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Perricone V, Schokker D, Bossers A, de Bruijn A, Kar SK, Te Pas MFW, Rebel JMJ, Wouters IM, de Jong IC. Dietary strategies can increase cloacal endotoxin levels and modulate the resident microbiota in broiler chickens. Poult Sci 2024; 103:103312. [PMID: 38100944 PMCID: PMC10762469 DOI: 10.1016/j.psj.2023.103312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Endotoxins released from poultry feces have been associated with impaired human health. Because endotoxins are released from gram-negative intestinal bacteria, it was hypothesized that dietary strategies may influence endotoxin excretion via modulation of gut microbiota. We therefore tested dietary strategies that could potentially reduce cloacal endotoxin levels in broiler chickens. One-day-old male Ross 308 (N = 1,344) broilers were housed in 48 pens (N = 8 pens/treatment, 28 chickens per pen) and fed 1 of 6 diets for 35 days (d) in a 3-phase feeding program: a basic diet (CON) that served as the reference diet, or basic diet supplemented with butyrate (BUT), inulin (INU), medium-chain fatty acids (MCFA) or Original XPC™LS (XPC), or a high-fiber-low-protein (HF-LP) diet. A significant (P < 0.05) increase in cloacal endotoxin concentration at d 35 was observed in BUT as compared to CON. Analysis of cloacal microbiota showed a trend (P < 0.07) for a higher gram-negative/gram-positive ratio and for a higher relative abundance of gram-negative bacteria at d 35 (P ≤ 0.08) in BUT and HF-LP as compared to CON. A significant (P < 0.05) increase in average daily gain (ADG) and improved feed conversion ratio (P < 0.05) were observed in MCFA during the grower phase (d 14-28), and a significant (P < 0.05) increase in average daily feed intake (ADFI) was observed in MCFA during d 0 to 28. Broilers fed HF-LP had a significantly (P < 0.05) higher FCR and lower ADG throughout the rearing period. No treatment effects were found on footpad dermatitis, but BUT had worst hock burn scores at d 35 (P < 0.01) and MCFA had worst cleanliness scores at d 21 but not at d 35 (treatment*age P < 0.05), while INU had better cleanliness as compared to CON at d 35 (P < 0.05). In conclusion, especially BUT and HF-LP were able to modulate resident microbiota and BUT also increased cloacal endotoxin levels, which was opposite to our hypothesis. The present study indicates that cloacal endotoxin release can be affected by the diet but further study is needed to find dietary treatments that can reduce cloacal endotoxin release.
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Affiliation(s)
- Vera Perricone
- Wageningen Livestock Research, Wageningen University and Research, 6700 AH Wageningen, the Netherlands
| | - Dirkjan Schokker
- Wageningen Livestock Research, Wageningen University and Research, 6700 AH Wageningen, the Netherlands; Wageningen Bioveterinary Research, Wageningen University and Research, 8221 RA Lelystad, the Netherlands
| | - Alex Bossers
- Wageningen Bioveterinary Research, Wageningen University and Research, 8221 RA Lelystad, the Netherlands; Institute for Risk Assessment Sciences (IRAS), Utrecht University, 3508 TD Utrecht, the Netherlands
| | - Anne de Bruijn
- Wageningen Livestock Research, Wageningen University and Research, 6700 AH Wageningen, the Netherlands
| | - Soumya K Kar
- Wageningen Livestock Research, Wageningen University and Research, 6700 AH Wageningen, the Netherlands
| | - Marinus F W Te Pas
- Wageningen Livestock Research, Wageningen University and Research, 6700 AH Wageningen, the Netherlands
| | - Johanna M J Rebel
- Wageningen Livestock Research, Wageningen University and Research, 6700 AH Wageningen, the Netherlands; Wageningen Bioveterinary Research, Wageningen University and Research, 8221 RA Lelystad, the Netherlands
| | - Inge M Wouters
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, 3508 TD Utrecht, the Netherlands
| | - Ingrid C de Jong
- Wageningen Livestock Research, Wageningen University and Research, 6700 AH Wageningen, the Netherlands.
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2
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Dou T, Yan S, Liu L, Wang K, Jian Z, Xu Z, Zhao J, Wang Q, Sun S, Talpur MZ, Duan X, Gu D, He Y, Du Y, Abdulwahid AM, Li Q, Rong H, Cao W, Su Z, Zhao G, Liu R, Zhao S, Huang Y, Te Pas MFW, Ge C, Jia J. Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens. BMC Genomics 2022; 23:173. [PMID: 35236293 PMCID: PMC8892760 DOI: 10.1186/s12864-022-08388-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 02/03/2022] [Indexed: 12/02/2022] Open
Abstract
Background Melanin is an important antioxidant in food and has been used in medicine and cosmetology. Chicken meat with high melanin content from black-boned chickens have been considered a high nutritious food with potential medicinal properties. The molecular mechanism of melanogenesis of skeletal muscle in black-boned chickens remain poorly understood. This study investigated the biological gene-metabolite associations regulating the muscle melanogenesis pathways in Wuliangshan black-boned chickens with two normal boned chicken breeds as control. Results We identified 25 differentially expressed genes and 11 transcription factors in the melanogenesis pathways. High levels of the meat flavor compounds inosine monophosphate, hypoxanthine, lysophospholipid, hydroxyoctadecadienoic acid, and nicotinamide mononucleotide were found in Wuliangshan black-boned chickens. Conclusion Integrative analysis of transcriptomics and metabolomics revealed the dual physiological functions of the PDZK1 gene, involved in pigmentation and/or melanogenesis and regulating the phospholipid signaling processes in muscle of black boned chickens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08388-w.
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Affiliation(s)
- Tengfei Dou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Shixiong Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Lixian Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.,Yunnan Vocational and Technical College of Agriculture, Kunming, 650031, Yunnan Province, People's Republic of China
| | - Kun Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Zonghui Jian
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Zhiqiang Xu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.,College of Food Science, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Jingying Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Qiuting Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Shuai Sun
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Mir Zulqarnain Talpur
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Xiaohua Duan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.,Yunnan University of Traditional Chinese Medical, Kunming, 650500, Yunnan Province, People's Republic of China
| | - Dahai Gu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.,College of Food Science, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Yang He
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Yanli Du
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Alsoufi Mohammed Abdulwahid
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Qihua Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Hua Rong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Weina Cao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, College of Computing and Informatics, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Guiping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Ranran Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Sumei Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Ying Huang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Marinus F W Te Pas
- Wageningen Livestock Research, Wageningen UR, Wageningen, 238050, The Netherlands. .,Visiting Professor Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.
| | - Changrong Ge
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.
| | - Junjing Jia
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.
