterization of paternally-contributed RNAs to pre-EGA embryos. Furthermore, a subset of 2-4 cell embryo-specific RNAs was identified.
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Affiliation(s)
- Nicole Gross
- University of Wisconsin, Department of Animal Sciences, Madison, WI, 53706, USA
| | | | | | - Hasan Khatib
- University of Wisconsin, Department of Animal Sciences, Madison, WI, 53706, USA.
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12
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Igoshin AV, Yurchenko AA, Belonogova NM, Petrovsky DV, Aitnazarov RB, Soloshenko VA, Yudin NS, Larkin DM. Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations. BMC Genet 2019; 20:26. [PMID: 30885142 PMCID: PMC6421640 DOI: 10.1186/s12863-019-0725-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Design of new highly productive livestock breeds, well-adapted to local climatic conditions is one of the aims of modern agriculture and breeding. The genetics underlying economically important traits in cattle are widely studied, whereas our knowledge of the genetic mechanisms of adaptation to local environments is still scarce. To address this issue for cold climates we used an integrated approach for detecting genomic intervals related to body temperature maintenance under acute cold stress. Our approach combined genome-wide association studies (GWAS) and scans for signatures of selection applied to a cattle population (Hereford and Kazakh Whiteheaded beef breeds) bred in Siberia. We utilized the GGP HD150K DNA chip containing 139,376 single nucleotide polymorphism markers. Results We detected a single candidate region on cattle chromosome (BTA)15 overlapping between the GWAS results and the results of scans for selective sweeps. This region contains two genes, MSANTD4 and GRIA4. Both genes are functional candidates to contribute to the cold-stress resistance phenotype, due to their indirect involvement in the cold shock response (MSANTD4) and body thermoregulation (GRIA4). Conclusions Our results point to a novel region on BTA15 which is a candidate region associated with the body temperature maintenance phenotype in Siberian cattle. The results of our research and the follow up studies might be used for the development of cattle breeds better adapted to cold climates of the Russian Federation and other Northern countries with similar climates. Electronic supplementary material The online version of this article (10.1186/s12863-019-0725-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander V Igoshin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia
| | - Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia
| | - Nadezhda M Belonogova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia
| | - Dmitry V Petrovsky
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia
| | - Ruslan B Aitnazarov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia
| | | | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia. .,Royal Veterinary College, University of London, London, NW1 0TU, UK.
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13
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Yang Y, Adeola AC, Xie HB, Zhang YP. Genomic and transcriptomic analyses reveal selection of genes for puberty in Bama Xiang pigs. Zool Res 2018; 39:424-430. [PMID: 29955027 PMCID: PMC6085766 DOI: 10.24272/j.issn.2095-8137.2018.068] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The Bama Xiang pig (BMX) is a famous early-maturing Chinese indigenous breed with a two-end black coat. To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and East Asian wild boars and Laiwu pigs, respectively. Genes under positive selection were enriched in pathways associated with gonadal hormone and melanin synthesis, consistent with the phenotypic changes observed during development in BMX pigs. We also performed differentially expressed gene analysis based on RNA-seq data from pituitary tissues of BMX and Large White pigs. The CTTNBP2NL, FRS2, KANK4, and KATNAL1 genes were under selection and exhibited expressional changes in the pituitary tissue, which may affect BMX pig puberty. Our study demonstrated the positive selection of early maturity in the development of BMX pigs and advances our knowledge on the role of regulatory elements in puberty evolution in pigs.
