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Liu Y, Wu X, Xu Q, Lan X, Li W. Temporal Transcriptome Dynamics of Longissimus dorsi Reveals the Mechanism of the Differences in Muscle Development and IMF Deposition between Fuqing Goats and Nubian Goats. Animals (Basel) 2024; 14:1770. [PMID: 38929389 PMCID: PMC11200590 DOI: 10.3390/ani14121770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/02/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
In this study, we measured the growth performance and intramuscular fat (IMF) content of the Longissimus dorsi (LD) of Fuqing goats (FQs) and Nubian goats (NBYs), which exhibit extreme phenotypic differences in terms of their production and meat quality traits. RNA-Seq analysis was performed, and transcriptome data were obtained from the LD tissue of 3-month fetuses (E3), 0-month lambs (0M), 3-month lambs (3M), and 12-month lambs (12M) to reveal the differences in the molecular mechanisms regulating the muscle development and IMF deposition between FQs and NBYs. The results showed that a higher body weight and average daily gain were observed in the NBYs at three developmental stages after birth, whereas a higher IMF content was registered in the FQs at 12M. Additionally, transcriptome profiles during the embryonic period and after birth were completely different for both FQs and NBYs. Moreover, DEGs (KIF23, CCDC69, CCNA2, MKI67, KIF11, RACGAP1, NUSAP1, SKP2, ZBTB18, NES, LOC102180034, CAPN6, TUBA1A, LOC102178700, and PEG10) significantly enriched in the cell cycle (ko04110) at E3 (FQs vs. NBYs), and DEGs (MRPS7, RPS8, RPL6, RPL4, RPS11, RPS10, RPL5, RPS6, RPL8, RPS13, RPS24, RPS15, RPL23) significantly enriched in ribosomes (ko03010) at 0M (FQs vs. NBYs) related to myogenic differentiation and fusion were identified. Meanwhile, the differences in glucose and lipid metabolism began at the E3 timepoint and continued to strengthen as growth proceeded in FQs vs. NBYs. DEGs (CD36, ADIROQR2, ACACA, ACACB, CPT1A, IGF1R, IRS2, LDH-A, PKM, HK2, PFKP, PCK1, GPI, FASN, FADS1, ELOVL6, HADHB, ACOK1, ACAA2, and ACSL4) at 3M (FQs vs. NBYs) and 12M (FQs vs. NBYs) significantly enriched in the AMPK signaling pathway (ko04152), insulin resistance (ko04931), the insulin signaling pathway (ko04910), fatty acid metabolism (ko01212), and glycolysis/gluconeogenesis (ko00010) related to IMF deposition were identified. Further, the results from this study provide the basis for future studies on the mechanisms regulating muscle development and IMF deposition in different breeds of goats, and the candidate genes identified could be used in the selection process.
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Affiliation(s)
- Yuan Liu
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.L.); (X.W.); (Q.X.)
| | - Xianfeng Wu
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.L.); (X.W.); (Q.X.)
| | - Qian Xu
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.L.); (X.W.); (Q.X.)
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Wenyang Li
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.L.); (X.W.); (Q.X.)
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Huo Y, Li X, Sun C, Pan Z, Li Q, Du X. From stability to reliability: Unveiling the un-biased reference genes in porcine ovarian granulosa cells under different conditions. Gene 2024; 897:148089. [PMID: 38123003 DOI: 10.1016/j.gene.2023.148089] [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: 10/31/2023] [Revised: 12/02/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Selection of optimal reference genes (RGs) is fundamental for functional genomics studies and gene expression analysis, which are two main approaches to identify functional genes and their expression patterns. However, no systematic study has identified the suitable RGs in porcine ovarian granulosa cells (GCs) which are essential for follicle fate and sow fertility. In this study, the expression profiles of 12 widely-used RGs (GAPDH, RPLP0, ACTB, TUBA1B, EIF3K, PPIA, ATP5F1, B2M, HPRT1, UBC, RPS3, and EEF1A1) in porcine GCs during follicular development and under different abiotic stresses were systematically investigated. Expression stability of the candidate RGs were comprehensively accessed by five statistical algorithms including ΔCt, NormFinder, BestKeeper, geNorm, and RefFinder, indicating that RPS3 and PPIA are the optimal RGs during follicular development, EEF1A1 and RPLP0 are most stable under oxidative stress and inflammation, while ATP5F1, B2M, and RPS3 have higher stability under starvation and heat stress. Notably, the most commonly used RGs (ACTB, GAPDH, and TUBA1B) exhibited low stability in GCs. Reliability of stable RGs was verified by RT-qPCR and showed that selection of the stable RGs significantly improved the detection accuracy of qPCR, which confirms once again that the stability of RGs should not be taken for granted. Our findings identified optimal RG sets in porcine GCs under different conditions, which is helpful in future studies to accurately identify the key regulators and their expression patterns during follicular development in sows.
