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Lee Y, Shim J, Ko N, Kim HJ, Kim JH, Kim H, Choi K. Docosahexaenoic acid supplementation during porcine oocyte in vitro maturation improves oocyte quality and embryonic development by enhancing the homeostasis of energy metabolism. Theriogenology 2024; 227:49-59. [PMID: 39013287 DOI: 10.1016/j.theriogenology.2024.07.002] [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: 02/25/2024] [Revised: 06/11/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
Although supplementation with docosahexaenoic acid (DHA) during porcine oocyte IVM is well-established, the available data are limited due to the lack of consistency. Moreover, to our knowledge, the anti-oxidant effects of DHA on porcine oocytes have not been reported. Hence, this study aimed to examine the effects of DHA supplementation on the regulation of energy metabolism during porcine oocyte maturation to improve oocyte maturation and embryonic development. By supplementing the IVM medium with various DHA concentrations, 25 μM DHA was identified as the optimal concentration which improved intraoocyte glutathione content and enhanced embryonic development after parthenogenesis. Compared to embryos derived from the control group, those derived from SCNT or IVF showed significantly improved blastocyst formation upon DHA supplementation during IVM. In addition, various transcription factors associated with oocyte development and apoptosis in mature oocytes were beneficially regulated in the DHA-treated oocytes. Moreover, DHA improved the AMP-activated protein kinase (AMPK)-regulatory ability of porcine oocytes and ameliorated nuclear maturation and embryonic development, which were decreased by artificially downregulating AMPK. To our knowledge, this is the first study to examine the effects of DHA as an AMPK regulator on oocyte maturation and embryo development in pigs. Furthermore, DHA addition to the IVM medium upregulated the relative expression of genes associated with mitochondrial potential and lipid metabolism. Therefore, the membrane potential of mitochondria (evaluated based on the JC-1 aggregate/JC-1 monomer ratio) and the levels of fatty acids and lipid droplets in matured oocytes increased, resulting in increased ATP synthesis. In conclusion, the DHA treatment of porcine oocytes with 25 μM DHA during IVM enhances the homeostasis of energy metabolism by improving mitochondrial function and lipid metabolism, leading to improved quality of matured oocytes and enhanced embryonic developmental potential of in vitro produced (IVP) embryos. Thus, 25 μM DHA supplementation could serve as a tool for improving the quality of IVP embryos. The study findings provide a basis for further research on improving the production efficiency of cloned animals by securing high-quality matured oocytes and enhancing energy metabolism in mammalian oocytes, including those of pigs.
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Affiliation(s)
- Yongjin Lee
- Optipharm Inc., 63, Osongsaengmyeong 6-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28158, Republic of Korea
| | - Joohyun Shim
- Optipharm Inc., 63, Osongsaengmyeong 6-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28158, Republic of Korea
| | - Nayoung Ko
- Optipharm Inc., 63, Osongsaengmyeong 6-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28158, Republic of Korea
| | - Hyoung-Joo Kim
- Optipharm Inc., 63, Osongsaengmyeong 6-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28158, Republic of Korea
| | - Jun-Hyeong Kim
- Optipharm Inc., 63, Osongsaengmyeong 6-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28158, Republic of Korea
| | - Hyunil Kim
- Optipharm Inc., 63, Osongsaengmyeong 6-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28158, Republic of Korea
| | - Kimyung Choi
- Optipharm Inc., 63, Osongsaengmyeong 6-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 28158, Republic of Korea.
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Kim EH, Kim GA, Taweechaipaisankul A, Ridlo MR, Lee SH, Ra K, Ahn C, Lee BC. Phytanic acid-derived peroxisomal lipid metabolism in porcine oocytes. Theriogenology 2020; 157:276-285. [PMID: 32823023 DOI: 10.1016/j.theriogenology.2020.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022]
Abstract
Lipid metabolism plays an important role in oocyte maturation. The peroxisome is the fundamental mediator for this mechanism. In this study, we investigated the peroxisomal lipid metabolism in porcine oocytes. Phytanic acid (PA) was chosen as an activator of alpha-oxidation in peroxisomes. Oocyte maturation, embryo development, immunocytochemistry of peroxisomal lipid activities, and staining of mitochondrial potentials were assessed. We found that 40 μM PA not only increased porcine oocyte maturation and embryonic development, but also upregulated the expression of genes and proteins related to activities of the peroxisomal lipid metabolism (PHYH, PEX19, and PEX subfamilies) and mitochondrial potentials (NRF1 and PGC1α). Moreover, PA upregulated the lipid droplet and fatty acid content in the oocytes. Moreover, mitochondria were activated and the mitochondrial membrane potential was increased after PA treatment, resulting in the production of more ATPs in the oocytes. Our findings suggest that the degradation of PA via alpha-oxidation in the peroxisome may potentiate oocyte maturation processes, peroxisomal lipid oxidation, and mitochondria activities.
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Affiliation(s)
- Eui Hyun Kim
- Department of Theriogenology and Biotechnology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Geon A Kim
- Department of Theriogenology and Biotechnology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea; Department of Biomedical Laboratory Science, School of Medicine, Eulji University, Daejeon, Republic of Korea
| | - Anukul Taweechaipaisankul
- Department of Theriogenology and Biotechnology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Muhammad Rosyid Ridlo
- Department of Theriogenology and Biotechnology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea; Department of Bioresource Technology and Veterinary, Vocational College, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Seok Hee Lee
- Department of Theriogenology and Biotechnology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Kihae Ra
- Department of Theriogenology and Biotechnology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Curie Ahn
- Division of Nephrology, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Byeong Chun Lee
- Department of Theriogenology and Biotechnology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
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Khan R, Raza SHA, Schreurs N, Xiaoyu W, Hongbao W, Ullah I, Rahman A, Suhail SM, Khan S, Linsen Z. Bioinformatics analysis and transcriptional regulation of TORC1 gene through transcription factors NRF1 and Smad3 in bovine preadipocytes. Genomics 2020; 112:1575-1587. [DOI: 10.1016/j.ygeno.2019.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/23/2019] [Accepted: 09/11/2019] [Indexed: 12/25/2022]
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Function and Transcriptional Regulation of Bovine TORC2 Gene in Adipocytes: Roles of C/EBP, XBP1, INSM1 and ZNF263. Int J Mol Sci 2019; 20:ijms20184338. [PMID: 31487963 PMCID: PMC6769628 DOI: 10.3390/ijms20184338] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/01/2019] [Accepted: 09/01/2019] [Indexed: 12/25/2022] Open
Abstract
The TORC2 gene is a member of the transducer of the regulated cyclic adenosine monophosphate (cAMP) response element binding protein gene family, which plays a key role in metabolism and adipogenesis. In the present study, we confirmed the role of TORC2 in bovine preadipocyte proliferation through cell cycle staining flow cytometry, cell counting assay, 5-ethynyl-2′-deoxyuridine staining (EdU), and mRNA and protein expression analysis of proliferation-related marker genes. In addition, Oil red O staining analysis, immunofluorescence of adiponectin, mRNA and protein level expression of lipid related marker genes confirmed the role of TORC2 in the regulation of bovine adipocyte differentiation. Furthermore, the transcription start site and sub-cellular localization of the TORC2 gene was identified in bovine adipocytes. To investigate the underlying regulatory mechanism of the bovine TORC2, we cloned a 1990 bp of the 5’ untranslated region (5′UTR) promoter region into a luciferase reporter vector and seven vector fragments were constructed through serial deletion of the 5′UTR flanking region. The core promoter region of the TORC2 gene was identified at location −314 to −69 bp upstream of the transcription start site. Based on the results of the transcriptional activities of the promoter vector fragments, luciferase activities of mutated fragments and siRNAs interference, four transcription factors (CCAAT/enhancer-binding protein C/BEPγ, X-box binding protein 1 XBP1, Insulinoma-associated 1 INSM1, and Zinc finger protein 263 ZNF263) were identified as the transcriptional regulators of TORC2 gene. These findings were further confirmed through Electrophoretic Mobility Shift Assay (EMSA) within nuclear extracts of bovine adipocytes. Furthermore, we also identified that C/EBPγ, XBP1, INSM1 and ZNF263 regulate TORC2 gene as activators in the promoter region. We can conclude that TORC2 gene is potentially a positive regulator of adipogenesis. These findings will not only provide an insight for the improvement of intramuscular fat in cattle, but will enhance our understanding regarding therapeutic intervention of metabolic syndrome and obesity in public health as well.