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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 Yunnan 650204, China; E-mails:; .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan 650204, 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 Yunnan 650204, China; E-mails:;
| | - 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 Yunnan 650204, China; E-mails:;
| | - 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 Yunnan 650204, China; E-mails:; .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan 650204, China
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14
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Reverter A, Porto-Neto LR, Fortes MRS, Kasarapu P, de Cara MAR, Burrow HM, Lehnert SA. Genomic inbreeding depression for climatic adaptation of tropical beef cattle1. J Anim Sci 2017. [DOI: 10.2527/jas.2017.1643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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15
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Liu A, Wang Y, Sahana G, Zhang Q, Liu L, Lund MS, Su G. Genome-wide Association Studies for Female Fertility Traits in Chinese and Nordic Holsteins. Sci Rep 2017; 7:8487. [PMID: 28814769 PMCID: PMC5559619 DOI: 10.1038/s41598-017-09170-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/20/2017] [Indexed: 12/18/2022] Open
Abstract
Reduced female fertility could cause considerable economic loss and has become a worldwide problem in the modern dairy industry. The objective of this study was to detect quantitative trait loci (QTL) for female fertility traits in Chinese and Nordic Holsteins using various strategies. First, single-trait association analyses were performed for female fertility traits in Chinese and Nordic Holsteins. Second, the SNPs with P-value < 0.005 discovered in Chinese Holsteins were validated in Nordic Holsteins. Third, the summary statistics from single-trait association analyses were combined into meta-analyses to: (1) identify common QTL for multiple fertility traits within each Holstein population; (2) detect SNPs which were associated with a female fertility trait across two Holstein populations. A large numbers of QTL were discovered or confirmed for female fertility traits. The QTL segregating at 31.4~34.1 Mb on BTA13, 48.3~51.9 Mb on BTA23 and 34.0~37.6 Mb on BTA28 shared between Chinese and Nordic Holsteins were further ascertained using a validation approach and meta-analyses. Furthermore, multiple novel variants identified in Chinese Holsteins were validated with Nordic data as well as meta-analyses. The genes IL6R, SLC39A12, CACNB2, ZEB1, ZMIZ1 and FAM213A were concluded to be strong candidate genes for female fertility in Holsteins.
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Affiliation(s)
- Aoxing Liu
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Yachun Wang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Qin Zhang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lin Liu
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark.
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16
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Parker Gaddis K, Dikmen S, Null D, Cole J, Hansen P. Evaluation of genetic components in traits related to superovulation, in vitro fertilization, and embryo transfer in Holstein cattle. J Dairy Sci 2017; 100:2877-2891. [DOI: 10.3168/jds.2016-11907] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/21/2016] [Indexed: 01/12/2023]
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17
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Brito LF, Kijas JW, Ventura RV, Sargolzaei M, Porto-Neto LR, Cánovas A, Feng Z, Jafarikia M, Schenkel FS. Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers. BMC Genomics 2017; 18:229. [PMID: 28288562 PMCID: PMC5348779 DOI: 10.1186/s12864-017-3610-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 03/07/2017] [Indexed: 01/08/2023] Open
Abstract
Background The detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation. Results The proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean HO and HE was 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures FEH, FVR, FLEUT, FROH and FPED was 0.129, −0.012, −0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis. Conclusions In general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds’ development history. The information reported here will be useful for the implementation of genomic selection and other genomic studies in goats. We also identified various genome regions under positive selection using smoothed FST and hapFLK statistics and suggested genes, which are potentially under selection. These results can now provide a foundation to formulate biological hypotheses related to selection processes in goats. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3610-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luiz F Brito
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.