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3
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Heida M, Schopen GCB, Te Pas MFW, Gredler-Grandl B, Veerkamp RF. Breeding goal traits accounting for feed intake capacity and roughage or concentrate intake separately. J Dairy Sci 2021; 104:8966-8982. [PMID: 34053766 DOI: 10.3168/jds.2020-19533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/20/2021] [Indexed: 11/19/2022]
Abstract
Current breeding tools aiming to improve feed efficiency use definitions based on total dry matter intake (DMI); for example, residual feed intake or feed saved. This research aimed to define alternative traits using existing data that differentiate between feed intake capacity and roughage or concentrate intake, and to investigate the phenotypic and genetic relationships among these traits. The data set contained 39,017 weekly milk yield, live weight, and DMI records of 3,164 cows. The 4 defined traits were as follows: (1) Feed intake capacity (FIC), defined as the difference between how much a cow ate and how much she was expected to eat based on diet satiety value and status of the cow (parity and lactation stage); (2) feed saved (FS), defined as the difference between the measured and the predicted DMI, based on the regression of DMI on milk components within experiment; (3) residual roughage intake (RRI), defined as the difference between the measured and the predicted roughage intake, based on the regression of roughage intake on milk components and concentrate intake within experiment; and (4) residual concentrate intake (RCI), defined as the difference between the measured and the predicted concentrate intake, based on the regression of concentrate intake on milk components and roughage intake within experiment. The phenotypic correlations were -0.72 between FIC and FS, -0.84 between FS and RRI, and -0.53 between FS and RCI. Heritability of FIC, FS, RRI, and RCI were estimated to be 0.21, 0.12, 0.15, and 0.03, respectively. The genetic correlations were -0.81 between FS and FIC, -0.96 between FS and RRI, and -0.25 between FS and RCI. Concentrate intake and RCI had low heritability. Genetic correlation between DMI and FIC was 0.98. Although the defined traits had moderate phenotypic correlations, the genetic correlations between DMI, FS, FIC, and RRI were above 0.79 (in absolute terms), suggesting that these traits are genetically similar. Therefore, selecting for FIC is expected to simply increase DMI and RRI, and there seems to be little advantage in separating concentrate and roughage intake in the genetic evaluation, because measured concentrate intake was determined by the feeding system in our data and not by the genetics of the cow.
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Affiliation(s)
- Margreet Heida
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH Wageningen, the Netherlands
| | - Ghyslaine C B Schopen
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH Wageningen, the Netherlands
| | - Marinus F W Te Pas
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH Wageningen, the Netherlands
| | - Birgit Gredler-Grandl
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH Wageningen, the Netherlands
| | - Roel F Veerkamp
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH Wageningen, the Netherlands.
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4
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Kar SK, Wells JM, Ellen ED, Te Pas MFW, Madsen O, Groenen MAM, Woelders H. Organoids: a promising new in vitro platform in livestock and veterinary research. Vet Res 2021; 52:43. [PMID: 33691792 PMCID: PMC7943711 DOI: 10.1186/s13567-021-00904-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/13/2021] [Indexed: 02/06/2023] Open
Abstract
Organoids are self-organizing, self-renewing three-dimensional cellular structures that resemble organs in structure and function. They can be derived from adult stem cells, embryonic stem cells, or induced pluripotent stem cells. They contain most of the relevant cell types with a topology and cell-to-cell interactions resembling that of the in vivo tissue. The widespread and increasing adoption of organoid-based technologies in human biomedical research is testament to their enormous potential in basic, translational- and applied-research. In a similar fashion there appear to be ample possibilities for research applications of organoids from livestock and companion animals. Furthermore, organoids as in vitro models offer a great possibility to reduce the use of experimental animals. Here, we provide an overview of studies on organoids in livestock and companion animal species, with focus on the methods developed for organoids from a variety of tissues/organs from various animal species and on the applications in veterinary research. Current limitations, and ongoing research to address these limitations, are discussed. Further, we elaborate on a number of fields of research in animal nutrition, host-microbe interactions, animal breeding and genomics, and animal biotechnology, in which organoids may have great potential as an in vitro research tool.
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Affiliation(s)
- Soumya K Kar
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands.
| | - Jerry M Wells
- Host-Microbe Interactomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Esther D Ellen
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Marinus F W Te Pas
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Henri Woelders
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
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5
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Corbett RJ, Te Pas MFW, van den Brand H, Groenen MAM, Crooijmans RPMA, Ernst CW, Madsen O. Genome-Wide Assessment of DNA Methylation in Chicken Cardiac Tissue Exposed to Different Incubation Temperatures and CO 2 Levels. Front Genet 2020; 11:558189. [PMID: 33193638 PMCID: PMC7655987 DOI: 10.3389/fgene.2020.558189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/30/2020] [Indexed: 12/26/2022] Open
Abstract
Temperature and CO2 concentration during incubation have profound effects on broiler chick development, and numerous studies have identified significant effects on hatch heart weight (HW) as a result of differences in these parameters. Early life environment has also been shown to affect broiler performance later in life; it has thus been suggested that epigenetic mechanisms may mediate long-term physiological changes induced by environmental stimuli. DNA methylation is an epigenetic modification that can confer heritable changes in gene expression. Using reduced-representation bisulfite sequencing (RRBS), we assessed DNA methylation patterns in cardiac tissue of 84 broiler hatchlings incubated at two egg shell temperatures (EST; 37.8°C and 38.9°C) and three CO2 concentrations (0.1%, 0.4%, and 0.8%) from day 8 of incubation onward. We assessed differential methylation between EST treatments and identified 2,175 differentially methylated (DM) CpGs (1,121 hypermethylated, 1,054 hypomethylated at 38.9° vs. 37.8°) in 269 gene promoters and 949 intragenic regions. DM genes (DMGs) were associated with heart developmental processes, including cardiomyocyte proliferation and differentiation. We identified enriched binding motifs among DM loci, including those for transcription factors associated with cell proliferation and heart development among hypomethylated CpGs that suggest increased binding ability at higher EST. We identified 9,823 DM CpGs between at least two CO2 treatments, with the greatest difference observed between 0.8 and 0.1% CO2 that disproportionately impacted genes involved in cardiac muscle development and response to low oxygen levels. Using HW measurements from the same chicks, we performed an epigenome-wide association study (EWAS) for HW, and identified 23 significantly associated CpGs, nine of which were also DM between ESTs. We found corresponding differences in transcript abundance between ESTs in three DMGs (ABLIM2, PITX2, and THRSP). Hypomethylation of an exonic CpG in PITX2 at 38.9°C was associated with increased expression, and suggests increased cell proliferation in broiler hatchlings incubated at higher temperatures. Overall, these results identified numerous epigenetic associations between chick incubation factors and heart development that may manifest in long-term differences in animal performance.