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Cloning and Expression Levels of TFAM and TFB2M Genes and their Correlation with Meat and Carcass Quality Traits in Jiaxing Black Pig. ANNALS OF ANIMAL SCIENCE 2019. [DOI: 10.2478/aoas-2018-0056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
The coding sequences (CDS) of TFAM and TFB2M genes from Jiaxing Black Pig (JBP) were first obtained by RT-PCR and DNA-seq in the present study. Sequence analyses showed that the TFAM gene contains a 741-bp CDS region encoding 246 amino acids sharing a 100% homology with the sequence on NCBI, while TFB2M gene contains a CDS region of 1176 bp encoding 391 amino acids with two missense mutations. The results of quantitative Real-Time PCR for TFAM and TFB2M revealed that transcripts of the genes were both presented at the highest levels in spleen tissue followed by liver tissue, while the least levels in longissimus dorsi muscle (LDM), and obviously the higher levels in two adipose tissues than those in LDM tissue (P<0.01). Meanwhile, a total of forty-two JBPs were employed in this experiment to investigate the effect of these two genes on the carcass, meat quality traits and flavor substances such as fatty acids, intramuscular fat (IMF) in LDM. As expected, some strong correlations of gene expression abundance of TFAM and TFB2M mRNA in particular tissues such as liver and LDM with carcass and meat quality traits including marbling score, as well as the content of saturated fatty acid (SFA), in JBP were found.
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Pirih N, Kunej T. An Updated Taxonomy and a Graphical Summary Tool for Optimal Classification and Comprehension of Omics Research. ACTA ACUST UNITED AC 2018; 22:337-353. [DOI: 10.1089/omi.2017.0186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Nina Pirih
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
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Raza SHA, Gui L, Khan R, Schreurs NM, Xiaoyu W, Wu S, Mei C, Wang L, Ma X, Wei D, Guo H, Zhang S, Wang X, Kaleri HA, Zan L. Association between FASN gene polymorphisms ultrasound carcass traits and intramuscular fat in Qinchuan cattle. Gene 2017; 645:55-59. [PMID: 29273553 DOI: 10.1016/j.gene.2017.12.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/05/2017] [Accepted: 12/18/2017] [Indexed: 11/18/2022]
Abstract
Fatty acid synthase (FASN) is an enzyme involved with fat deposition and fatty acid composition in cattle. This study was conducted to detect single nucleotide polymorphisms (SNPs) of the FASN gene and explore their relationships with ultrasound carcass traits in order to assess the potential use of the FASN gene for the breeding selection of Qinchuan cattle for desirable carcass traits. The frequencies of SNP g.12740C>T, g.13192T>C and g.13232C>T were identified in 525 individual Qinchuan cattle which were also assessed for backfat depth, eye muscle area and intramuscular fat by ultrasound. According to the PIC values, g.13192T>C possessed an intermediate polymorphism (0.25<PIC<0.5). The SNPs of g.13232C>T, g.12740C>T possessed low polymorphism (PIC<0.25). Chi-square tests showed that g.13192T>C were in Hardy-Weinberg disequilibrium (c2<c0.052). Two SNPs were found to be associated with variation in ultrasound carcass traits. The H2H2 diplotypes had a greater back fat depth than H1H1, H1H4 and H1H2 (P<0.01). The TT genotype at g.13192T>C was associated with a greater eye muscle area and the TT genotype at g.13232C>T was associated with greater intramuscular fat. When these genotypes were combined there was no difference in eye muscle area and intramuscular fat between the diplotypes. The H2H2 diplotype was associated with carcass traits that are likely to provide economic advantage in Qinchuan cattle. Variations in the FASN genes and their corresponding genotypes may be considered as molecular markers for economic traits in cattle breeding.
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Affiliation(s)
- Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; National Beef Cattle Improvement Center of Northwest A&F University, Yangling 712100, PR China
| | - Linsheng Gui
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai 810016, People's Republic of China
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Nicola M Schreurs
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Wang Xiaoyu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Sen Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Li Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xueyao Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Dawei Wei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Hongfang Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Song Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xingping Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Hubdar Ali Kaleri
- Department of Animal Science and Aquaculture, Dalhousie University, Canada
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; National Beef Cattle Improvement Center of Northwest A&F University, Yangling 712100, PR China.
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Jin JX, Lee S, Taweechaipaisankul A, Kim GA, Lee BC. Melatonin regulates lipid metabolism in porcine oocytes. J Pineal Res 2017; 62. [PMID: 28095627 DOI: 10.1111/jpi.12388] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/11/2017] [Indexed: 12/22/2022]
Abstract
It is being increasingly recognized that the processes of lipogenesis and lipolysis are important for providing an essential energy source during oocyte maturation and embryo development. Recent studies demonstrated that melatonin has a role in lipid metabolism regulation, including lipogenesis, lipolysis, and mitochondrial biogenesis. In this study, we attempted to investigate the effects of melatonin on lipid metabolism during porcine oocyte in vitro maturation. Melatonin treatment significantly enhanced the number of lipid droplets (LDs) and upregulated gene expression related to lipogenesis (ACACA, FASN, PPARγ, and SREBF1). Oocytes treated with melatonin formed smaller LDs and abundantly expressed several genes associated with lipolysis, including ATGL, CGI-58, HSL, and PLIN2. Moreover, melatonin significantly increased the content of fatty acids, mitochondria, and ATP, as indicated by fluorescent staining. Concomitantly, melatonin treatment upregulated gene expression related to fatty acid β-oxidation (CPT1a, CPT1b, CPT2, and ACADS) and mitochondrial biogenesis (PGC-1α, TFAM, and PRDX2). Overall, melatonin treatment not only altered both the morphology and amount of LDs, but also increased the content of fatty acids, mitochondria, and ATP. In addition, melatonin upregulated mRNA expression levels of lipogenesis, lipolysis, β-oxidation, and mitochondrial biogenesis-related genes in porcine oocytes. These results indicated that melatonin promoted lipid metabolism and thereby provided an essential energy source for oocyte maturation and subsequent embryonic development.