| | - James W Kijas
- CSIRO Agriculture & Food, Brisbane, Queensland, Australia
| | - Ricardo V Ventura
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Beef Improvement Opportunities, Guelph, Ontario, Canada
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,The Semex Alliance, Guelph, Ontario, Canada
| | | | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Zeny Feng
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada
| | - Mohsen Jafarikia
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Canadian Centre for Swine Improvement Inc., Ottawa, Ontario, Canada
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
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18
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Pinet-Charvet C, Geller S, Desroziers E, Ottogalli M, Lomet D, Georgelin C, Tillet Y, Franceschini I, Vaudin P, Duittoz A. GnRH Episodic Secretion Is Altered by Pharmacological Blockade of Gap Junctions: Possible Involvement of Glial Cells. Endocrinology 2016; 157:304-22. [PMID: 26562259 DOI: 10.1210/en.2015-1437] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Episodic release of GnRH is essential for reproductive function. In vitro studies have established that this episodic release is an endogenous property of GnRH neurons and that GnRH secretory pulses are associated with synchronization of GnRH neuron activity. The cellular mechanisms by which GnRH neurons synchronize remain largely unknown. There is no clear evidence of physical coupling of GnRH neurons through gap junctions to explain episodic synchronization. However, coupling of glial cells through gap junctions has been shown to regulate neuron activity in their microenvironment. The present study investigated whether glial cell communication through gap junctions plays a role in GnRH neuron activity and secretion in the mouse. Our findings show that Glial Fibrillary Acidic Protein-expressing glial cells located in the median eminence in close vicinity to GnRH fibers expressed Gja1 encoding connexin-43. To study the impact of glial-gap junction coupling on GnRH neuron activity, an in vitro model of primary cultures from mouse embryo nasal placodes was used. In this model, GnRH neurons possess a glial microenvironment and were able to release GnRH in an episodic manner. Our findings show that in vitro glial cells forming the microenvironment of GnRH neurons expressed connexin-43 and displayed functional gap junctions. Pharmacological blockade of the gap junctions with 50 μM 18-α-glycyrrhetinic acid decreased GnRH secretion by reducing pulse frequency and amplitude, suppressed neuronal synchronization and drastically reduced spontaneous electrical activity, all these effects were reversed upon 18-α-glycyrrhetinic acid washout.
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Affiliation(s)
- Caroline Pinet-Charvet
- Unité Mixte de Recherche (UMR) 85 Physiologie de la Reproduction et des Comportements (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Institut National de la Recherche Agronomique (INRA); UMR7247 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Centre National de la Recherche Scientifique (CNRS); and Institut Français du Cheval et de l'Equitation (IFCE) (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37380 Nouzilly, France; Physiologie de la Reproduction et des Comportements (PRC) UMR7247 INRA CNRS IFCE (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.) and CNRS UMR7350 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Laboratoire de Mathématiques et Physiques Théoriques, Université François Rabelais, F-37041 Tours, France; Fédération Denis Poisson (C.G.), F-37000 Tours, France; Structure Fédérative de Recherche (SFR) FED4226 Neuro-Imagerie Fonctionnelle (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37044 Tours, France; and Université de Poitiers (C.P.-C.), Unité de Formation et de Recherche (UFR) Pharmacie, F-86000 Poitiers, France
| | - Sarah Geller
- Unité Mixte de Recherche (UMR) 85 Physiologie de la Reproduction et des Comportements (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Institut National de la Recherche Agronomique (INRA); UMR7247 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Centre National de la Recherche Scientifique (CNRS); and Institut Français du Cheval et de l'Equitation (IFCE) (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37380 Nouzilly, France; Physiologie de la Reproduction et des Comportements (PRC) UMR7247 INRA CNRS IFCE (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.) and CNRS UMR7350 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Laboratoire de Mathématiques et Physiques Théoriques, Université François Rabelais, F-37041 Tours, France; Fédération Denis Poisson (C.G.), F-37000 Tours, France; Structure Fédérative de Recherche (SFR) FED4226 Neuro-Imagerie Fonctionnelle (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37044 Tours, France; and Université de Poitiers (C.P.-C.), Unité de Formation et de Recherche (UFR) Pharmacie, F-86000 Poitiers, France
| | - Elodie Desroziers