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Affiliation(s)
- Yangan Huo
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiaoxue Li
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Chen Sun
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zengxiang Pan
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Qifa Li
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xing Du
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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Wang Y, Zhang YQ, Wu ZW, Fang T, Wang F, Zhao H, Du ZQ, Yang CX. Selection of reference genes for RT-qPCR analysis in developing chicken embryonic ovary. Mol Biol Rep 2023; 50:3379-3387. [PMID: 36729208 DOI: 10.1007/s11033-023-08280-0] [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: 10/19/2022] [Accepted: 01/12/2023] [Indexed: 02/03/2023]
Abstract
BACKGROUND Normalization of the expression profiling of target genes, in a tissue-specific manner and under different experimental conditions, requires stably expressed gene(s) to be used as internal reference(s). However, to study the molecular regulation of oocyte meiosis initiation during ovary development in chicken embryos, stable reference gene(s) still need to be compared and confirmed. METHODS AND RESULTS Six candidate genes previously used as internal references for the chicken embryo (Actb, Cvh, Dazl, Eef1a, Gapdh and Rpl15) were chosen, and their expression profiles in left ovaries dissected at five chicken embryonic days (E12.5, E15.5, E17.5, E18.5 and E20.5) were evaluated, respectively. Separately, GeNorm, NormFinder, BestKeeper and Comparative ΔCt methods were used to assess the stability of candidate reference genes, and all results were combined to give the final rank by RefFinder. All methods identified that Eef1a and Rpl15 were the two most stable internal reference genes, whereas Cvh is the most unstable one. Moreover, expression levels of three marker genes for chicken oocyte meiosis entry (Stra8, Scp3 and Dmc1) were normalized, based on Eef1a, Rpl15, or their combinations, respectively. CONCLUSION Our findings provide the most suitable internal reference genes (Eef1a and Rpl15), to investigate further molecular regulation of ovary development and oocyte meiosis initiation in chicken embryos.
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Affiliation(s)
- Yi Wang
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China
| | - Yu-Qing Zhang
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China
| | - Zi-Wei Wu
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China
| | - Ting Fang
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China
| | - Fang Wang
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China
| | - Han Zhao
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China
| | - Zhi-Qiang Du
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China.
| | - Cai-Xia Yang
- College of Animal Science, Yangtze University, 434025, Jingzhou, Hubei, China.
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Cheng TY, Zimmerman JJ, Giménez-Lirola LG. Internal reference genes with the potential for normalizing quantitative PCR results for oral fluid specimens. Anim Health Res Rev 2022; 23:147-156. [PMID: 36330795 DOI: 10.1017/s1466252322000044] [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] [Indexed: 11/06/2022]
Abstract
In basic research, testing of oral fluid specimens by real-time quantitative polymerase chain reaction (qPCR) has been used to evaluate changes in gene expression levels following experimental treatments. In diagnostic medicine, qPCR has been used to detect DNA/RNA transcripts indicative of bacterial or viral infections. Normalization of qPCR using endogenous and exogenous reference genes is a well-established strategy for ensuring result comparability by controlling sample-to-sample variation introduced during sampling, storage, and qPCR testing. In this review, the majority of recent publications in human (n = 136) and veterinary (n = 179) medicine did not describe the use of internal reference genes in qPCRs for oral fluid specimens (52.9% animal studies; 57.0% human studies). However, the use of endogenous reference genes has not been fully explored or validated for oral fluid specimens. The lack of valid internal reference genes inherent to the oral fluid matrix will continue to hamper the reliability, reproducibility, and generalizability of oral fluid qPCR assays until this issue is addressed.