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Affiliation(s)
- Ryan J Corbett
- Genetics and Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, United States
| | - Marinus F W Te Pas
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Henry van den Brand
- Adaptation Physiology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | | | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
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6
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Te Pas MFW, Jansman AJM, Kruijt L, van der Meer Y, Vervoort JJM, Schokker D. Sanitary Conditions Affect the Colonic Microbiome and the Colonic and Systemic Metabolome of Female Pigs. Front Vet Sci 2020; 7:585730. [PMID: 33195612 PMCID: PMC7649119 DOI: 10.3389/fvets.2020.585730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/22/2020] [Indexed: 12/04/2022] Open
Abstract
Differences in sanitary conditions, as model to induce differences in subclinical immune stimulation, affect the growth performance and nutrient metabolism in pigs. The objective of the present study was to evaluate the colonic microbiota and the colonic and systemic metabolome of female pigs differing in health status induced by sanitary conditions. We analyzed blood and colon digesta metabolite profiles using Nuclear Magnetic Resonance (1H NMR) and Triple quadrupole mass spectrometry, as well as colonic microbiota profiles. 1H NMR is a quantitative metabolomics technique applicable to biological samples. Weaned piglets of 4 weeks of age were kept under high or low sanitary conditions for the first 9 weeks of life. The microbiota diversity in colon digesta was higher in pigs subjected to low sanitary conditions (n = 18 per treatment group). The abundance of 34 bacterial genera was higher in colon digesta of low sanitary condition pigs, while colon digesta of high sanitary status pigs showed a higher abundance for four bacterial groups including the Megasphaera genus (p < 0.003) involved in lactate fermentation. Metabolite profiles (n = 18 per treatment group) in blood were different between both groups of pigs. These different profiles suggested changes in general nutrient metabolism, and more specifically in amino acid metabolism. Moreover, differences in compounds related to the immune system and responses to stress were observed. Microbiome-specific metabolites in blood were also affected by sanitary status of the pigs. We conclude that the microbiome composition in colon and the systemic metabolite profiles are affected by sanitary conditions and related to suboptimal health. These data are useful for exploring further relationships between health, metabolic status and performance and for the identification of biomarkers related to health (indices) and performance.
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Affiliation(s)
- Marinus F W Te Pas
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Alfons J M Jansman
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Leo Kruijt
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Yvonne van der Meer
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Jacques J M Vervoort
- Department of Agrotechnology and Food Sciences, Biochemistry, Wageningen University, Wageningen, Netherlands
| | - Dirkjan Schokker
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
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7
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Lim B, Kim S, Lim KS, Jeong CG, Kim SC, Lee SM, Park CK, Te Pas MFW, Gho H, Kim TH, Lee KT, Kim WI, Kim JM. Integrated time-serial transcriptome networks reveal common innate and tissue-specific adaptive immune responses to PRRSV infection. Vet Res 2020; 51:128. [PMID: 33050948 PMCID: PMC7552595 DOI: 10.1186/s13567-020-00850-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/13/2020] [Indexed: 12/17/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) infection is the most important viral disease causing severe economic losses in the swine industry. However, mechanisms underlying gene expression control in immunity-responsible tissues at different time points during PRRSV infection are poorly understood. We constructed an integrated gene co-expression network and identified tissue- and time-dependent biological mechanisms of PRRSV infection through bioinformatics analysis using three tissues (lungs, bronchial lymph nodes [BLNs], and tonsils) via RNA-Seq. Three groups with specific expression patterns (i.e., the 3-dpi, lung, and BLN groups) were discovered. The 3 dpi-specific group showed antiviral and innate-immune signalling similar to the case for influenza A infection. Moreover, we observed adaptive immune responses in the lung-specific group based on various cytokines, while the BLN-specific group showed down-regulated AMPK signalling related to viral replication. Our study may provide comprehensive insights into PRRSV infection, as well as useful information for vaccine development.
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Affiliation(s)
- Byeonghwi Lim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Sangwook Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Chang-Gi Jeong
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Jeollabuk-do, 54596, Republic of Korea
| | - Seung-Chai Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Jeollabuk-do, 54596, Republic of Korea
| | - Sang-Myeong Lee
- College of Veterinary Medicine, Chungbuk National University, Cheongju, Chungcheongbuk-do, 28644, Republic of Korea
| | - Choi-Kyu Park
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu, 41566, Republic of Korea
| | | | - Haesu Gho
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Tae-Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea.
| | - Won-Il Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Jeollabuk-do, 54596, Republic of Korea.
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea.
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8
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Te Pas MFW, Borg R, Buddiger NJH, Wood BJ, Rebel JMJ, van Krimpen MM, Calus MPL, Park JE, Schokker D. Regulating appetite in broilers for improving body and muscle development - A review. J Anim Physiol Anim Nutr (Berl) 2020; 104:1819-1834. [PMID: 32592266 PMCID: PMC7754290 DOI: 10.1111/jpn.13407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022]
Abstract
Appetite is the desire for feed and water and the voluntary intake of feed and is an important regulator of livestock productivity and animal health. Economic traits such as growth rate and muscle development (meat deposition) in broilers are directly correlated to appetite. Factors that may influence appetite include environmental factors, such as stress and temperature variation, and animal‐specific factors, such as learning period, eating capacity and preferences. Feed preferences have been reported to be determined in early life, and this period is important in broilers due to their fast growth and relatively short growth trajectories. This may be of importance when contemplating the use of more circular and sustainable feeds and the optimization of appetite for these feeds. The objective of this review was to review the biological mechanisms underlying appetite using data from human, animal and bird models and to consider the option for modulating appetite particularly as it relates to broiler chickens.