- Unité Mixte de Recherche (UMR) 85 Physiologie de la Reproduction et des Comportements (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Institut National de la Recherche Agronomique (INRA); UMR7247 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Centre National de la Recherche Scientifique (CNRS); and Institut Français du Cheval et de l'Equitation (IFCE) (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37380 Nouzilly, France; Physiologie de la Reproduction et des Comportements (PRC) UMR7247 INRA CNRS IFCE (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.) and CNRS UMR7350 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Laboratoire de Mathématiques et Physiques Théoriques, Université François Rabelais, F-37041 Tours, France; Fédération Denis Poisson (C.G.), F-37000 Tours, France; Structure Fédérative de Recherche (SFR) FED4226 Neuro-Imagerie Fonctionnelle (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37044 Tours, France; and Université de Poitiers (C.P.-C.), Unité de Formation et de Recherche (UFR) Pharmacie, F-86000 Poitiers, France
| | - Monique Ottogalli
- Unité Mixte de Recherche (UMR) 85 Physiologie de la Reproduction et des Comportements (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Institut National de la Recherche Agronomique (INRA); UMR7247 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Centre National de la Recherche Scientifique (CNRS); and Institut Français du Cheval et de l'Equitation (IFCE) (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37380 Nouzilly, France; Physiologie de la Reproduction et des Comportements (PRC) UMR7247 INRA CNRS IFCE (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.) and CNRS UMR7350 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Laboratoire de Mathématiques et Physiques Théoriques, Université François Rabelais, F-37041 Tours, France; Fédération Denis Poisson (C.G.), F-37000 Tours, France; Structure Fédérative de Recherche (SFR) FED4226 Neuro-Imagerie Fonctionnelle (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37044 Tours, France; and Université de Poitiers (C.P.-C.), Unité de Formation et de Recherche (UFR) Pharmacie, F-86000 Poitiers, France
| | - Didier Lomet
- Unité Mixte de Recherche (UMR) 85 Physiologie de la Reproduction et des Comportements (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Institut National de la Recherche Agronomique (INRA); UMR7247 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Centre National de la Recherche Scientifique (CNRS); and Institut Français du Cheval et de l'Equitation (IFCE) (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37380 Nouzilly, France; Physiologie de la Reproduction et des Comportements (PRC) UMR7247 INRA CNRS IFCE (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.) and CNRS UMR7350 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Laboratoire de Mathématiques et Physiques Théoriques, Université François Rabelais, F-37041 Tours, France; Fédération Denis Poisson (C.G.), F-37000 Tours, France; Structure Fédérative de Recherche (SFR) FED4226 Neuro-Imagerie Fonctionnelle (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37044 Tours, France; and Université de Poitiers (C.P.-C.), Unité de Formation et de Recherche (UFR) Pharmacie, F-86000 Poitiers, France
| | - Christine Georgelin
- Unité Mixte de Recherche (UMR) 85 Physiologie de la Reproduction et des Comportements (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Institut National de la Recherche Agronomique (INRA); UMR7247 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Centre National de la Recherche Scientifique (CNRS); and Institut Français du Cheval et de l'Equitation (IFCE) (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37380 Nouzilly, France; Physiologie de la Reproduction et des Comportements (PRC) UMR7247 INRA CNRS IFCE (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.) and CNRS UMR7350 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Laboratoire de Mathématiques et Physiques Théoriques, Université François Rabelais, F-37041 Tours, France; Fédération Denis Poisson (C.G.), F-37000 Tours, France; Structure Fédérative de Recherche (SFR) FED4226 Neuro-Imagerie Fonctionnelle (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37044 Tours, France; and Université de Poitiers (C.P.-C.), Unité de Formation et de Recherche (UFR) Pharmacie, F-86000 Poitiers, France
| | - Yves Tillet
- Unité Mixte de Recherche (UMR) 85 Physiologie de la Reproduction et des Comportements (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Institut National de la Recherche Agronomique (INRA); UMR7247 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Centre National de la Recherche Scientifique (CNRS); and Institut Français du Cheval et de l'Equitation (IFCE) (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37380 Nouzilly, France; Physiologie de la Reproduction et des Comportements (PRC) UMR7247 INRA CNRS IFCE (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.) and CNRS UMR7350 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Laboratoire de Mathématiques et Physiques Théoriques, Université François Rabelais, F-37041 Tours, France; Fédération Denis Poisson (C.G.), F-37000 Tours, France; Structure Fédérative de Recherche (SFR) FED4226 Neuro-Imagerie Fonctionnelle (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37044 Tours, France; and Université de Poitiers (C.P.-C.), Unité de Formation et de Recherche (UFR) Pharmacie, F-86000 Poitiers, France
| | - Isabelle Franceschini
- Unité Mixte de Recherche (UMR) 85 Physiologie de la Reproduction et des Comportements (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Institut National de la Recherche Agronomique (INRA); UMR7247 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Centre National de la Recherche Scientifique (CNRS); and Institut Français du Cheval et de l'Equitation (IFCE) (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37380 Nouzilly, France; Physiologie de la Reproduction et des Comportements (PRC) UMR7247 INRA CNRS IFCE (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.) and CNRS UMR7350 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Laboratoire de Mathématiques et Physiques Théoriques, Université François Rabelais, F-37041 Tours, France; Fédération Denis Poisson (C.G.), F-37000 Tours, France; Structure Fédérative de Recherche (SFR) FED4226 Neuro-Imagerie Fonctionnelle (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37044 Tours, France; and Université de Poitiers (C.P.-C.), Unité de Formation et de Recherche (UFR) Pharmacie, F-86000 Poitiers, France