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Affiliation(s)
- Ting-Yu Cheng
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jeffrey J Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Luis G Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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Wang Y, Wu Z, Fang T, Zhang Y, Chen L, Du Z, Yang C. Identification of internal reference genes for porcine immature Sertoli cells under heat stress. Reprod Domest Anim 2022; 57:1344-1352. [DOI: 10.1111/rda.14211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Yi Wang
- College of Animal Science Yangtze University 434025 Jingzhou Hubei China
| | - Zi‐Wei Wu
- College of Animal Science Yangtze University 434025 Jingzhou Hubei China
| | - Ting Fang
- College of Animal Science Yangtze University 434025 Jingzhou Hubei China
| | - Yu‐Qing Zhang
- College of Animal Science Yangtze University 434025 Jingzhou Hubei China
| | - Lu Chen
- College of Animal Science and Technology Northeast Agricultural University 150030 Harbin Heilongjiang China
| | - Zhi‐Qiang Du
- College of Animal Science Yangtze University 434025 Jingzhou Hubei China
| | - Cai‐Xia Yang
- College of Animal Science Yangtze University 434025 Jingzhou Hubei China
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Hul LM, Ibelli AMG, Savoldi IR, Marcelino DEP, Fernandes LT, Peixoto JO, Cantão ME, Higa RH, Giachetto PF, Coutinho LL, Ledur MC. Differentially expressed genes in the femur cartilage transcriptome clarify the understanding of femoral head separation in chickens. Sci Rep 2021; 11:17965. [PMID: 34504189 PMCID: PMC8429632 DOI: 10.1038/s41598-021-97306-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
Locomotor problems are among one of the main concerns in the current poultry industry, causing major economic losses and affecting animal welfare. The most common bone anomalies in the femur are dyschondroplasia, femoral head separation (FHS), and bacterial chondronecrosis with osteomyelitis (BCO), also known as femoral head necrosis (FHN). The present study aimed to identify differentially expressed (DE) genes in the articular cartilage (AC) of normal and FHS-affected broilers by RNA-Seq analysis. In the transcriptome analysis, 12,169 genes were expressed in the femur AC. Of those, 107 genes were DE (FDR < 0.05) between normal and affected chickens, of which 9 were downregulated and 98 were upregulated in the affected broilers. In the gene-set enrichment analysis using the DE genes, 79 biological processes (BP) were identified and were grouped into 12 superclusters. The main BP found were involved in the response to biotic stimulus, gas transport, cellular activation, carbohydrate-derived catabolism, multi-organism regulation, immune system, muscle contraction, multi-organism process, cytolysis, leukocytes and cell adhesion. In this study, the first transcriptome analysis of the broilers femur articular cartilage was performed, and a set of candidate genes (AvBD1, AvBD2, ANK1, EPX, ADA, RHAG) that could trigger changes in the broiler´s femoral growth plate was identified. Moreover, these results could be helpful to better understand FHN in chickens and possibly in humans.
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Affiliation(s)
- Ludmila Mudri Hul
- grid.412329.f0000 0001 1581 1066Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, PR 85040-080 Brazil
| | - Adriana Mércia Guaratini Ibelli
- grid.412329.f0000 0001 1581 1066Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, PR 85040-080 Brazil ,Embrapa Suínos e Aves, Concórdia, SC 89715-899 Brazil
| | - Igor Ricardo Savoldi
- grid.412287.a0000 0001 2150 7271Programa de Pós-Graduação em Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, Chapecó, SC 89815-630 Brazil
| | | | | | - Jane Oliveira Peixoto
- grid.412329.f0000 0001 1581 1066Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, PR 85040-080 Brazil ,Embrapa Suínos e Aves, Concórdia, SC 89715-899 Brazil
| | | | - Roberto Hiroshi Higa
- grid.460200.00000 0004 0541 873XEmbrapa Informática Agropecuária, Campinas, SP 70770-901 Brazil
| | | | - Luiz Lehmann Coutinho
- grid.11899.380000 0004 1937 0722Departamento de Zootecnia, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, SP 13418-900 Brazil
| | - Mônica Corrêa Ledur
- Embrapa Suínos e Aves, Concórdia, SC 89715-899 Brazil ,grid.412287.a0000 0001 2150 7271Programa de Pós-Graduação em Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, Chapecó, SC 89815-630 Brazil
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Validation of the Reference Genes for the Gene Expression Studies in Different Cell Lines of Pig. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5364190. [PMID: 34458368 PMCID: PMC8390154 DOI: 10.1155/2021/5364190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/20/2021] [Indexed: 11/30/2022]
Abstract
Reverse transcription quantitative real-time polymerase chain reaction is one of the important methods to investigate gene expression in cells and tissues. However, if the data cannot be normalized with appropriate reference genes, the results may be unreliable. In this study, we detected the expression of 15 reference genes in three pig cell lines. The results showed that SDHA and ALDOA were the most stable reference genes in 3D4/21 cells. TOP2B, TBP, and PPIA were the most stable reference genes in PK-15 cells. SDHA and ALDOA were the most stable reference genes in IPEC-J2 cells. In addition, each cell line only needs to use two reference genes to standardize the expression of target genes. Taken together, this study provides a reference for different pig cell lines to select reference genes and also provides a theoretical basis for the use of these cell lines in related functional researches.