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Affiliation(s)
- Jun-Xue Jin
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Sanghoon Lee
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Anukul Taweechaipaisankul
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Geon A Kim
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Byeong Chun Lee
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Institutes of Green Bio Science and Technology, Seoul National University, Seoul, Korea
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Granados JB, Méndez JP, Feria-Bernal G, García-García E, Tejeda ME, Rojano-Mejía D, Tapia A, Canto P. Association of a TFAM haplotype with aggressive prostate cancer in overweight or obese Mexican Mestizo men. Urol Oncol 2017; 35:111.e9-111.e14. [DOI: 10.1016/j.urolonc.2016.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 10/10/2016] [Accepted: 10/11/2016] [Indexed: 01/05/2023]
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Association study and expression analysis of MTNR1A as a candidate gene for body measurement and meat quality traits in Qinchuan cattle. Gene 2015; 570:199-204. [DOI: 10.1016/j.gene.2015.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/29/2015] [Accepted: 06/05/2015] [Indexed: 11/23/2022]
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11
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Yamada T. Genetic dissection of marbling trait through integration of mapping and expression profiling. Anim Sci J 2014; 85:349-55. [DOI: 10.1111/asj.12179] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/19/2013] [Indexed: 01/28/2023]
Affiliation(s)
- Takahisa Yamada
- Department of Agrobiology, Faculty of Agriculture; Niigata University; Niigata Japan
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12
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Tang C, Liu H, Tang Y, Guo Y, Liang X, Guo L, Pi R, Yang J. Analysis of mitochondrial transcription factor A SNPs in alcoholic cirrhosis. Exp Ther Med 2013; 7:73-79. [PMID: 24348767 PMCID: PMC3861118 DOI: 10.3892/etm.2013.1353] [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: 06/06/2013] [Accepted: 10/04/2013] [Indexed: 11/13/2022] Open
Abstract
Genetic susceptibility to alcoholic cirrhosis (AC) exists. We previously demonstrated hepatic mitochondrial DNA (mtDNA) damage in patients with AC compared with chronic alcoholics without cirrhosis. Mitochondrial transcription factor A (mtTFA) is central to mtDNA expression regulation and repair; however, it is unclear whether there are specific mtTFA single nucleotide polymorphisms (SNPs) in patients with AC and whether they affect mtDNA repair. In the present study, we screened mtTFA SNPs in patients with AC and analyzed their impact on the copy number of mtDNA in AC. A total of 50 patients with AC, 50 alcoholics without AC and 50 normal subjects were enrolled in the study. SNPs of full-length mtTFA were analyzed using the polymerase chain reaction (PCR) combined with gene sequencing. The hepatic mtTFA mRNA and mtDNA copy numbers were measured using quantitative PCR (qPCR), and mtTFA protein was measured using western blot analysis. A total of 18 mtTFA SNPs specific to patients with AC with frequencies >10% were identified. Two were located in the coding region and 16 were identified in non-coding regions. Conversely, there were five SNPs that were only present in patients with AC and normal subjects and had a frequency >10%. In the AC group, the hepatic mtTFA mRNA and protein levels were significantly lower than those in the other two groups. Moreover, the hepatic mtDNA copy number was significantly lower in the AC group than in the controls and alcoholics without AC. Based on these data, we conclude that AC-specific mtTFA SNPs may be responsible for the observed reductions in mtTFA mRNA, protein levels and mtDNA copy number and they may also increase the susceptibility to AC.
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Affiliation(s)
- Chun Tang
- Department of Hepatobiliary Surgery, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing 400042, P.R. China
| | - Hongming Liu
- Department of Hepatobiliary Surgery, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing 400042, P.R. China
| | - Yongliang Tang
- Department of Hepatobiliary Surgery, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing 400042, P.R. China
| | - Yong Guo
- Department of Hepatobiliary Surgery, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing 400042, P.R. China
| | - Xianchun Liang
- Department of Hepatobiliary Surgery, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing 400042, P.R. China
| | - Liping Guo
- Department of Hepatobiliary Surgery, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing 400042, P.R. China
| | - Ruxian Pi
- Department of Hepatobiliary Surgery, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing 400042, P.R. China
| | - Juntao Yang
- Department of Hepatobiliary Surgery, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing 400042, P.R. China
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Kunej T, Jevsinek Skok D, Zorc M, Ogrinc A, Michal JJ, Kovac M, Jiang Z. Obesity gene atlas in mammals. J Genomics 2013; 1:45-55. [PMID: 25031655 PMCID: PMC4091431 DOI: 10.7150/jgen.3996] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Obesity in humans has increased at an alarming rate over the past two decades and has become one of the leading public health problems worldwide. Studies have revealed a large number of genes/markers that are associated with obesity and/or obesity-related phenotypes, indicating an urgent need to develop a central database for helping the community understand the genetic complexity of obesity. In the present study, we collected a total of 1,736 obesity associated loci and created a freely available obesity database, including 1,515 protein-coding genes and 221 microRNAs (miRNAs) collected from four mammalian species: human, cattle, rat, and mouse. These loci were integrated as orthologs on comparative genomic views in human, cattle, and mouse. The database and genomic views are freely available online at: http://www.integratomics-time.com/fat_deposition. Bioinformatics analyses of the collected data revealed some potential novel obesity related molecular markers which represent focal points for testing more targeted hypotheses and designing experiments for further studies. We believe that this centralized database on obesity and adipogenesis will facilitate development of comparative systems biology approaches to address this important health issue in human and their potential applications in animals.
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Affiliation(s)
- Tanja Kunej
- 1. Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Dasa Jevsinek Skok
- 1. Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Minja Zorc
- 1. Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia; ; 2. Centre for Mathematical and Computational Biology, Rothamsted Research, Harpenden, Herts, AL5, 2JQ, UK
| | - Ana Ogrinc
- 1. Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Jennifer J Michal
- 3. Department of Animal Sciences, Washington State University, Pullman, Washington 99164-6351, USA
| | - Milena Kovac
- 1. Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Zhihua Jiang
- 3. Department of Animal Sciences, Washington State University, Pullman, Washington 99164-6351, USA
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Liu Y, Zan L, Li L, Xin Y. Proopiomelanocortin gene polymorphisms and its association with meat quality traits by ultrasound measurement in Chinese cattle. Gene X 2013; 529:138-43. [DOI: 10.1016/j.gene.2013.06.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 11/15/2022] Open
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15
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Wathes DC, Clempson AM, Pollott GE. Associations between lipid metabolism and fertility in the dairy cow. Reprod Fertil Dev 2013; 25:48-61. [PMID: 23244828 DOI: 10.1071/rd12272] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Dairy cows mobilise body tissues to support milk production and, because glucose supplies are limited, lipids are used preferentially for energy production. Lipogenic activity is switched off and lipolytic mechanisms in adipose tissue increase through changes in the expression of several key enzymes. This results in a loss of body condition, together with high circulating concentrations of non-esterified fatty acids. Changes in the synthesis, secretion and signalling pathways of somatotrophic hormones (insulin, growth hormone, insulin-like growth factor 1) and adipokines (e.g. leptin) are central to the regulation of these processes. A high reliance on fatty acids as an energy source in the peripartum period causes oxidative damage to mitochondria in metabolically active tissues, including the liver and reproductive tract. The expression of genes involved in insulin resistance (PDK4, AHSG) is increased, together with expression of TIEG1, a transcription factor that can induce apoptosis via the mitochondrial pathway. Polymorphisms in TFAM and UCP2, two autosomal mitochondrial genes, have been associated with longevity in dairy cows. Polymorphisms in many other genes that affect lipid metabolism also show some associations with fertility traits. These include DGAT1, SCD1, DECR1, CRH, CBFA2T1, GH, LEP and NPY. Excess lipid accumulation in oocytes and the regenerating endometrium reduces fertility via reductions in embryo survival and increased inflammatory changes, respectively.
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Affiliation(s)
- D Claire Wathes
- Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Herts AL9 7TA, UK.