| | - Pascal Vaudin
- Unité Mixte de Recherche (UMR) 85 Physiologie de la Reproduction et des Comportements (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Institut National de la Recherche Agronomique (INRA); UMR7247 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Centre National de la Recherche Scientifique (CNRS); and Institut Français du Cheval et de l'Equitation (IFCE) (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37380 Nouzilly, France; Physiologie de la Reproduction et des Comportements (PRC) UMR7247 INRA CNRS IFCE (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.) and CNRS UMR7350 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Laboratoire de Mathématiques et Physiques Théoriques, Université François Rabelais, F-37041 Tours, France; Fédération Denis Poisson (C.G.), F-37000 Tours, France; Structure Fédérative de Recherche (SFR) FED4226 Neuro-Imagerie Fonctionnelle (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37044 Tours, France; and Université de Poitiers (C.P.-C.), Unité de Formation et de Recherche (UFR) Pharmacie, F-86000 Poitiers, France
| | - Anne Duittoz
- Unité Mixte de Recherche (UMR) 85 Physiologie de la Reproduction et des Comportements (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Institut National de la Recherche Agronomique (INRA); UMR7247 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Centre National de la Recherche Scientifique (CNRS); and Institut Français du Cheval et de l'Equitation (IFCE) (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37380 Nouzilly, France; Physiologie de la Reproduction et des Comportements (PRC) UMR7247 INRA CNRS IFCE (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.) and CNRS UMR7350 (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), Laboratoire de Mathématiques et Physiques Théoriques, Université François Rabelais, F-37041 Tours, France; Fédération Denis Poisson (C.G.), F-37000 Tours, France; Structure Fédérative de Recherche (SFR) FED4226 Neuro-Imagerie Fonctionnelle (C.P.-C., S.G., E.D., M.O., D.L., Y.T., I.F., P.V., A.D.), F-37044 Tours, France; and Université de Poitiers (C.P.-C.), Unité de Formation et de Recherche (UFR) Pharmacie, F-86000 Poitiers, France
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Sasaki S, Ibi T, Matsuhashi T, Takeda K, Ikeda S, Sugimoto M, Sugimoto Y. Genetic variants in the upstream region of activin receptor IIA are associated with female fertility in Japanese Black cattle. BMC Genet 2015; 16:123. [PMID: 26486459 PMCID: PMC4618343 DOI: 10.1186/s12863-015-0282-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 10/16/2015] [Indexed: 12/24/2022] Open
Abstract
Background Female fertility, a fundamental trait required for animal reproduction, has gradually declined in the last 2 decades in Japanese Black cattle. To identify associated genetic variants in Japanese Black cattle, we evaluated female fertility as a metric to describe the average inverse of the number of artificial inseminations required for conception from the first through the fourth parity (ANAI4) and conducted a genome-wide association study (GWAS) using 430 animals with extreme ANAI4 values from 10,399 animals. Results We found that 2 variants, namely a single-nucleotide polymorphisms (SNP; g.48476925C > T) and a 3-bp indel (g.48476943_48476946insGGC), in the upstream region of the activin receptor IIA gene (ACVR2A) were associated with ANAI4. ACVR2A transcripts from Japanese Black cattle of the Q haplotype, defined by the SNP and the 3-bp indel, with increased ANAI4 were 1.29–1.32-fold more abundant than q-derived transcripts. In agreement, reporter assay results revealed that the activity of the ACVR2A promoter was higher in reporter constructs with the Q haplotype than in those with the q haplotype by approximately 1.2 fold. Expression of exogenous ACVR2A induced dose-dependent increases of reporter activity from the follicle-stimulating hormone, beta polypeptide (FSHB) promoter in response to activin A in a pituitary gonadotrophic cell line. The findings suggested that sequence variations in the upstream region of ACVR2A with the Q haplotype increased ACVR2A transcription, which in turn induced FSHB expression. This association was replicated using a sample population size of 1,433 animals; the frequency of the Q haplotype was 0.39, and Q-to-q haplotype substitution resulted in an increase of 0.02 in terms of ANAI4. Conclusions This GWAS identified variants in the upstream region of ACVR2A, which were associated with female fertility in Japanese Black cattle. The variants affected the level of ACVR2A mRNA expression, which could lead to an allelic imbalance. This association was replicated with a sample population of 1,433 animals. Thus, the results suggest that the Q haplotype could serve as a useful marker to select Japanese Black cattle with superior female fertility. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0282-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shinji Sasaki
- National Livestock Breeding Center, Odakura, Nishigo, Fukushima, 961-8511, Japan.