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The Selection of Reliable Reference Genes for RT-qPCR Analysis of Anisakis simplex Sensu Stricto Gene Expression from Different Developmental Stages. Acta Parasitol 2020; 65:837-842. [PMID: 32488545 PMCID: PMC7679296 DOI: 10.2478/s11686-020-00220-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/23/2020] [Indexed: 01/28/2023]
Abstract
BACKGROUND Anisakis simplex s. s. is a parasitic nematode with a complex life cycle in which humans can become accidental hosts by consuming raw or not fully cooked fish containing L3 larvae. The growing popularity of raw fish dishes has contributed to an increase in the incidence of anisakiasis, which has spurred scientific efforts to develop new methods for diagnosing and treating the disease and also to investigate the gene expression at different developmental stages of this parasite. The identification of reference genes suitable for the normalization of RT-qPCR data has not been studied with respect to A. simplex s. s. METHODS In the present study, eight candidate reference genes were analyzed in A. simplex s. s. at two different developmental stages: L3 and L4. The expression stability of these genes was assessed by geNorm and NormFinder softwares. RESULTS In general, our results identified translation elongation factor 1α (ef-1α) and peptidyl-prolyl isomerase 12 (ppi12) as the most stable genes in L3 and L4 developmental stages of A. simplex s. s. Validation of the selected reference genes was performed by profiling the expression of the nuclear hormone receptor gene (nhr 48) in different developmental stages. CONCLUSIONS This first analysis selecting suitable reference genes for RT-qPCR in A. simplex s. s. will facilitate future functional analyses and deep mining of genetic resources in this parasitic nematode.
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Hul LM, Ibelli AMG, Peixoto JDO, Souza MR, Savoldi IR, Marcelino DEP, Tremea M, Ledur MC. Reference genes for proximal femoral epiphysiolysis expression studies in broilers cartilage. PLoS One 2020; 15:e0238189. [PMID: 32841273 PMCID: PMC7447007 DOI: 10.1371/journal.pone.0238189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 08/11/2020] [Indexed: 12/18/2022] Open
Abstract
The use of reference genes is required for relative quantification in gene expression analysis and the stability of these genes can be variable depending on the experimental design. Therefore, it is indispensable to test the reliability of endogenous genes previously to their use. This study evaluated nine candidate reference genes to select the most stable genes to be used as reference in gene expression studies with the femoral cartilage of normal and epiphysiolysis-affected broilers. The femur articular cartilage of 29 male broilers with 35 days of age was collected, frozen and further submitted to RNA extraction and quantitative PCR (qPCR) analysis. The candidate reference genes evaluated were GAPDH, HMBS, HPRT1, MRPS27, MRPS30, RPL30, RPL4, RPL5, and RPLP1. For the gene stability evaluation, three software were used: GeNorm, BestKeeper and NormFinder, and a global ranking was generated using the function RankAggreg. In this study, the RPLP1 and RPL5 were the most reliable endogenous genes being recommended for expression studies with femur cartilage in broilers with epiphysiolysis and possible other femur anomalies.