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16
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Wathes DC. Mechanisms Linking Metabolic Status and Disease with Reproductive Outcome in the Dairy Cow. Reprod Domest Anim 2012; 47 Suppl 4:304-12. [DOI: 10.1111/j.1439-0531.2012.02090.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Shin SC, Heo JP, Chung ER. Genetic variants of the FABP4 gene are associated with marbling scores and meat quality grades in Hanwoo (Korean cattle). Mol Biol Rep 2011; 39:5323-30. [DOI: 10.1007/s11033-011-1331-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 12/03/2011] [Indexed: 12/16/2022]
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18
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Polymorphisms in the autosomal genes for mitochondrial function TFAM and UCP2 are associated with performance and longevity in dairy cows. Animal 2011; 5:1335-43. [DOI: 10.1017/s1751731111000346] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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19
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Daniels TF, Wu XL, Pan Z, Michal JJ, Wright RW, Killinger KM, MacNeil MD, Jiang Z. The reverse cholesterol transport pathway improves understanding of genetic networks for fat deposition and muscle growth in beef cattle. PLoS One 2010; 5:e15203. [PMID: 21151936 PMCID: PMC2997077 DOI: 10.1371/journal.pone.0015203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 11/01/2010] [Indexed: 01/23/2023] Open
Abstract
In the present study, thirteen genes involved in the reverse cholesterol transport (RCT) pathway were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population, including 6 F1 bulls, 113 F1 dams, and 246 F2 progeny. A total of 37 amplicons were used to screen single nucleotide polymorphisms (SNPs) on 6 F1 bulls. Among 36 SNPs detected in 11 of these 13 genes, 19 were selected for genotyping by the Sequenom assay design on all F2 progeny. Single-marker analysis revealed seven SNPs in ATP binding cassette A1, apolipoproteins A1, B and E, phospholipid transfer protein and paraoxinase 1 genes significantly associated with nine phenotypes (P<0.05). Previously, we reported genetic networks associated with 19 complex phenotypes based on a total of 138 genetic polymorphisms derived from 71 known functional genes. Therefore, after Bonferroni correction, these significant (adjusted P<0.05) and suggestive (adjusted P<0.10) associations were then used to identify genetic networks related to the RCT pathway. Multiple-marker analysis suggested possible genetic networks involving the RCT pathway for kidney-pelvic-heart fat percentage, rib-eye area, and subcutaneous fat depth phenotypes with markers derived from paraoxinase 1, apolipoproteins A1 and E, respectively. The present study confirmed that genes involved in cholesterol homeostasis are useful targets for investigating obesity in humans as well as for improving meat quality phenotypes in a livestock production.
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Affiliation(s)
- Tyler F Daniels
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
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20
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Dodson MV, Jiang Z, Chen J, Hausman GJ, Guan LL, Novakofski J, Thompson DP, Lorenzen CL, Fernyhough ME, Mir PS, Reecy JM. Allied industry approaches to alter intramuscular fat content and composition in beef animals. J Food Sci 2010; 75:R1-8. [PMID: 20492190 DOI: 10.1111/j.1750-3841.2009.01396.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biochemical and biophysical research tools are used to define the developmental dynamics of numerous cell lineages from a variety of tissues relevant to meat quality. With respect to the adipose cell lineage, much of our present understanding of adipogenesis and lipid metabolism was initially determined through the use of these methods, even though the in vitro or molecular environments are far removed from the tissues of meat animals. This concise review focuses on recent cellular and molecular biology-related research with adipocytes, and how the research might be extended to the endpoint of altering red meat quality. Moreover, economic and policy impacts of such in animal production regimens is discussed. These issues are important, not only with respect to palatability, but also to offer enhanced health benefits to the consumer by altering content of bioactive components in adipocytes.
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Affiliation(s)
- Michael V Dodson
- Dept. of Animal Science, Washington State Univ., Pullman, WA 99164, USA.
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21
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Yamada T, Sasaki S, Sukegawa S, Miyake T, Fujita T, Kose H, Morita M, Takahagi Y, Murakami H, Morimatsu F, Sasaki Y. Association of a single nucleotide polymorphism in ribosomal protein L27a gene with marbling in Japanese Black beef cattle. Anim Sci J 2010; 80:631-5. [PMID: 20163651 DOI: 10.1111/j.1740-0929.2009.00688.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Marbling, defined by the amount and distribution of intramuscular fat, is an economically important trait of beef cattle in Japan. The c2-11#2 expressed sequence tag (EST) has been previously shown to possess expression difference in musculus longissimus muscle between low-marbled and high-marbled steer groups, and to be located within genomic region of a quantitative trait locus for marbling. Thus, the ribosomal protein L27a (RPL27A) gene containing the c2-11#2 EST sequence was considered as a positional candidate for the gene responsible for marbling. In the present study, a single nucleotide polymorphism (SNP) in the promoter region of the RPL27A, referred to as g.3109537C>T, was detected between the 2 steer groups. The SNP was associated with the predicted breeding value for beef marbling standard number by the analyses using Japanese Black beef cattle population. The effect of genotypes of the SNP on the predicted breeding value for subcutaneous fat thickness was not statistically significant. These findings suggest that the RPL27A SNP may be useful for effective marker-assisted selection to increase the levels of marbling in Japanese Black beef cattle.
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Affiliation(s)
- Takahisa Yamada
- Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyoku, Kyoto, Japan.
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22
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Genome-wide transcription factor binding site/promoter databases for the analysis of gene sets and co-occurrence of transcription factor binding motifs. BMC Genomics 2010; 11:145. [PMID: 20193056 PMCID: PMC2841680 DOI: 10.1186/1471-2164-11-145] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 03/01/2010] [Indexed: 12/25/2022] Open
Abstract
Background The use of global gene expression profiling is a well established approach to understand biological processes. One of the major goals of these investigations is to identify sets of genes with similar expression patterns. Such gene signatures may be very informative and reveal new aspects of particular biological processes. A logical and systematic next step is to reduce the identified gene signatures to the regulatory components that induce the relevant gene expression changes. A central issue in this context is to identify transcription factors, or transcription factor binding sites (TFBS), likely to be of importance for the expression of the gene signatures. Results We develop a strategy that efficiently produces TFBS/promoter databases based on user-defined criteria. The resulting databases constitute all genes in the Santa Cruz database and the positions for all TFBS provided by the user as position weight matrices. These databases are then used for two purposes, to identify significant TFBS in the promoters in sets of genes and to identify clusters of co-occurring TFBS. We use two criteria for significance, significantly enriched TFBS in terms of total number of binding sites for the promoters, and significantly present TFBS in terms of the fraction of promoters with binding sites. Significant TFBS are identified by a re-sampling procedure in which the query gene set is compared with typically 105 gene lists of similar size randomly drawn from the TFBS/promoter database. We apply this strategy to a large number of published ChIP-Chip data sets and show that the proposed approach faithfully reproduces ChIP-Chip results. The strategy also identifies relevant TFBS when analyzing gene signatures obtained from the MSigDB database. In addition, we show that several TFBS are highly correlated and that co-occurring TFBS define functionally related sets of genes. Conclusions The presented approach of promoter analysis faithfully reproduces the results from several ChIP-Chip and MigDB derived gene sets and hence may prove to be an important method in the analysis of gene signatures obtained through ChIP-Chip or global gene expression experiments. We show that TFBS are organized in clusters of co-occurring TFBS that together define highly coherent sets of genes.