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Affiliation(s)
- Marinus F W Te Pas
- Wageningen University and Research, Wageningen Livestock Research, Wageningen, The Netherlands
| | | | | | - Benjamin J Wood
- Hendrix Genetics North America Office, Kitchener, ON, Canada
| | - Johanna M J Rebel
- Wageningen University and Research, Wageningen Livestock Research, Wageningen, The Netherlands
| | - Marinus M van Krimpen
- Wageningen University and Research, Wageningen Livestock Research, Wageningen, The Netherlands
| | - Mario P L Calus
- Wageningen University and Research, Wageningen Livestock Research, Wageningen, The Netherlands
| | - Jong-Eun Park
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Jeonju, Korea
| | - Dirkjan Schokker
- Wageningen University and Research, Wageningen Livestock Research, Wageningen, The Netherlands
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Srikanth K, Kumar H, Park W, Byun M, Lim D, Kemp S, Te Pas MFW, Kim JM, Park JE. Corrigendum: Cardiac and Skeletal Muscle Transcriptome Response to Heat Stress in Kenyan Chicken Ecotypes Adapted to Low and High Altitudes Reveal Differences in Thermal Tolerance and Stress Response. Front Genet 2020; 11:197. [PMID: 32194645 PMCID: PMC7063063 DOI: 10.3389/fgene.2020.00197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/19/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Himansu Kumar
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Mijeong Byun
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Steve Kemp
- Animal Biosciences, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Marinus F W Te Pas
- Wageningen UR Livestock Research, Animal Breeding and Genomics, Wageningen, Netherlands
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
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Srikanth K, Kumar H, Park W, Byun M, Lim D, Kemp S, Te Pas MFW, Kim JM, Park JE. Cardiac and Skeletal Muscle Transcriptome Response to Heat Stress in Kenyan Chicken Ecotypes Adapted to Low and High Altitudes Reveal Differences in Thermal Tolerance and Stress Response. Front Genet 2019; 10:993. [PMID: 31681427 PMCID: PMC6798392 DOI: 10.3389/fgene.2019.00993] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/18/2019] [Indexed: 12/30/2022] Open
Abstract
Heat stress (HS) negatively affects chicken performance. Agricultural expansion will happen in regions that experience high ambient temperatures, where fast-growing commercial chickens are vulnerable. Indigenous chickens of such regions, due to generations of exposure to environmental challenges, might have higher thermal tolerance. In this study, two indigenous chicken ecotypes, from the hot and humid Mombasa (lowland) and the colder Naivasha (highland) regions, were used to investigate the effects of acute (5 h, 35°C) and chronic (3 days of 35°C for 8 h/day) HS on the cardiac and skeletal muscle, through RNA sequencing. The rectal temperature gain and the number of differentially expressed genes (DEGs) [False Discovery Rate (FDR) < 0.05] were two times higher in the acute stage than in the chronic stage in both ecotypes, suggesting that cyclic exposure to HS can lead to adaptation. A tissue- and stage-specific difference in response to HS was observed, with peroxisome proliferator-activated-receptor (PPAR) signaling and mitogen-activate protein kinase (MAPK) signaling pathways, enriched in heart and skeletal muscle, respectively, and the p53 pathway enriched only in the acute stage in both tissues. The acute and chronic stage DEGs were integrated by a region-specific gene coexpression network (GCN), and genes with the highest number of connections (hub genes) were identified. The hub genes in the lowland network were CCNB2, Crb2, CHST9, SESN1, and NR4A3, while COMMD4, TTC32, H1F0, ACYP1, and RPS28 were the hub genes in the highland network. Pathway analysis of genes in the GCN showed that p53 and PPAR signaling pathways were enriched in both low and highland networks, while MAPK signaling and protein processing in endoplasmic reticulum were enriched only in the gene network of highland chickens. This shows that to dissipate the accumulated heat, to reduce heat induced apoptosis, and to promote DNA damage repair, the ecotypes activated or suppressed different genes, indicating the differences in thermal tolerance and HS response mechanisms between the ecotypes. This study provides information on the HS response of chickens, adapted to two different agro climatic environments, extending our understanding of the mechanisms of HS response and the effect of adaptation in counteracting HS.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Himansu Kumar
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Mijeong Byun
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
| | - Steve Kemp
- Animal Biosciences, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Marinus F W Te Pas
- Wageningen UR Livestock Research, Animal Breeding and Genomics, Wageningen, Netherlands
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, South Korea
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11
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Te Pas MFW, Park W, Srikanth K, Kemp S, Kim JM, Lim D, Park JE. Transcriptomic profiles of muscle, heart, and spleen in reaction to circadian heat stress in Ethiopian highland and lowland male chicken. Cell Stress Chaperones 2019; 24:175-194. [PMID: 30565091 PMCID: PMC6363629 DOI: 10.1007/s12192-018-0954-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 11/14/2018] [Accepted: 11/24/2018] [Indexed: 01/25/2023] Open
Abstract
Temperature stress impacts both welfare and productivity of livestock. Global warming is expected to increase the impact, especially in tropical areas. We investigated the biological mechanisms regulated by temperature stress due to the circadian temperature cycle in temperature adapted and non-adapted chicken under tropical conditions. We studied transcriptome profiles of heart, breast muscle, and spleen tissues of Ethiopian lowland chicken adapted to high circadian temperatures and non-adapted Ethiopian highland chicken under lowland conditions at three points during the day: morning, noon, and evening. Functional annotations and network analyses of genes differentially expressed among the time points of the day indicate major differences in the reactions of the tissues to increasing and decreasing temperatures, and also the two chickens lines differ. However, epigenetic changes of chromatin methylation and histone (de)acetylation seemed to be central regulatory mechanisms in all tissues in both chicken lines. Finally, all tissues showed differentially expressed genes between morning and evening times indicating biological mechanisms that need to change during the night to reach morning levels again the next day.