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Affiliation(s)
- Ludmila Mudri Hul
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, Paraná, Brazil
| | - Adriana Mércia Guaratini Ibelli
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, Paraná, Brazil
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Jane de Oliveira Peixoto
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, Paraná, Brazil
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Mayla Regina Souza
- Programa de Pós-Graduação em Zootecnia, UDESC-Oeste, Chapecó, Santa Catarina, Brazil
| | - Igor Ricardo Savoldi
- Programa de Pós-Graduação em Zootecnia, UDESC-Oeste, Chapecó, Santa Catarina, Brazil
| | | | - Mateus Tremea
- Universidade Federal de Santa Maria, campus Palmeira das Missões, Rio Grande do Sul, Brazil
| | - Mônica Corrêa Ledur
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
- Programa de Pós-Graduação em Zootecnia, UDESC-Oeste, Chapecó, Santa Catarina, Brazil
- * E-mail:
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Wang T, Li J, Shao Y, Yao W, Xia J, He Q, Huang F. The effect of dietary garcinol supplementation on oxidative stability, muscle postmortem glycolysis and meat quality in pigs. Meat Sci 2019; 161:107998. [PMID: 31707156 DOI: 10.1016/j.meatsci.2019.107998] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 01/19/2023]
Abstract
The objective of this study was to evaluate the effects of dietary garcinol (0, 200, 400 and 600 mg/kg) on the growth performance, meat quality, postmortem glycolysis and antioxidative capacity of finishing pigs. Dietary garcinol increased pigs' average daily gain, pH 24h, a* and myoglobin content of longissimus dorsi (LM) (P < 0.05), and decreased feed/gain ratio, the L*24h, glycolytic potential, drip loss, shear force, and backfat depth (P < 0.05). The glutathione peroxidase (GPx), catalase (CAT) and total antioxidative capacity (T-AOC) were significantly increased by garcinol (P < 0.05), while the activity of lactate dehydrogenase (LDH) and malonaldehyde (MDA) content were decreased (P < 0.05). Moreover, garcinol decreased the p300/CBP-associated factor (PCAF) activity, the acetylation level and activities of glycolysis enzymes phosphoglycerate kinase 1 (PGK1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and 6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase-3 (PFKFB3) (P < 0.05). The results of this study showed that garcinol decreased postmortem glycolysis, and this may be due to the mechanism of decreasing glycolytic enzyme acetylation induced by PCAF. The present study indicates that garcinol can facilitate the growth performance of pigs and improve pork quality by changing postmortem glycolysis and antioxidative capacity.
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Affiliation(s)
- Tongxin Wang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Juan Li
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yafei Shao
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Weilei Yao
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Xia
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiongyu He
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Feiruo Huang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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11
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Wang S, Wang B, He H, Sun A, Guo C. A new set of reference housekeeping genes for the normalization RT-qPCR data from the intestine of piglets during weaning. PLoS One 2018; 13:e0204583. [PMID: 30256841 PMCID: PMC6157878 DOI: 10.1371/journal.pone.0204583] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 09/11/2018] [Indexed: 01/09/2023] Open
Abstract
The intestinal mucosal development of piglets (Sus scrofa) during the weaning stage is important to their disease susceptibility and later growth. Quantitative real-time PCR (RT-qPCR) is commonly used to screen for differentially expressed genes and, for accurate results, proper reference housekeeping genes are essential. Here we assessed the mRNA expression of 18 well-known candidate reference genes at different parts of the gastrointestinal tract (GIT) of piglets during the weaning process by RT-qPCR assay. GeNorm analysis revealed that B2M/HMBS/HPRT1 were the three most stable reference genes and GAPDH was the least stable gene in the duodenum, jejunum, ileum, colon, and whole GIT. BestKeeper analysis found that B2M/HMBS/PGK11, HMBS/B2M/HPRT1, B2M/HMBS/HSPCB, B2M/HPRT1/HMBS, and B2M/HMBS/HPRT1 were the most stable genes in the duodenum, jejunum, ileum, colon, and whole GIT, respectively, whereas GAPDH, B-actin, and 18S rRNA were the least stable genes at different parts of the GIT. To confirm the crucial role of appropriate housekeeping genes in obtaining reliable results, we analyzed the expression of ALP using each of the 18 reference genes to normalize the RT-qPCR data. We found that the expression levels of ALP normalized using the most stable reference genes (B2M/HMBS/HPRT1) differed greatly from the expression levels obtained when the data were normalized using the least stable genes (GAPDH, B-actin, and 18S). We concluded that B2M/HMBS/HPRT1 were the optimal reference genes for gene expression analysis by RT-qPCR in the intestinal mucosal development stages of piglets at weaning. Our findings provide a set of porcine housekeeping reference genes for studies of mRNA expression in different parts of the pig intestine.