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MacNeil MD, Nkrumah JD, Woodward BW, Northcutt SL. Genetic evaluation of Angus cattle for carcass marbling using ultrasound and genomic indicators. J Anim Sci 2009; 88:517-22. [PMID: 19897629 DOI: 10.2527/jas.2009-2022] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The objectives were to estimate genetic parameters needed to elucidate the relationships of a molecular breeding value (MBV) for marbling, intramuscular fat (IMF) of yearling bulls measured with ultrasound, and marbling score (MRB) of slaughtered steers, and to assess the utility of MBV and IMF in predicting the breeding value for MRB. Records for MRB (n = 38,296) and IMF (n = 6,594) were from the American Angus Association database used for national cattle evaluation. A total of 1,006 records of MBV were used in this study. (Co)variance components were estimated with ASREML, fitting an animal model with fixed contemporary groups for MRB and IMF similar to those used in the Angus national genetic evaluation. The overall mean was the only fixed effect included in the model for MBV. Heritability estimates for carcass measures were 0.48 +/- 0.03, 0.31 +/- 0.03, and 0.98 +/- 0.05 for MRB, IMF, and MBV, respectively. Genetic correlations of IMF and MBV with MRB were 0.56 +/- 0.09 and 0.38 +/- 0.10, respectively. The genetic correlation between IMF and MBV was 0.80 +/- 0.22. These results indicate the MBV evaluated may yield a greater genetic advance of approximately 20% when used as an indicator trait for genetic prediction of MRB compared with IMF. However, neither of these indicators alone provides sufficient information to produce highly accurate prediction of breeding value for the economically relevant trait MRB. Given that the goal is a highly accurate prediction of true breeding value for MRB, results of this work point to the need to 1) continue progeny testing, and 2) continue increasing the genetic correlation between the MBV and MRB.
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24
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Cheong HS, Yoon DH, Bae JS, Kim LH, Kim EM, Kim JO, Hong J, Kim N, Shin HD. ADFP promoter polymorphism associated with marbling score in Korean cattle. BMB Rep 2009; 42:529-34. [PMID: 19712591 DOI: 10.5483/bmbrep.2009.42.8.529] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marbling score (MS) is the major trait that affects carcass quality in beef cattle. In this study, we investigated the association between genetic polymorphisms of the adipose differentiation-related protein gene (ADFP) and carcass traits in Korean cattle (also known as Hanwoo). Using direct DNA sequencing in 24 unrelated Korean cattle, 25 novel polymorphisms were identified within all exons and their flanking regions of ADFP, including the promoter region (1.5 kb). Among them, 21 polymorphic sites were selected for genotyping in the beef cattle (n = 425). Statistical analyses revealed that one promoter polymorphism (c.-56-18A > G) was associated with MS (P = 0.009). The "A" allele of c.-56-18A > G exerted a lowering effect on MS, e.g., the lowest MS was found in "A/A" (MS = 2.09 +/- 1.23), intermediate in "A/G" (MS = 2.11 +/- 1.31), and the highest in "G/G" (MS = 2.47 +/- 1.47). Our findings suggest that these polymorphisms in ADFP might be important genetic factors involved in carcass quality in beef cattle.
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Affiliation(s)
- Hyun Sub Cheong
- Department of Life Science, Sogang University, Seoul 121-742, Korea
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25
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Jiang Z, Michal JJ, Chen J, Daniels TF, Kunej T, Garcia MD, Gaskins CT, Busboom JR, Alexander LJ, Wright RW, Macneil MD. Discovery of novel genetic networks associated with 19 economically important traits in beef cattle. Int J Biol Sci 2009; 5:528-42. [PMID: 19727437 PMCID: PMC2726579 DOI: 10.7150/ijbs.5.528] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 07/16/2009] [Indexed: 11/20/2022] Open
Abstract
Quantitative or complex traits are determined by the combined effects of many loci, and are
affected by genetic networks or molecular pathways. In the present study, we genotyped a total
of 138 mutations, mainly single nucleotide polymorphisms derived from 71 functional genes on a
Wagyu x Limousin reference population. Two hundred forty six F2 animals were
measured for 5 carcass, 6 eating quality and 8 fatty acid composition traits. A total of 2,280
single marker-trait association runs with 120 tagged mutations selected based on the HAPLOVIEW
analysis revealed 144 significant associations (P < 0.05), but 50 of them were removed
from the analysis due to the small number of animals (≤ 9) in one genotype group or
absence of one genotype among three genotypes. The remaining 94 single-trait associations were
then placed into three groups of quantitative trait modes (QTMs) with additive, dominant and
overdominant effects. All significant markers and their QTMs associated with each of these 19
traits were involved in a linear regression model analysis, which confirmed single-gene
associations for 4 traits, but revealed two-gene networks for 8 traits and three-gene networks
for 5 traits. Such genetic networks involving both genotypes and QTMs resulted in high
correlations between predicted and actual values of performance, thus providing evidence that
the classical Mendelian principles of inheritance can be applied in understanding genetic
complexity of complex phenotypes. Our present study also indicated that carcass, eating quality
and fatty acid composition traits rarely share genetic networks. Therefore, marker-assisted
selection for improvement of one category of these traits would not interfere with improvement
of another.
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Affiliation(s)
- Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA.
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Yamada T, Sasaki S, Sukegawa S, Yoshioka S, Takahagi Y, Morita M, Murakami H, Morimatsu F, Fujita T, Miyake T, Sasaki Y. Association of a single nucleotide polymorphism in titin gene with marbling in Japanese Black beef cattle. BMC Res Notes 2009; 2:78. [PMID: 19419586 PMCID: PMC2683863 DOI: 10.1186/1756-0500-2-78] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 05/07/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Marbling defined by the amount and distribution of intramuscular fat is an economically important trait of beef cattle in Japan. We have recently reported that single nucleotide polymorphisms (SNPs) in the endothelial differentiation, sphingolipid G-protein-coupled receptor, 1 (EDG1) gene were associated with marbling in Japanese Black beef cattle. As well as EDG1, the titin (TTN) gene, involved in myofibrillogenesis, has been previously shown to possess expression difference in musculus longissimus muscle between low-marbled and high-marbled steer groups, and to be located within genomic region of a quantitative trait locus for marbling. Thus TTN was considered as a positional functional candidate for the gene responsible for marbling. In this study, we explored SNP in TTN and analyzed association of the SNP with marbling. FINDINGS A SNP in the promoter region of TTN, referred to as g.231054C>T, was the only difference detected between high- and low-marbled steer groups. The SNP was associated with marbling in 3 experiments using 101 sires (P = 0.004), 848 paternal half-sib progeny steers from 5 sires heterozygous for the g.231054C>T (P = 0.046), and 820 paternal half-sib progeny steers from 3 sires homozygous for C allele at the g.231054C>T (P = 0.051), in Japanese Black beef cattle. The effect of genotypes of the SNP on subcutaneous fat thickness was not statistically significant (P > 0.05). CONCLUSION These findings suggest that in addition to the EDG1 SNPs, the TTN SNP polymorphism is associated with marbling and may be useful for effective marker-assisted selection to increase the levels of marbling in Japanese Black beef cattle. Further replicate studies will be needed to confirm the allelic association observed here, and to expand the results to evaluate all possible genotypic combinations of alleles.