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Affiliation(s)
- Marinus F W Te Pas
- Wageningen UR Livestock Research, Animal Breeding and Genomics, Wageningen, The Netherlands.
| | - Woncheoul Park
- Department of Animal Biotechnology and Environment, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Krishnamoorthy Srikanth
- Department of Animal Biotechnology and Environment, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Steve Kemp
- Animal Biosciences, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Dajeong Lim
- Department of Animal Biotechnology and Environment, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Jong-Eun Park
- Department of Animal Biotechnology and Environment, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea.
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12
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Dou T, Li Z, Wang K, Liu L, Rong H, Xu Z, Huang Y, Gu D, Chen X, Hu W, Zhang J, Zhao S, Jois M, Li Q, Ge C, Te Pas MFW, Jia J. Regulation of myostatin expression is associated with growth and muscle development in commercial broiler and DMC muscle. Mol Biol Rep 2018; 45:511-522. [PMID: 29740785 PMCID: PMC6060753 DOI: 10.1007/s11033-018-4187-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/26/2018] [Indexed: 11/17/2022]
Abstract
Myostatin is a negative regulator of skeletal muscle growth. Muscle tissue is the largest tissue in the body and influences body growth. Commercial Avian broiler chickens are selected for high growth rate and muscularity. Daweishan mini chickens are a slow growing small-sized chicken breed. We investigated the relations between muscle (breast and leg) myostatin mRNA expression and body and muscle growth. Twenty chickens per breed were slaughtered at 0, 30, 60, 90, 120, and 150 days of age. Body and muscle weights were higher at all times in Avian chickens. Breast muscle myostatin expression was higher in Avian chickens than in Daweishan mini chickens at day 30. Myostatin expression peaked at day 60 in Daweishan mini chickens and expression remained higher in breast muscle. Daweishan mini chickens myostatin expression correlated positively with carcass weight, breast and leg muscle weight from day 0 to 60, and correlated negatively with body weight from day 90 to 150, while myostatin expression in Avian chickens was negatively correlated with carcass and muscle weight from day 90 to 150. The results suggest that myostatin expression is related to regulation of body growth and muscle development, with two different regulatory mechanisms that switch between days 30 and 60.
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Affiliation(s)
- Tengfei Dou
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Zhengtian Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Kun Wang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Lixian Liu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Hua Rong
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Zhiqiang Xu
- Faculty of Food Science, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Ying Huang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Dahai Gu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Xiaobo Chen
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Wenyuan Hu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Jiarong Zhang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Sumei Zhao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Markandeya Jois
- Department of Agricultural Sciences, School of Life Sciences, Faculty of Science, Technology and Engineering, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Qihua Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Changrong Ge
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Marinus F W Te Pas
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Wageningen University and Research Centre, Building 107, Radix, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. .,Kunming Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China. .,Dali University, Dali, People's Republic of China.
| | - Junjing Jia
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
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13
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Kim JM, Park JE, Yoo I, Han J, Kim N, Lim WJ, Cho ES, Choi B, Choi S, Kim TH, Te Pas MFW, Ka H, Lee KT. Integrated transcriptomes throughout swine oestrous cycle reveal dynamic changes in reproductive tissues interacting networks. Sci Rep 2018; 8:5436. [PMID: 29615657 PMCID: PMC5882957 DOI: 10.1038/s41598-018-23655-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 03/12/2018] [Indexed: 12/22/2022] Open
Abstract
Female fertility is a highly regulated process involving the synchronized activities of multiple tissues. The underlying genomic regulation of the tissue synchronization is poorly understood. To understand this better we investigated the transcriptomes of the porcine ovary, endometrium, and oviduct at days 0, 3, 6, 9, 12, 15, or 18 of the oestrous cycle. We analysed the transcriptome profiles of the individual tissues and focus on the bridging genes shared by two or more tissues. The three tissue-networks were connected forming a triangular shape. We identified 65 bridging genes with a high level of connectivity to all other genes in the network. The expression levels showed negative correlations between the ovary and the other two tissues, and low correlations between endometrium and oviduct. The main functional annotations involved biosynthesis of steroid hormones, cell-to-cell adhesion, and cell apoptosis, suggesting that regulation of steroid hormone synthesis and tissue viability are major regulatory mechanisms.
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Affiliation(s)
- Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Inkyu Yoo
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea
| | - Jisoo Han
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea
| | - Namshin Kim
- Personalized Genomic Medicine Research Center Genome Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Won-Jun Lim
- Personalized Genomic Medicine Research Center Genome Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Eun-Seok Cho
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Bonghwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Sunho Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Tae-Hun Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Marinus F W Te Pas
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea.,Animal Breeding and Genomics, Wageningen UR Livestock Research, 6700AH, Wageningen, The Netherlands
| | - Hakhyun Ka
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea.
| | - Kyung-Tai Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
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14
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Dou T, Zhao S, Rong H, Gu D, Li Q, Huang Y, Xu Z, Chu X, Tao L, Liu L, Ge C, Te Pas MFW, Jia J. Biological mechanisms discriminating growth rate and adult body weight phenotypes in two Chinese indigenous chicken breeds. BMC Genomics 2017. [PMID: 28633640 PMCID: PMC5477733 DOI: 10.1186/s12864-017-3845-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background Intensive selection has resulted in increased growth rates and muscularity in broiler chickens, in addition to adverse effects, including delayed organ development, sudden death syndrome, and altered metabolic rates. The biological mechanisms underlying selection responses remain largely unknown. Non-artificially-selected indigenous Chinese chicken breeds display a wide variety of phenotypes, including differential growth rate, body weight, and muscularity. The Wuding chicken breed is a fast growing large chicken breed, and the Daweishan mini chicken breed is a slow growing small chicken breed. Together they form an ideal model system to study the biological mechanisms underlying broiler chicken selection responses in a natural system. The objective of this study was to study the biological mechanisms underlying differential phenotypes between the two breeds in muscle and liver tissues, and relate these to the growth rate and body development phenotypes of the two breeds. Results The muscle tissue in the Wuding breed showed higher expression of muscle development genes than muscle tissue in the Daweishan chicken breed. This expression was accompanied by higher expression of acute inflammatory response genes in Wuding chicken than in Daweishan chicken. The muscle tissue of the Daweishan mini chicken breed showed higher expression of genes involved in several metabolic mechanisms including endoplasmic reticulum, protein and lipid metabolism, energy metabolism, as well as specific immune traits than in the Wuding chicken. The liver tissue showed fewer differences between the two breeds. Genes displaying higher expression in the Wuding breed than in the Daweishan breed were not associated with a specific gene network or biological mechanism. Genes highly expressed in the Daweishan mini chicken breed compared to the Wuding breed were enriched for protein metabolism, ABC receptors, signal transduction, and IL6-related mechanisms. Conclusions We conclude that faster growth rates and larger body size are related to increased expression of genes involved in muscle development and immune response in muscle, while slower growth rates and smaller body size are related to increased general cellular metabolism. The liver of the Daweishan breed displayed increased expression of metabolic genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3845-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tengfei Dou
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Sumei Zhao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Hua Rong
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Dahai Gu
- Department of Food Science, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Qihua Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Ying Huang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Zhiqiang Xu
- Department of Food Science, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Xiaohui Chu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Linli Tao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Lixian Liu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Changrong Ge
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Marinus F W Te Pas
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Building 107, Radix, Droevendaalsesteeg 1, P.O. Box 338, 6708 PB, 6700 AH, Wageningen, The Netherlands. .,Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China. .,Dali University, Dali, People's Republic of China.