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Affiliation(s)
- Shujin Wang
- College of Life Science and Technology, Southwest Miznu University, Chengdu, China.,Department of Molecular Genetics and Cell Biology, Maastricht University, Maastricht, The Netherlands
| | - Binxing Wang
- College of Life Science and Technology, Southwest Miznu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, China
| | - Huan He
- College of Life Science and Technology, Southwest Miznu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, China
| | - Aomin Sun
- Department of Molecular Genetics and Cell Biology, Maastricht University, Maastricht, The Netherlands
| | - Chunhua Guo
- College of Life Science and Technology, Southwest Miznu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, China
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12
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Lorenzetti WR, Ibelli AMG, Peixoto JDO, Mores MAZ, Savoldi IR, do Carmo KB, de Oliveira HC, Ledur MC. Identification of endogenous normalizing genes for expression studies in inguinal ring tissue for scrotal hernias in pigs. PLoS One 2018; 13:e0204348. [PMID: 30235332 PMCID: PMC6147718 DOI: 10.1371/journal.pone.0204348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/06/2018] [Indexed: 02/06/2023] Open
Abstract
The use of reference genes is required for relative quantification in gene expression analysis and since the stability of these genes could be variable depending on the experimental design, it has become indispensable to test the reliability of endogenous genes. Therefore, this study evaluated 10 reference candidate genes in two different experimental conditions in order to obtain stable genes to be used as reference in expression studies related to scrotal hernias in pigs. Two independent experiments were performed: one with 30 days-old MS115 pigs and the other with 60 days-old Landrace pigs. The inguinal ring/canal was collected, frozen and further submitted to real-time PCR analysis (qPCR). For the reference genes stability evaluation, four tools were used: GeNorm in the SLqPCR, BestKeeper, NormFinder and Comparative CT. A general ranking was generated using the BruteAggreg function of R environment. In this study, the RPL19 was one of the most reliable endogenous genes for both experiments. The breed/age effects influenced the expression stability of candidate reference genes evaluated in the inguinal ring of pigs. Therefore, this study reinforces the importance of evaluating the stability of several endogenous genes previous their use, since a consensual set of reference genes is not easily obtained. Here, two sets of genes are recommended: RPL19, RPL32 and H3F3A for 30-days MS115 and PPIA and RPL19 for the 60 days-old Landrace pigs. This is the first study using the inguinal ring tissue and the results can be useful as an indicative for other studies working with gene expression in this tissue.
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Affiliation(s)
- William Raphael Lorenzetti
- Programa de Pós-graduação em Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, Chapecó, Santa Catarina, Brazil
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | | | | | | | | | | | | | - Mônica Corrêa Ledur
- Programa de Pós-graduação em Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, Chapecó, Santa Catarina, Brazil
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
- * E-mail:
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13
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Selection and validation of suitable reference genes for qRT-PCR analysis in pear leaf tissues under distinct training systems. PLoS One 2018; 13:e0202472. [PMID: 30138340 PMCID: PMC6107188 DOI: 10.1371/journal.pone.0202472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/04/2018] [Indexed: 12/13/2022] Open
Abstract
Training systems generally alter tree architecture, which modulates light microclimate within the canopy, for the purpose of improving photosynthetic efficiency and fruit quality. Gene expression quantification is one of the most important methods for exploring the molecular mechanisms underlying the influence of training systems on pear photosynthesis, and suitable reference genes for gene expression normalization are a prerequisite for this method. In this study, the expression stability of nine common and four novel candidate genes were evaluated in 14 different pear leaf samples in two training systems, including those at four developmental stages (training_period) and from different parts of the trees (training_space), using two distinct algorithms, geNorm and NormFinder. Our results revealed that SKD1 (Suppressor of K+Transport Growth Defect1)/ YLS8 (Yellow Leaf Specific 8) and ARM (Armadillo) were the most stable single reference genes for the ‘training_period’ and ‘training_space’ subsets, respectively, although these single genes were not as stable as the optimal pairs of reference genes, SKD1+YLS8 and ARM+YLS8, respectively. Furthermore, the expression levels of the PpsAPX (Ascorbate peroxidase) gene showed that the arbitrary use of reference genes without previous testing could lead to misinterpretation of data. This work constitutes the first systematic analysis regarding the selection of superior reference genes in training system studies, facilitating the elucidation of gene function in pear and providing valuable information for similar studies in other higher plants.