| | - Takayuki Ibi
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan.
| | - Tamako Matsuhashi
- Gifu Prefectural Livestock Research Institute, Kiyomi, Takayama, Gifu, 506-0101, Japan.
| | - Kenji Takeda
- Gifu Prefectural Livestock Research Institute, Kiyomi, Takayama, Gifu, 506-0101, Japan.
| | - Shogo Ikeda
- Cattle Breeding Development Institute of Kagoshima Prefecture, Osumi, So, Kagoshima, 899-8212, Japan.
| | - Mayumi Sugimoto
- National Livestock Breeding Center, Odakura, Nishigo, Fukushima, 961-8511, Japan.
| | - Yoshikazu Sugimoto
- Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Odakura, Nishigo, Fukushima, 961-8061, Japan.
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Sharma A, Lee JS, Dang CG, Sudrajad P, Kim HC, Yeon SH, Kang HS, Lee SH. Stories and Challenges of Genome Wide Association Studies in Livestock - A Review. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1371-9. [PMID: 26194229 PMCID: PMC4554843 DOI: 10.5713/ajas.14.0715] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/09/2014] [Accepted: 01/30/2015] [Indexed: 11/27/2022]
Abstract
Undoubtedly livestock is one of the major contributors to the economy of any country. The economic value of livestock includes meat, dairy products, fiber, fertilizer etc. Understanding and identifying the associations of quantitative trait loci (QTL) with the economically important traits is believed to substantially benefit the livestock industry. The past two decades have seen a flurry of interest in mapping the QTL associated with traits of economic importance on the genome. With the availability of single nucleotide polymorphism chip of various densities it is possible to identify regions, QTL and genes on the genome that explain the association and its effect on the phenotype under consideration. Remarkable advancement has been seen in genome wide association studies (GWAS) since its inception till the present day. In this review we describe the progress and challenges of GWAS in various livestock species.