| | - Junjing Jia
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.
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15
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Te Pas MFW, Madsen O, Calus MPL, Smits MA. The Importance of Endophenotypes to Evaluate the Relationship between Genotype and External Phenotype. Int J Mol Sci 2017; 18:E472. [PMID: 28241430 PMCID: PMC5344004 DOI: 10.3390/ijms18020472] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 02/02/2017] [Accepted: 02/13/2017] [Indexed: 02/06/2023] Open
Abstract
With the exception of a few Mendelian traits, almost all phenotypes (traits) in livestock science are quantitative or complex traits regulated by the expression of many genes. For most of the complex traits, differential expression of genes, rather than genomic variation in the gene coding sequences, is associated with the genotype of a trait. The expression profiles of the animal's transcriptome, proteome and metabolome represent endophenotypes that influence/regulate the externally-observed phenotype. These expression profiles are generated by interactions between the animal's genome and its environment that range from the cellular, up to the husbandry environment. Thus, understanding complex traits requires knowledge about not only genomic variation, but also environmental effects that affect genome expression. Gene products act together in physiological pathways and interaction networks (of pathways). Due to the lack of annotation of the functional genome and ontologies of genes, our knowledge about the various biological systems that contribute to the development of external phenotypes is sparse. Furthermore, interaction with the animals' microbiome, especially in the gut, greatly influences the external phenotype. We conclude that a detailed understanding of complex traits requires not only understanding of variation in the genome, but also its expression at all functional levels.
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Affiliation(s)
- Marinus F W Te Pas
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700AH Wageningen, The Netherlands.
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University, 6700AH Wageningen, The Netherlands.
| | - Mario P L Calus
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700AH Wageningen, The Netherlands.
| | - Mari A Smits
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700AH Wageningen, The Netherlands.
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16
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Ogłuszka M, Szostak A, Te Pas MFW, Poławska E, Urbański P, Blicharski T, Pareek CS, Juszczuk-Kubiak E, Dunkelberger JR, Horbańczuk JO, Pierzchała M. A porcine gluteus medius muscle genome-wide transcriptome analysis: dietary effects of omega-6 and omega-3 fatty acids on biological mechanisms. Genes Nutr 2017; 12:4. [PMID: 28163789 PMCID: PMC5282897 DOI: 10.1186/s12263-017-0552-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/09/2017] [Indexed: 01/27/2023]
Abstract
Background The level of omega-6 and omega-3 polyunsaturated fatty acids can affect many cellular systems and function via nuclear receptors or the bioactive lipid regulation of gene expression. The objective of this study was to investigate changes in the muscle transcriptome and the biological functions regulated by increased consumption of omega-3 and omega-6 fatty acids in the pig gluteus medius muscle. Results The transcriptome of the gluteus medius muscle was studied for pigs subjected to either a control diet or a diet supplemented with linseed and rapeseed oil to increase polyunsaturated fatty acid content. Next-generation sequencing (NGS) was used to generate the muscle tissue transcriptome database pointing differentially expressed genes (DEG). Comparative expression analyses identified 749 genes significantly differing at least in the twofold of change between two groups of animals fed with divergent level of omega-3 and omega-6 fatty acids. The expression of 219 genes was upregulated, and the expression of 530 genes was downregulated in the group of pigs supplemented with omega-3 and omega-6 fatty acids in relation to control group pigs. Results of RNA-seq indicated a role of fatty acid in the regulation of the expression of genes which are essential for muscle tissue development and functioning. Functional analysis revealed that the identified genes were important for a number of biological processes including inflammatory response, signaling, lipid metabolism, and homeostasis. Conclusions Summarizing, obtained results provide strong evidence that omega-6 and omega-3 fatty acids regulate fundamental metabolic processes in muscle tissue development and functioning. Electronic supplementary material The online version of this article (doi:10.1186/s12263-017-0552-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Magdalena Ogłuszka
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Postępu 36A, 05-552 Jastrzębiec, Poland
| | - Agnieszka Szostak
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Postępu 36A, 05-552 Jastrzębiec, Poland
| | - Marinus F W Te Pas
- Breeding and Genomic Centre, Wageningen UR Livestock Research, 6700 AH Wageningen, The Netherlands
| | - Ewa Poławska
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Postępu 36A, 05-552 Jastrzębiec, Poland
| | - Paweł Urbański
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Postępu 36A, 05-552 Jastrzębiec, Poland
| | - Tadeusz Blicharski
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Postępu 36A, 05-552 Jastrzębiec, Poland
| | - Chandra S Pareek
- Division of Functional Genomics in Biological and Biomedical Research, Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Edyta Juszczuk-Kubiak
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Postępu 36A, 05-552 Jastrzębiec, Poland
| | - Jenelle R Dunkelberger
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011 USA
| | - Jarosław O Horbańczuk
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Postępu 36A, 05-552 Jastrzębiec, Poland
| | - Mariusz Pierzchała
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Postępu 36A, 05-552 Jastrzębiec, Poland
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17
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Szostak A, Ogłuszka M, Te Pas MFW, Poławska E, Urbański P, Juszczuk-Kubiak E, Blicharski T, Pareek CS, Dunkelberger JR, Horbańczuk JO, Pierzchała M. Effect of a diet enriched with omega-6 and omega-3 fatty acids on the pig liver transcriptome. Genes Nutr 2016; 11:9. [PMID: 27482299 PMCID: PMC4959555 DOI: 10.1186/s12263-016-0517-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 11/28/2015] [Indexed: 01/10/2023]
Abstract
The optimal ratio of omega-6 to omega-3 polyunsaturated fatty acids (PUFAs) is important for keeping the homeostasis of biological processes and metabolism, yet the underlying biological mechanism is poorly understood. The objective of this study was to identify changes in the pig liver transcriptome induced by a diet enriched with omega-6 and omega-3 fatty acids and to characterize the biological mechanisms related to PUFA metabolism. Polish Landrace pigs (n = 12) were fed diet enriched with linoleic acid (LA, omega-6) and α-linolenic acid (ALA, omega-3) or standard diet as a control. The fatty acid profiling was assayed in order to verify how feeding influenced the fatty acid content in the liver, and subsequently next-generation sequencing (NGS) was used to identify differentially expressed genes (DEG) between transcriptomes between dietary groups. The biological mechanisms and pathway interaction networks were identified using DAVID and Cytoscape tools. Fatty acid profile analysis indicated a higher contribution of PUFAs in the liver for LA- and ALA-enriched diet group, particularly for the omega-3 fatty acid family, but not omega-6. Next-generation sequencing identified 3565 DEG, 1484 of which were induced and 2081 were suppressed by PUFA supplementation. A low ratio of omega-6/omega-3 fatty acids resulted in the modulation of fatty acid metabolism pathways and over-representation of genes involved in energy metabolism, signal transduction, and immune response pathways. In conclusion, a diet enriched with omega-6 and omega-3 fatty acids altered the transcriptomic profile of the pig liver and would influence animal health status.