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14
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Zhou L, Chen F, Ye J, Pan H. Selection of Reliable Reference Genes for RT-qPCR Analysis of Bursaphelenchus mucronatus Gene Expression From Different Habitats and Developmental Stages. Front Genet 2018; 9:269. [PMID: 30083182 PMCID: PMC6064934 DOI: 10.3389/fgene.2018.00269] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/02/2018] [Indexed: 12/13/2022] Open
Abstract
Quantitative reverse transcription polymerase chain reaction (RT-qPCR), a sensitive technique for gene expression analysis, depends on the stability of the reference genes used for data normalization under different experimental conditions. Bursaphelenchus mucronatus, a pine-parasitic nematode varying in virulence, is widely distributed in natural pine forests throughout the northern hemisphere, but has not been investigated with respect to the identification of reference genes suitable for the normalization of RT-qPCR data. In the present study, eight candidate reference genes were analyzed in B. mucronatus under different habitat conditions and at different developmental stages. The expression stability of these genes was assessed by geNorm, NormFinder, BestKeeper, delta Cq, and RefFinder algorithms. In general, our results identified encoding beta-tubulin as the most stable gene. Moreover, pairwise analysis showed that three reference genes were sufficient to normalize the gene expression data under each set of conditions, with genes encoding beta-tubulin, 18S ribosomal RNA and ubiquitin-conjugating enzyme being the most suitable reference genes for different habitat conditions, whereas genes encoding beta-tubulin, histone, and 18S ribosomal RNA exhibited the most stable expression at different developmental stages. Validation of the selected reference genes was performed by profiling the expression of the fatty acid- and retinol-binding protein gene in different habitats, and by profiling the expression of the arginine kinase gene at different developmental stages. This first systematic analysis for the selection of suitable reference genes for RT-qPCR in B. mucronatus will facilitate future functional analyses and deep mining of genetic resources in this nematode.
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Affiliation(s)
| | - Fengmao Chen
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jianren Ye
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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15
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Wang YK, Li X, Song ZQ, Yang CX. Methods of RNA preparation affect mRNA abundance quantification of reference genes in pig maturing oocytes. Reprod Domest Anim 2017; 52:722-730. [PMID: 28407308 DOI: 10.1111/rda.12972] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/25/2017] [Indexed: 11/28/2022]
Abstract
To ensure accurate normalization and quantification of target RNA transcripts using reverse transcription quantitative polymerase chain reaction (RT-qPCR), most studies focus on the identification of stably expressed gene(s) as internal reference. However, RNA preparation methods could also be an important factor, especially for test samples of limited quantity (e.g. oocytes). In this study, we aimed to select appropriate reference gene(s), and evaluate the effect of RNA preparation methods on gene expression quantification in porcine oocytes and cumulus cells during in vitro maturation. Expression profiles of seven genes (GAPDH, 18S, YWHAG, BACT, RPL4, HPRT1 and PPIA) were examined, on RNA samples extracted from cumulus cells (RNeasy Kit) and oocytes (RNeasy Kit and Lysis Kit) during in vitro maturation, respectively. Interestingly, different RNA preparation methods were found to potentially affect the quantification of reference gene expression in pig oocytes cultured in vitro. After geNorm analyses, the most suitable genes for normalization were identified, GAPDH/18S for cumulus cells and YWHAG/BACT for oocytes, respectively. Thus, our results provide useful data and information on the selection of better reference genes and RNA preparation method for related functional studies.
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Affiliation(s)
- Y-K Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - X Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Z-Q Song
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - C-X Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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16
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Niu G, Yang Y, Zhang Y, Hua C, Wang Z, Tang Z, Li K. Identifying suitable reference genes for gene expression analysis in developing skeletal muscle in pigs. PeerJ 2016; 4:e2428. [PMID: 27994956 PMCID: PMC5157201 DOI: 10.7717/peerj.2428] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/11/2016] [Indexed: 11/20/2022] Open
Abstract
The selection of suitable reference genes is crucial to accurately evaluate and normalize the relative expression level of target genes for gene function analysis. However, commonly used reference genes have variable expression levels in developing skeletal muscle. There are few reports that systematically evaluate the expression stability of reference genes across prenatal and postnatal developing skeletal muscle in mammals. Here, we used quantitative PCR to examine the expression levels of 15 candidate reference genes (ACTB, GAPDH, RNF7, RHOA, RPS18, RPL32, PPIA, H3F3, API5, B2M, AP1S1, DRAP1, TBP, WSB, and VAPB) in porcine skeletal muscle at 26 different developmental stages (15 prenatal and 11 postnatal periods). We evaluated gene expression stability using the computer algorithms geNorm, NormFinder, and BestKeeper. Our results indicated that GAPDH and ACTB had the greatest variability among the candidate genes across prenatal and postnatal stages of skeletal muscle development. RPS18, API5, and VAPB had stable expression levels in prenatal stages, whereas API5, RPS18, RPL32, and H3F3 had stable expression levels in postnatal stages. API5 and H3F3 expression levels had the greatest stability in all tested prenatal and postnatal stages, and were the most appropriate reference genes for gene expression normalization in developing skeletal muscle. Our data provide valuable information for gene expression analysis during different stages of skeletal muscle development in mammals. This information can provide a valuable guide for the analysis of human diseases.