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Affiliation(s)
- Takahisa Yamada
- Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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27
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Yamada T, Itoh M, Nishimura S, Taniguchi Y, Miyake T, Sasaki S, Yoshioka S, Fujita T, Shiga K, Morita M, Sasaki Y. Association of single nucleotide polymorphisms in the endothelial differentiation sphingolipid G-protein-coupled receptor 1 gene with marbling in Japanese Black beef cattle. Anim Genet 2008; 40:209-16. [PMID: 19133939 DOI: 10.1111/j.1365-2052.2008.01822.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Marbling defined by the amount and distribution of intramuscular fat, so-called Shimofuri, is an economically important trait of beef cattle in Japan. The endothelial differentiation sphingolipid G-protein-coupled receptor 1 (EDG1) gene, involved in blood vessel formation, has been previously shown to be expressed at different levels in musculus longissimus muscle between low-marbled and high-marbled steer groups. It is located within the genomic region of a quantitative trait locus for marbling, and thus was considered as a positionally functional candidate for the gene responsible for marbling. In this study, two single nucleotide polymorphisms (SNPs) in the 5' untranslated region (UTR) and the 3' UTR of EDG1, referred to as c.-312A>G and c.*446G>A, respectively, were detected between the two steer groups. The two SNPs were associated with the predicted breeding value for beef marbling standard number by analyses using a population of Japanese Black beef cattle. The effect of genotypes at each of the SNPs on the predicted breeding value for subcutaneous fat thickness was not statistically significant (P > 0.05). Reporter gene assays revealed no significant differences in gene expression between alleles at each of the SNPs. These findings suggest that EDG1 SNPs, although they may not be regarded as a causal mutation, may be useful for effective marker-assisted selection to increase the levels of marbling in Japanese Black beef cattle.
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Affiliation(s)
- T Yamada
- Laboratory of Animal Breeding and Genetics, Graduate School of Agriculture, Kyoto University, Sakyoku, Kyoto 606-8502, Japan
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Wang X, Xue C, Wang X, Liu H, Xu Y, Zhao R, Jiang Z, Dodson MV, Chen J. Differential display of expressed genes reveals a novel function of SFRS18 in regulation of intramuscular fat deposition. Int J Biol Sci 2008; 5:28-33. [PMID: 19119313 PMCID: PMC2605576 DOI: 10.7150/ijbs.5.28] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Accepted: 12/15/2008] [Indexed: 01/29/2023] Open
Abstract
Intramuscular fat (IMF) content plays a key role in establishing pork quality. In the present study, differential-display reverse transcription-polymerase chain reaction (DDRT-PCR) was used to identify differentially expressed (DE) genes between longissimus dorsi (LD) muscles with extremely different IMF content. A major DE gene associated with IMF content was identified as splicing factor serine-arginine rich protein (SFRS18) gene, also known as SRrp130. The gene exhibited relatively higher expression levels in LD muscles with higher IMF content. A full-length cDNA sequence of pig SFRS18 gene was obtained by in silico comparative cloning coupled with PCR target sequencing, while the current EST (expressed sequence tag) database supported two transcript variants of the pig gene. Differential expression of the SFRS18 gene was further confirmed using quantitative PCR. The mRNA levels of SFRS18 gene showed significant and positive correlation with IMF content in LD muscle (r = 0.54, P < 0.01). Collectively, these results suggest that the SFRS18 gene is involved in the regulation of IMF deposition in pig and that it may be a useful tool in selecting animals for desired amounts of fatness for high quality pork.
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Affiliation(s)
- Xiuxing Wang
- College of Animal Science & Technology, Nanjing Agricultural University, Nanjing, China
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29
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Abe T, Saburi J, Hasebe H, Nakagawa T, Kawamura T, Saito K, Nade T, Misumi S, Okumura T, Kuchida K, Hayashi T, Nakane S, Mitsuhasi T, Nirasawa K, Sugimoto Y, Kobayashi E. Bovine quantitative trait loci analysis for growth, carcass, and meat quality traits in an F2 population from a cross between Japanese Black and Limousin. J Anim Sci 2008; 86:2821-32. [PMID: 18599673 DOI: 10.2527/jas.2007-0676] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- T Abe
- National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan.
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30
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Hausman GJ, Dodson MV, Ajuwon K, Azain M, Barnes KM, Guan LL, Jiang Z, Poulos SP, Sainz RD, Smith S, Spurlock M, Novakofski J, Fernyhough ME, Bergen WG. Board-invited review: the biology and regulation of preadipocytes and adipocytes in meat animals. J Anim Sci 2008; 87:1218-46. [PMID: 18849378 DOI: 10.2527/jas.2008-1427] [Citation(s) in RCA: 235] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The quality and value of the carcass in domestic meat animals are reflected in its protein and fat content. Preadipocytes and adipocytes are important in establishing the overall fatness of a carcass, as well as being the main contributors to the marbling component needed for consumer preference of meat products. Although some fat accumulation is essential, any excess fat that is deposited into adipose depots other than the marbling fraction is energetically unfavorable and reduces efficiency of production. Hence, this review is focused on current knowledge about the biology and regulation of the important cells of adipose tissue: preadipocytes and adipocytes.
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Affiliation(s)
- G J Hausman
- USDA-ARS, Richard B. Russell Agricultural Research Station, Athens, GA 30604, USA
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31
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Jiang Z, Michal JJ, Tobey DJ, Daniels TF, Rule DC, Macneil MD. Significant associations of stearoyl-CoA desaturase (SCD1) gene with fat deposition and composition in skeletal muscle. Int J Biol Sci 2008; 4:345-51. [PMID: 18825276 PMCID: PMC2556050 DOI: 10.7150/ijbs.4.345] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Accepted: 09/25/2008] [Indexed: 11/05/2022] Open
Abstract
Gene expression studies in humans and animals have shown that elevated stearoyl-CoA desaturase (SCD1) activity is associated with increased fat accumulation and monounsaturation of saturated fatty acids in skeletal muscle. However, results of the two reported association studies in humans are inconsistent. In the present study, we annotated the bovine SCD1 gene and identified 3 single nucleotide polymorphisms (SNPs) in its 3'untranslated region (UTR). Genotyping these SNPs on a Wagyu x Limousin reference population revealed that the SCD1 gene was significantly associated with six fat deposition and fatty acid composition traits in skeletal muscle, but not with subcutaneous fat depth and percent kidney-pelvic-heart fat. In particular, we confirmed that the high stearoyl-CoA desaturase activities/alleles were positively correlated with beef marbling score, amount of monounsaturated fatty acids and conjugated linoleic acid content, but negatively with amount of saturated fatty acids. The inconsistent associations between human studies might be caused by using different sets of markers because we observed that most associated markers are located near the end of 3'UTR. We found that the proximity of the polyadenylation signal site is highly conserved among human, cattle and pig, indicating that the region might contain functional elements involved in posttranscriptional control of SCD1 activity. In conclusion, our cross species study provided solid evidence to support SCD1 gene as a critical player in skeletal muscle fat metabolism.
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Affiliation(s)
- Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA.
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32
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Jiang Z, Michal JJ, Tobey DJ, Wang Z, Macneil MD, Magnuson NS. Comparative understanding of UTS2 and UTS2R genes for their involvement in type 2 diabetes mellitus. Int J Biol Sci 2008; 4:96-102. [PMID: 18463714 PMCID: PMC2359900 DOI: 10.7150/ijbs.4.96] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Accepted: 04/22/2008] [Indexed: 11/26/2022] Open
Abstract
Several reports have shown that urotensin 2 (UTS2) and its receptor (UTS2R) are involved in glucose metabolism and insulin resistance, which lead to development of type 2 diabetes mellitus (T2DM) in humans. In the present study, we annotated both bovine UTS2 and UTS2R genes and identified 5 single nucleotide polymorphisms (SNPs) for the former gene and 14 mutations for the latter gene. Four mutations were genotyped on a Wagyu x Limousin reference population, including 6 F1 bulls, 113 F1 dams and ~250 F2 progeny. Among 12 phenotypes related to fat deposition and fatty acid composition, we observed that the UTS2 gene was significantly associated with the amount of skeletal saturated fatty acids, while its receptor (UTS2R) gene had significant effects on amounts of saturated and monounsaturated fatty acids, Δ9 desaturase activity for converting 16:0 into 16:1, muscle fat (marbling) score and Longissimus Dorsi muscle area. However, in this population, these markers were not associated with subcutaneous fat depth or percent kidney, pelvic and heart fat. We also found that mutations in the promoter regions altered the promoter activities in both genes and coding SNPs might affect the mRNA stability in the UTS2R gene. Overall, our present study provides the first evidence that both UTS2 and UTS2R genes regulate skeletal muscle fat accumulation and fatty acid metabolism, thus indicating their potential pathological functions related to obesity and T2DM in humans.