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Affiliation(s)
- Aditi Sharma
- Corresponding Authors: Aditi Sharma. Tel: +82-33-330-0600 (719), E-mail: / Seung-Hwan Lee. Tel: +82-033-330-0600 (717), E-mail:
| | | | | | | | | | | | | | - Seung-Hwan Lee
- Department of Animal Science and Biotechnology, Chung Nam National University, Daejeon 305-764,
Korea
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Molecular Effects of Polymorphism in the 3'UTR of Unc-5 homolog C Associated with Conception Rate in Holsteins. PLoS One 2015; 10:e0131283. [PMID: 26147436 PMCID: PMC4493121 DOI: 10.1371/journal.pone.0131283] [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: 10/05/2014] [Accepted: 06/01/2015] [Indexed: 11/20/2022] Open
Abstract
Conception rates among dairy cows in Japan have declined in recent decades. To enhance our understanding of the genes involved in conception rates, we conducted a genome-wide association study (GWAS) using 822 Holsteins and identified a single-nucleotide polymorphism (SNP) associated with conception rate: A+169G in the 3’ untranslated region (UTR) of unc-5 homolog C (UNC5C). Cows with higher conception rates carried the A polymorphism in the UNC5C 3’UTR. Luciferase assays and quantitative analysis of allele ratios revealed that UNC5C transcripts with the A polymorphism were expressed at higher levels than those carrying the G polymorphism. UNC5C transmits either pro- or anti-apoptotic signals depending on the availability of its ligand, Netrin-1. UNC5C expression is negatively regulated by reproductive homeobox X-linked 5 (Rhox5), and the Rhox5 locus is methylated by G9a methyltransferase. G9a-knockout mice have previously been demonstrated to be subfertile, and we found that UNC5C, G9a, and Netrin-1 expression levels increased from the 4-cell stage to the blastocyst stage in fertilized murine embryos, whereas Rhox5 expression decreased. Repression of UNC5C, G9a, or Netrin-1 or forced expression of Rhox5 in the anterior nucleus stage inhibited development to the blastocyst stage, suggesting that cows carrying the G polymorphism in UNC5C might have lower conception rates because of the poor development of preimplantation embryos. This study provides novel insights into the role of UNC5C during embryonic development.
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Serrano-Velez JL, Rodriguez-Alvarado M, Torres-Vazquez II, Fraser SE, Yasumura T, Vanderpool KG, Rash JE, Rosa-Molinar E. Abundance of gap junctions at glutamatergic mixed synapses in adult Mosquitofish spinal cord neurons. Front Neural Circuits 2014; 8:66. [PMID: 25018700 PMCID: PMC4072101 DOI: 10.3389/fncir.2014.00066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 05/28/2014] [Indexed: 11/13/2022] Open
Abstract
"Dye-coupling", whole-mount immunohistochemistry for gap junction channel protein connexin 35 (Cx35), and freeze-fracture replica immunogold labeling (FRIL) reveal an abundance of electrical synapses/gap junctions at glutamatergic mixed synapses in the 14th spinal segment that innervates the adult male gonopodium of Western Mosquitofish, Gambusia affinis (Mosquitofish). To study gap junctions' role in fast motor behavior, we used a minimally-invasive neural-tract-tracing technique to introduce gap junction-permeant or -impermeant dyes into deep muscles controlling the gonopodium of the adult male Mosquitofish, a teleost fish that rapidly transfers (complete in <20 mS) spermatozeugmata into the female reproductive tract. Dye-coupling in the 14th spinal segment controlling the gonopodium reveals coupling between motor neurons and a commissural primary ascending interneuron (CoPA IN) and shows that the 14th segment has an extensive and elaborate dendritic arbor and more gap junctions than do other segments. Whole-mount immunohistochemistry for Cx35 results confirm dye-coupling and show it occurs via gap junctions. Finally, FRIL shows that gap junctions are at mixed synapses and reveals that >50 of the 62 gap junctions at mixed synapses are in the 14th spinal segment. Our results support and extend studies showing gap junctions at mixed synapses in spinal cord segments involved in control of genital reflexes in rodents, and they suggest a link between mixed synapses and fast motor behavior. The findings provide a basis for studies of specific roles of spinal neurons in the generation/regulation of sex-specific behavior and for studies of gap junctions' role in regulating fast motor behavior. Finally, the CoPA IN provides a novel candidate neuron for future studies of gap junctions and neural control of fast motor behaviors.
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Affiliation(s)
| | | | | | - Scott E Fraser
- Molecular and Computational Biology Section, University of Southern California Los Angeles, CA, USA
| | - Thomas Yasumura
- Department of Biomedical Sciences, Colorado State University Fort Collins, CO, USA
| | | | - John E Rash
- Department of Biomedical Sciences, Colorado State University Fort Collins, CO, USA ; Program in Molecular, Cellular and Integrative Neurosciences, Colorado State University Fort Collins, CO, USA
| | - Eduardo Rosa-Molinar
- Biological Imaging Group, University of Puerto Rico San Juan, PR, USA ; Institute of Neurobiology, School of Medicine, University of Puerto Rico San Juan, PR, USA
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