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Affiliation(s)
- Guanglin Niu
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yalan Yang
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - YuanYuan Zhang
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaoju Hua
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zishuai Wang
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonglin Tang
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kui Li
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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17
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Gong H, Sun L, Chen B, Han Y, Pang J, Wu W, Qi R, Zhang TM. Evaluation of candidate reference genes for RT-qPCR studies in three metabolism related tissues of mice after caloric restriction. Sci Rep 2016; 6:38513. [PMID: 27922100 PMCID: PMC5138604 DOI: 10.1038/srep38513] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/09/2016] [Indexed: 12/24/2022] Open
Abstract
Reverse transcription quantitative-polymerase chain reaction (RT-qPCR) is a routine method for gene expression analysis, and reliable results depend on proper normalization by stable reference genes. Caloric restriction (CR) is a robust lifestyle intervention to slow aging and delay onset of age-associated diseases via inducing global changes in gene expression. Reliable normalization of RT-qPCR data becomes crucial in CR studies. In this study, the expression stability of 12 candidate reference genes were evaluated in inguinal white adipose tissue (iWAT), skeletal muscle (Sk.M) and liver of CR mice by using three algorithms, geNorm, NormFinder, and Bestkeeper. Our results showed β2m, Ppia and Hmbs as the most stable genes in iWAT, Sk.M and liver, respectively. Moreover, two reference genes were sufficient to normalize RT-qPCR data in each tissue and the suitable pair of reference genes was β2m-Hprt in iWAT, Ppia-Gusb in Sk.M and Hmbs-β2m in liver. By contrast, the least stable gene in iWAT or Sk.M was Gapdh, and in liver was Pgk1. Furthermore, the expression of Leptin and Ppar-γ were profiled in these tissues to validate the selected reference genes. Our data provided a basis for gene expression analysis in future CR studies.
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Affiliation(s)
- Huan Gong
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Liang Sun
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Beidong Chen
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Yiwen Han
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Jing Pang
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Wei Wu
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Ruomei Qi
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Tie-Mei Zhang
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
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18
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Sinha P, Saxena RK, Singh VK, Krishnamurthy L, Varshney RK. Selection and Validation of Housekeeping Genes as Reference for Gene Expression Studies in Pigeonpea (Cajanus cajan) under Heat and Salt Stress Conditions. FRONTIERS IN PLANT SCIENCE 2015; 6:1071. [PMID: 27242803 PMCID: PMC4865767 DOI: 10.3389/fpls.2015.01071] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/16/2015] [Indexed: 05/22/2023]
Abstract
To identify stable housekeeping genes as a reference for expression analysis under heat and salt stress conditions in pigeonpea, the relative expression variation for 10 commonly used housekeeping genes (EF1α, UBQ10, GAPDH, 18Sr RNA, 25Sr RNA, TUB6, ACT1, IF4α, UBC, and HSP90) was studied in root, stem, and leaves tissues of Asha (ICPL 87119), a leading pigeonpea variety. Three statistical algorithms geNorm, NormFinder, and BestKeeper were used to define the stability of candidate genes. Under heat stress, UBC, HSP90, and GAPDH were found to be the most stable reference genes. In the case of salinity stress, GAPDH followed by UBC and HSP90 were identified to be the most stable reference genes. Subsequently, the above identified genes were validated using qRT-PCR based gene expression analysis of two universal stress-resposive genes namely uspA and uspB. The relative quantification of these two genes varied according to the internal controls (most stable, least stable, and combination of most stable and least stable housekeeping genes) and thus confirmed the choice as well as validation of internal controls in such experiments. The identified and validated housekeeping genes will facilitate gene expression studies under heat and salt stress conditions in pigeonpea.
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Affiliation(s)
- Pallavi Sinha
- Applied Genomics, Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Rachit K. Saxena
- Applied Genomics, Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Vikas K. Singh
- Applied Genomics, Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - L. Krishnamurthy
- Applied Genomics, Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Rajeev K. Varshney
- Applied Genomics, Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- School of Plant Biology and Institute of Agriculture, The University of Western Australia, PerthWA, Australia
- *Correspondence: Rajeev K. Varshney,
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