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Affiliation(s)
- Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA.
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Kunej T, Wang Z, Michal JJ, Daniels TF, Magnuson NS, Jiang Z. Functional UQCRC1 polymorphisms affect promoter activity and body lipid accumulation. Obesity (Silver Spring) 2007; 15:2896-901. [PMID: 18198295 DOI: 10.1038/oby.2007.344] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Obesity and type 2 diabetes constitute leading public health problems worldwide. Studies have shown that insulin resistance affiliated with these conditions is associated with skeletal muscle lipid accumulation, while the latter is associated with mitochondrial dysfunctions. However, the initiation and regulation of mitochondrial biogenesis rely heavily on approximately 1000 nuclear-encoded mitochondrial regulatory proteins. In this study, we targeted the ubiquinol-cytochrome c reductase core protein I gene, a nuclear-encoded component of mitochondrial complex III, for its association with subcutaneous fat depth (SFD) and skeletal muscle lipid accumulation (SMLA) using cattle as a model. Four promoter polymorphisms were identified and genotyped on approximately 250 Wagyu x Limousin F2 progeny. Statistical analysis revealed that two completely linked polymorphic sites, g.13487C>T and g.13709G>C (r2 = 1), were significantly associated with both SFD (p < 0.01) and SMLA (p < 0.0001). The difference between TTCC and CCGG haplotypes was 0.178 cm for SFD and 0.624 scores for SMLA. Interestingly, the former haplotype produced higher promoter activities than the latter by 43% to 49% in three cell lines (p < 0.05). In addition to Rett syndrome and breast/ovarian cancer observed in other studies, we report evidence for the first time, to our knowledge, that overexpression of ubiquinol-cytochrome c reductase core protein I might affect mitochondrial morphology and/or physiology and lead to development of obesity and related conditions.
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Affiliation(s)
- Tanja Kunej
- Department of Animal Sciences, East Wilson Road, Washington State University, Pullman, WA 99164-6351, USA
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34
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Alexander LJ, Macneil MD, Geary TW, Snelling WM, Rule DC, Scanga JA. Quantitative trait loci with additive effects on palatability and fatty acid composition of meat in a Wagyu-Limousin F2 population. Anim Genet 2007; 38:506-13. [PMID: 17894565 DOI: 10.1111/j.1365-2052.2007.01643.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A whole-genome scan was conducted on 328 F(2) progeny in a Wagyu x Limousin cross to identify quantitative trait loci (QTL) affecting palatability and fatty acid composition of beef at an age-constant endpoint. We have identified seven QTL on five chromosomes involved in lipid metabolism and tenderness. None of the genes encoding major enzymes involved in fatty acid metabolism, such as fatty acid synthase (FASN), acetyl-CoA carboxylase alpha (ACACA), solute carrier family 2 (facilitated glucose transporter) member 4 (SLC2A4), stearoyl-CoA desaturase (SCD) and genes encoding the subunits of fatty acid elongase, was located in these QTL regions. The present study may lead to a better-tasting and healthier product for consumers through improved selection for palatability and lipid content of beef.
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Affiliation(s)
- L J Alexander
- U.S. Department of Agriculture-Agricultural Research Service, Miles City, MT 59301, USA.
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35
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Wibowo TA, Michal JJ, Jiang Z. Corticotropin releasing hormone is a promising candidate gene for marbling and subcutaneous fat depth in beef cattle. Genome 2007; 50:939-45. [DOI: 10.1139/g07-075] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The gene corticotropin releasing hormone (CRH) is mapped on bovine chromosome 14 (BTA14), where more than 30 fat-related quantitative trait loci (QTLs) have been reported in dairy and beef cattle. The gene product regulates secretion of adrenocorticotrophin hormone, the hypothalamic–pituitary–adrenal axis, and multiple hypothalamic functions; therefore, we hypothesized that CRH is a promising candidate gene for beef marbling score (BMS) and subcutaneous fat depth (SFD) in a Wagyu × Limousin F2 population. Two pairs of primers were designed and a total of 5 single nucleotide polymorphisms (SNPs) were identified: g.9657C>T, c.10718G>C, c.10841G>A, c.10893A>C, and c.10936G>C (AAFC03076794.1). Among the 4 cSNPs, c.10718G>C, c.10841G>A, and c.10936G>C are missense mutations leading to amino acid changes from arginine to proline, from serine to asparagine, and from aspartic acid to histidine, respectively. These 5 SNPs were genotyped on ~250 F2 progeny, but only 4 were selected as tagging SNPs for association analysis because no historical recombination was observed between c.10718G>C and c.10893A>C. Statistical analysis showed that g.9657C>T, c.10718G>C, and c.10936G>C and their haplotypes had significant effects on SFD, but only c.10936G>C was significantly associated with BMS. The SNP in the promoter (g.9657C>T) led to gain/loss of a CpG site and 4 potential regulatory binding sites. Different haplotypes among the 4 cSNPs significantly affected mRNA secondary structures but were not associated with phenotypes. Overall, our results provide further evidence that CRH is a promising candidate gene for a concordant QTL related to lipid metabolism in mammals.
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Affiliation(s)
- Tito A. Wibowo
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
| | - Jennifer J. Michal
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
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Feng Z, Tang ZL, Li K, Liu B, Yu M, Zhao SH. Molecular characterization of the BTG2 and BTG3 genes in fetal muscle development of pigs. Gene 2007; 403:170-7. [PMID: 17890019 DOI: 10.1016/j.gene.2007.08.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 07/03/2007] [Accepted: 08/10/2007] [Indexed: 11/19/2022]
Abstract
BTG2 and BTG3 are two members of the B-cell translocation gene family with anti-proliferative properties. BTG1 gene in this gene family has been reported to play a key role in muscle growth. In this study, we identified and characterized the porcine BTG2 and BTG3 genes, mapped the two genes to porcine chromosomes, and analyzed their expression differences in the longissimus dorci muscle of 33 dpc (day postconception), 65 dpc and 90 dpc in the lean Landrace and fatty Chinese Tongcheng pig breeds. Expression changes in differentiated C2C12 cells were also investigated with myogenin as internal control. The results showed that the porcine BTG2 and BTG3 genes were mapped on SSC9q21-25 and SSC13q47, respectively. BTG2 gene expressed at high levels in skeletal muscle and heart in both Tongcheng and Landrace pigs whereas BTG3 gene expressed at lower levels in skeletal muscle and heart than in other tissues. Furthermore, BTG3 expressed at higher levels in skeletal muscle of Tonghceng compared with Landrace pig. The expression of BTG2 and BTG3 was significantly different in skeletal muscle among different developmental stages and between the two breeds. Expression analysis in murine myoblast cells showed that both genes were induced in differentiated C2C12 cells, suggesting a role of them in myogenic differentiation. Our study indicated that BTG2 and BTG3, especially BTG3 gene, may be important genes for skeletal muscle growth.