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Affiliation(s)
- Agnieszka Szostak
- Institute of Genetics and Animal Breeding, Polish Academy of Science, Jastrzębiec, Poland
| | - Magdalena Ogłuszka
- Institute of Genetics and Animal Breeding, Polish Academy of Science, Jastrzębiec, Poland
| | - Marinus F W Te Pas
- Animal Breeding and Genetics Centre, Wageningen UR Livestock Research, Lelystad, The Netherlands
| | - Ewa Poławska
- Institute of Genetics and Animal Breeding, Polish Academy of Science, Jastrzębiec, Poland
| | - Paweł Urbański
- Institute of Genetics and Animal Breeding, Polish Academy of Science, Jastrzębiec, Poland
| | - Edyta Juszczuk-Kubiak
- Institute of Genetics and Animal Breeding, Polish Academy of Science, Jastrzębiec, Poland
| | - Tadeusz Blicharski
- Institute of Genetics and Animal Breeding, Polish Academy of Science, Jastrzębiec, Poland
| | - Chandra Shekhar Pareek
- Functional Genomics Laboratory, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Toruń, Poland
| | | | - Jarosław O Horbańczuk
- Institute of Genetics and Animal Breeding, Polish Academy of Science, Jastrzębiec, Poland
| | - Mariusz Pierzchała
- Institute of Genetics and Animal Breeding, Polish Academy of Science, Jastrzębiec, Poland
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Te Pas MFW, Hulsegge I, Schokker D, Smits MA, Fife M, Zoorob R, Endale ML, Rebel JMJ. Meta-analysis of chicken--salmonella infection experiments. BMC Genomics 2012; 13:146. [PMID: 22531008 PMCID: PMC3411418 DOI: 10.1186/1471-2164-13-146] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 04/24/2012] [Indexed: 11/10/2022] Open
Abstract
Background Chicken meat and eggs can be a source of human zoonotic pathogens, especially Salmonella species. These food items contain a potential hazard for humans. Chickens lines differ in susceptibility for Salmonella and can harbor Salmonella pathogens without showing clinical signs of illness. Many investigations including genomic studies have examined the mechanisms how chickens react to infection. Apart from the innate immune response, many physiological mechanisms and pathways are reported to be involved in the chicken host response to Salmonella infection. The objective of this study was to perform a meta-analysis of diverse experiments to identify general and host specific mechanisms to the Salmonella challenge. Results Diverse chicken lines differing in susceptibility to Salmonella infection were challenged with different Salmonella serovars at several time points. Various tissues were sampled at different time points post-infection, and resulting host transcriptional differences investigated using different microarray platforms. The meta-analysis was performed with the R-package metaMA to create lists of differentially regulated genes. These gene lists showed many similarities for different chicken breeds and tissues, and also for different Salmonella serovars measured at different times post infection. Functional biological analysis of these differentially expressed gene lists revealed several common mechanisms for the chicken host response to Salmonella infection. The meta-analysis-specific genes (i.e. genes found differentially expressed only in the meta-analysis) confirmed and expanded the biological functional mechanisms. Conclusions The meta-analysis combination of heterogeneous expression profiling data provided useful insights into the common metabolic pathways and functions of different chicken lines infected with different Salmonella serovars.
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Affiliation(s)
- Marinus F W Te Pas
- Animal Breeding and Genetics Centre (ABGC), Wageningen UR Livestock Research, Animal Sciences Group, Wageningen University and Research Centre, P.O. Box 65, 8200 AB Lelystad, The Netherlands.
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Jungerius BJ, Gu J, Crooijmans RPMA, van der Poel JJ, Groenen MAM, van Oost BA, Te Pas MFW. ESTIMATION OF THE EXTENT OF LINKAGE DISEQUILIBRIUM IN SEVEN REGIONS OF THE PORCINE GENOME. Anim Biotechnol 2007; 16:41-54. [PMID: 28881173 DOI: 10.1081/abio-200053402] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Linkage disequilibrium (LD) refers to the correlation among neighboring alleles, reflecting non-random patterns of association between alleles at (nearby) loci. A better understanding of LD in the porcine genome is of direct relevance for identification of genes and mutations with a certain effect on the traits of interest. Here, 215 SNPs in seven genomic regions were genotyped in individuals of three breeds. Pairwise linkage disequilibrium was calculated for all marker pairs. To estimate the extent of LD, all pairwise LD values were plotted against the distance between the markers. Based on SNP markers in four genomic regions analyzed in three panels from populations of Large White, Dutch Landrace, and Meishan origin, useful LD is estimated to extend for approximately 40 to 60 kb in the porcine genome.