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Affiliation(s)
- Zheng Feng
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, PR China
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37
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Jiang Z, Wang Z, Kunej T, Williams GA, Michal JJ, Wu XL, Magnuson NS. A novel type of sequence variation: multiple-nucleotide length polymorphisms discovered in the bovine genome. Genetics 2007; 176:403-7. [PMID: 17409076 PMCID: PMC1893069 DOI: 10.1534/genetics.106.069401] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three types of sequence variations--single-nucleotide polymorphisms (SNPs), insertions and deletions (indels), and short tandem repeats (STRs)--have been extensively reported in mammalian genomes. In this study, we discovered a novel type of sequence variation, i.e., multiple-nucleotide length polymorphisms (MNLPs) in bovine UCN3 (Urocortin 3) and its receptor CRHR2 (corticotropin-releasing hormone receptor 2) genes. Both MNLPs featured involvement of multiple-nucleotide length polymorphisms (5-18 bases), low sequence identity, and 1.7- to 11-fold changes in promoter activity between two alleles. Therefore, this novel genetic complexity would contribute significantly to the evolutionary, functional, and phenotypic complexity of genomes within or among species.
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Affiliation(s)
- Zhihua Jiang
- Department of Animal Science, Washington State University, Pullman, WA 99164-6351, USA.
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Xiao Q, Wibowo TA, Wu XL, Michal JJ, Reeves JJ, Busboom JR, Thorgaard GH, Jiang Z. A simplified QTL mapping approach for screening and mapping of novel AFLP markers associated with beef marbling. J Biotechnol 2007; 127:177-87. [PMID: 16901568 DOI: 10.1016/j.jbiotec.2006.06.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Revised: 06/15/2006] [Accepted: 06/26/2006] [Indexed: 11/20/2022]
Abstract
Genome screening of quantitative trait loci (QTL) for a complex trait is usually costly and highly laborious, as it requires a large number of markers spanning the whole genome. Here we present a simplified approach for screening and mapping of QTL-linked markers for beef marbling using a WagyuxLimousin F(2) reference population. This simplified approach involves integration of the amplified fragment length polymorphism (AFLP) with DNA pooling and selective genotyping and comparative bioinformatics tools. AFLP analysis on two high and two low marbling DNA pools yielded ten visually different markers. Among them, four were confirmed based on individual AFLP validation. Sequencing and in silico characterization assigned two of these AFLP markers to bovine chromosomes 1 (BTA1) and 13 (BTA13), which are orthologous to human chromosomes HSA21q22.2 and HSA10p11.23 with both regions harboring QTL for obesity-related phenotypes. Both AFLP markers showed significantly large additive genetic effects (0.28+/-0.11 on BTA1 and 0.54+/-0.21 on BTA13) on beef-marbling score (BMS) (P<0.05). Overall, this approach is less time consuming, inexpensive and in particular, suitable for screening and mapping QTL-linked markers when targeting one or a few complex traits.
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Affiliation(s)
- Qianjun Xiao
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
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39
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Recent advances in cattle functional genomics and their application to beef quality. Animal 2007; 1:159-73. [DOI: 10.1017/s1751731107658042] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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40
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Jiang Z, Michal JJ, Williams GA, Daniels TF, Kunej T. Cross species association examination of UCN3 and CRHR2 as potential pharmacological targets for antiobesity drugs. PLoS One 2006; 1:e80. [PMID: 17183713 PMCID: PMC1762311 DOI: 10.1371/journal.pone.0000080] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2006] [Accepted: 11/14/2006] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Obesity now constitutes a leading global public health problem. Studies have shown that insulin resistance affiliated with obesity is associated with intramyocellular lipid (IMCL) accumulation. Therefore, identification of genes associated with the phenotype would provide a clear target for pharmaceutical intervention and care for the condition. We hypothesized that urocortin 3 (UCN3) and corticotropin-releasing hormone receptor 2 (CRHR2) are associated with IMCL and subcutaneous fat depth (SFD), because the corticotropin-releasing hormone family of peptides are capable of strong anorectic and thermogenic effects. METHODOLOGY/PRINCIPAL FINDINGS We annotated both bovine UCN3 and CRHR2 genes and identified 12 genetic mutations in the former gene and 5 genetic markers in the promoter region of the latter gene. Genotyping of these 17 markers on Wagyu times Limousin F(2) progeny revealed significant associations between promoter polymorphisms and SFD (P = 0.0203-0.0685) and between missense mutations of exon 2 and IMCL (P = 0.0055-0.0369) in the bovine UCN3 gene. The SFD associated promoter SNPs caused a gain/loss of 12 potential transcription regulatory binding sites, while the IMCL associated coding SNPs affected the secondary structure of UCN3 mRNA. However, none of five polymorphisms in CRHR2 gene clearly co-segregated with either trait in the population (P>0.6000). CONCLUSIONS/SIGNIFICANCE Because UCN3 is located on human chromosome 10p15.1 where quantitative trait loci for obesity have been reported, our cross species study provides further evidence that it could be proposed as a potential target for developing antiobesity drugs. None of the markers in CRHR2 was associated with obesity-type traits in cattle, which is consistent with findings in human. Therefore, CRHR2 does not lend itself to the development of antiobesity drugs.
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Affiliation(s)
- Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America.
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Xiao Q, Wu XL, Michal JJ, Reeves JJ, Busboom JR, Thorgaard GH, Jiang Z. A novel nuclear-encoded mitochondrial poly(A) polymerase PAPD1 is a potential candidate gene for the extreme obesity related phenotypes in mammals. Int J Biol Sci 2006; 2:171-8. [PMID: 16810331 PMCID: PMC1483122 DOI: 10.7150/ijbs.2.171] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Accepted: 05/14/2006] [Indexed: 11/23/2022] Open
Abstract
People with obesity, especially extreme obesity, are at risk for many health problems. However, the responsible genes remain unknown in >95% of severe obesity cases. Our previous genome-wide scan of Wagyu x Limousin F2 cattle crosses with extreme phenotypes revealed a molecular marker significantly associated with intramuscular fat deposition. Characterization of this marker showed that it is orthologous to the human gene KIAA1462 located on HSA10p11.23, where a major quantitative trait locus for morbid obesity has been reported. The newly identified mitochondrial poly(A) polymerase associated domain containing 1 (PAPD1) gene, which is located near this marker, is particularly interesting because the polymerase is required for the polyadenylation and stabilization of mammalian mitochondrial mRNAs. In the present study, both cDNA and genomic DNA sequences were annotated for the bovine PAPD1 gene and ten genetic markers were detected in the promoter and exon 1 region. Among seven markers assayed on ~ 250 Wagyu x Limousin F2 animals, two single nucleotide polymorphisms (SNPs) in the promoter region were significantly associated with intramuscular fat (P<0.05). However, there was a significant interaction (P<0.05) between a third SNP, which causes an amino acid change in coding exon 1, and each of these two promoter SNPs on intramuscular fat deposition. In particular, the differences between double heterozygous animals at two polymorphic sites and the slim genotype animals exceeded 2.3 standard deviations for the trait in both cases. Our study provides evidence for a new mechanism – the involvement of compound heterosis in extreme obesity, which warrants further examination.
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Affiliation(s)
- Qianjun Xiao
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164- 6351, USA
| | - Xiao-Lin Wu
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164- 6351, USA
| | - Jennifer J. Michal
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164- 6351, USA
| | - Jerry J. Reeves
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164- 6351, USA
| | - Jan R. Busboom
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164- 6351, USA
| | - Gary H. Thorgaard
- 2. School of Biological Sciences, Washington State University, Pullman, WA 99164- 4236 USA
| | - Zhihua Jiang
- 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164- 6351, USA
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