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Affiliation(s)
- Bart J Jungerius
- a Department of Animal Breeding and Genetics , Wageningen University , Wageningen , Netherlands
| | - Jingjing Gu
- a Department of Animal Breeding and Genetics , Wageningen University , Wageningen , Netherlands
| | | | - Jan J van der Poel
- a Department of Animal Breeding and Genetics , Wageningen University , Wageningen , Netherlands
| | - Martien A M Groenen
- a Department of Animal Breeding and Genetics , Wageningen University , Wageningen , Netherlands
| | - Bernard A van Oost
- b Department of Laboratory Animal Sciences , Utrecht University , Utrecht , Netherlands
| | - Marinus F W Te Pas
- c Animal Sciences Group , Wageningen University and Research Centre , Lelystad , Netherlands
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Te Pas MFW, De Wit AAW, Priem J, Cagnazzo M, Davoli R, Russo V, Pool MH. Transcriptome expression profiles in prenatal pigs in relation to myogenesis. J Muscle Res Cell Motil 2005; 26:157-65. [PMID: 15999225 DOI: 10.1007/s10974-005-7004-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Accepted: 05/09/2005] [Indexed: 11/24/2022]
Abstract
Myogenesis, the formation of muscle fibers, is a complex process. Pigs have been selected for efficient muscle growth for the past decades making them interesting to study myogenesis. We studied expression profiles of genes known to affect myogenesis, muscle structural proteins, and energy metabolism in prenatal pigs from 14 to 91 days of gestation. Primary and secondary muscle fiber formation takes place during days 30-60 and 54-90 of gestation, respectively. Differential expression and expression levels of the genes were studied using microarray technology. Gene activation and repression profiles were studied counting the number of spots with detectable signal. The number of spots for muscle tissue structural protein genes showing upregulated expression increased constantly from day 14 until day 91 of gestation indicating continued activation of genes during this period. The mRNA expression level of the genes showed a peak around day 35 of gestation. The expression levels of genes affecting myogenic differentiation (stimulating and inhibiting) showed a peak at day 35 of gestation. The number of spots for differentiation-stimulating genes showing differential expression reaches a first peak around day 35 of gestation and a nadir at day 49 of gestation while the number of spots for differentiation-inhibiting genes reaches a nadir at day 35 of gestation. Myogenic differentiation seems less a matter of the expression level of genes affecting differentiation, but depends on the balance between the number of significantly activated genes for stimulating and inhibiting differentiation. Genes stimulating myoblast proliferation showed a small peak expression prior to day 35 of gestation indicating myoblast proliferation before differentiation. The number of spots and the expression levels of genes for glycolysis and ATP-metabolism are at a nadir around days 35 and 49-63 of gestation suggesting that the energy metabolism is low during fusion of myoblasts into multinucleated muscle fibers.
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Affiliation(s)
- Marinus F W Te Pas
- Division of Animal Resource Development, Wageningen University and Research, Animal Sciences Group ID-Lelystad, Animal Genomics Group, P.O. Box 65, 8200 AB Lelystad, The Netherlands.
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Jungerius BJ, van Laere AS, Te Pas MFW, van Oost BA, Andersson L, Groenen MAM. The IGF2-intron3-G3072A substitution explains a major imprinted QTL effect on backfat thickness in a Meishan×European white pig intercross. Genet Res (Camb) 2004; 84:95-101. [PMID: 15678747 DOI: 10.1017/s0016672304007098] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A paternally expressed QTL for muscle growth and backfat thickness (BFT) has previously been identified near the IGF2 locus on the distal tip of pig chromosome 2 (SSC2p) in three experimental F2 populations. Recently, a mutation in a regulatory element of the IGF2 gene was identified as the quantitative trait nucleotide (QTN) underlying the major QTL effect on muscle growth and BFT in crosses between Large White and Wild Boar or Pietrain. This study demonstrates that the IGF2 mutation also controls the paternally expressed QTL for backfat thickness in a cross between Meishan and European Whites. In addition, a comparison of QTL of backfat thickness measured by Hennessy grading probe (HGP) and by ultrasound measurement (USM) was made. In the USM analyses, the IFG2 mutation explains the entire QTL effect on SSC2p, whereas in the HGP analysis the presence of a second minor QTL can not be excluded. Finally, this study shows that this particular IGF2 mutation does not cause the paternally expressed QTL for teat number mapping to the same region of SSC2p as the BFT QTL.
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Affiliation(s)
- Bart J Jungerius
- Department of Animal Breeding and Genetics, Wageningen University, P.O. Box 40, 6700 AH Wageningen, The Netherlands.
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Jungerius BJ, Veenendaal A, Van Oost BA, Te Pas MFW, Groenen MAM. Typing single-nucleotide polymorphisms using a gel-based sequencer: a new data analysis tool and suggestions for improved efficiency. Mol Biotechnol 2004; 25:283-8. [PMID: 14668541 DOI: 10.1385/mb:25:3:283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) are increasingly used as genetic markers. Although a high number of SNP-genotyping techniques have been described, most techniques still have low throughput or require major investments. For laboratories that have access to an automated sequencer, a single-base extension (SBE) assay can be implemented using the ABI SNaPshot trade mark kit. Here we present a modified protocol comprising multiplex template generation, multiplex SBE reaction, and multiplex sample analysis on a gel-based sequencer such as the ABI 377. These sequencers run on a Macintosh platform, but on this platform the software available for analysis of data from the ABI 377 has limitations. First, analysis of the size standard included with the kit is not facilitated. Therefore a new size standard was designed. Second, using Genotyper (ABI), the analysis of the data is very tedious and time consuming. To enable automated batch analysis of 96 samples, with 10 SNPs each, we developed SNPtyper. This is a spreadsheet-based tool that uses the data from Genotyper and offers the user a convenient interface to set parameters required for correct allele calling. In conclusion, the method described will enable any lab having access to an ABI sequencer to genotype up to 1000 SNPs per day for a single experimenter, without investing in new equipment.
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Affiliation(s)
- Bart J Jungerius
- Animal Breeding and Genetics Group, PO Box 338, 6700 AH Wageningen, The Netherlands.
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