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Zhan S, Zhang L, Zhong T, Wang L, Guo J, Cao J, Li L, Zhang H. Evaluation of Reference Gene Stability in Goat Skeletal Muscle Satellite Cells during Proliferation and Differentiation Phases. Animals (Basel) 2024; 14:2479. [PMID: 39272264 PMCID: PMC11394193 DOI: 10.3390/ani14172479] [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: 07/23/2024] [Revised: 08/16/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
The process of skeletal muscle development is intricate and involves the regulation of a diverse array of genes. Accurate gene expression profiles are crucial for studying muscle development, making it essential to choose the right reference genes for real-time quantitative PCR (RT-qPCR). In the present study, eight candidate reference genes were identified from our previous transcriptome sequencing analysis of caprine skeletal muscle satellite cells (MuSCs), and two traditional reference genes (ACTB and GAPDH) were assessed. The quantitative levels of the candidate reference genes were determined through the RT-qPCR technique, while the stability of their expression was evaluated utilizing the GeNorm, NormFinder, BestKeeper, and RefFinder programs. Furthermore, the chosen reference genes were utilized for the normalization of the gene expression levels of PCNA and Myf5. It was determined that conventional reference genes, including ACTB and GAPDH, were not appropriate for normalizing target gene expression. Conversely, RPL14 and RPS15A, identified through RNA sequencing analysis, exhibited minimal variability and were identified as the optimal reference genes for normalizing gene expression during the proliferation and differentiation of goat MuSCs. Our research offers a validated panel of optimal reference genes for the detection of differentially expressed genes in goat muscle satellite cells using RT-qPCR.
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Affiliation(s)
- Siyuan Zhan
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lufei Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Zhong
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Linjie Wang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaxue Cao
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongping Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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Ahlawat S, Vasu M, Choudhary V, Arora R, Sharma R, Mir MA, Singh MK. Comprehensive evaluation and validation of optimal reference genes for normalization of qPCR data in different caprine tissues. Mol Biol Rep 2024; 51:268. [PMID: 38302649 DOI: 10.1007/s11033-024-09268-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/18/2024] [Indexed: 02/03/2024]
Abstract
BACKGROUND Quantitative real-time PCR (qPCR) is a highly reliable method for validating gene expression data in molecular studies due to its sensitivity, specificity, and efficiency. To ensure accurate qPCR results, it's essential to normalize the expression data using stable reference genes. METHODS This study aimed to identify suitable reference genes for qPCR studies in goats by evaluating 18 candidate reference genes (ACTB, BACH1, B2M, GAPDH, HMBS, HPRT1, PGK1, PPIA, PPIB, RPLP0, RPL19, RPS9, RPS15, RPS28, SDHA, TBP, UXT, and YWHAZ) in 10 different caprine tissues (heart, intestine, kidney, liver, lung, muscle, rumen, skin, spleen, and testis). An integrated tool called RefFinder, which incorporates various algorithms like NormFinder, GeNorm, BestKeeper, and ΔCt, was used to assess the stability of expression among these genes. RESULTS After thorough analysis, ACTB, PPIB, and B2M emerged as the most stable reference genes, while RPL19, RPS15, and RPS9 were found to be the least stable. The suitability of the selected internal control genes was further validated through target gene analysis, confirming their efficacy in ensuring accurate gene expression profiling in goats. CONCLUSION The study determined that the geometric average of ACTB, PPIB, and B2M creates an appropriate normalization factor for gene expression studies in goat tissues.
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Affiliation(s)
- Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
- Animal Biotechnology Division, ICAR-NBAGR, Karnal, India.
| | - Mahanthi Vasu
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Vikas Choudhary
- District Disease Diagnostic Laboratory, Department of Animal Husbandry and Dairying, Karnal, Haryana, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - M A Mir
- Mountain Research Centre for Sheep and Goat, SKUAST, Shuhama (Aulestang), Kashmir, India
| | - Manoj Kumar Singh
- ICAR-Central Institute for Research on Goats, Makhdoom, Mathura, India
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Min Q, Yang L, Wang Y, Liu Y, Jiang M. Transcriptome-Based Evaluation of Optimal Reference Genes for Quantitative Real-Time PCR in Yak Stomach throughout the Growth Cycle. Animals (Basel) 2023; 13:ani13050925. [PMID: 36899781 PMCID: PMC10000025 DOI: 10.3390/ani13050925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/21/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Efficient nutritional assimilation and energy metabolism in the stomachs of yaks contribute to their adaption to harsh environments. Accurate gene expression profile analysis will help further reveal the molecular mechanism of nutrient and energy metabolism in the yak stomach. RT-qPCR is regarded as an accurate and dependable method for analyzing gene expression. The selection of reference genes is essential to obtain meaningful RT-qPCR results, especially in longitudinal gene expression studies of tissues and organs. Our objective was to select and validate optimal reference genes from across the transcriptome as internal controls for longitudinal gene expression studies in the yak stomach. In this study, 15 candidate reference genes (CRGs) were determined according to transcriptome sequencing (RNA-seq) results and the previous literature. The expression levels of these 15 CRGs were quantified using RT-qPCR in the yak stomach, including the rumen, reticulum, omasum and abomasum at five stages: 0 days, 20 days, 60 days, 15 months and three years old (adult). Subsequently, the expression stabilities of these 15 CRGs were evaluated via four algorithms: geNorm, NormFinder, BestKeeper and the comparative CT method. Furthermore, RefFinder was employed to obtain a comprehensive ranking of the stability of CRGs. The analysis results indicate that RPS15, MRPL39 and RPS23 are the most stable genes in the yak stomach throughout the growth cycle. In addition, to verify the reliability of the selected CRGs, the relative expression levels of HMGCS2 were quantified via RT-qPCR using the three most stable or the three least stable CRGs. Overall, we recommend combining RPS15, MRPL39 and RPS23 as reference genes for the normalization of RT-qPCR data in the yak stomach throughout the growth cycle.
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Affiliation(s)
- Qi Min
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610041, China
| | - Lu Yang
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Yu Wang
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Yili Liu
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Mingfeng Jiang
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
- Correspondence:
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Zhao L, Yang H, Li X, Zhou Y, Liu T, Zhao Y. Transcriptome-based selection and validation of optimal reference genes in perirenal adipose developing of goat ( Capra hircus). Front Vet Sci 2022; 9:1055866. [PMID: 36467654 PMCID: PMC9712442 DOI: 10.3389/fvets.2022.1055866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/02/2022] [Indexed: 06/15/2024] Open
Abstract
Brown adipose tissue (BAT) is mainly present in young mammals and is important for maintaining body temperature in neonatal mammals because of its ability to produce non-shivering thermogenesis. There is usually a large amount of BAT around the kidneys of newborn kids, but the BAT gradually "whiting" after birth. Screening and validating appropriate reference genes is a prerequisite for further studying the mechanism of goat brown adipose tissue "whiting" during the early stages. In this study, the expression stability of 17 candidate reference genes: 12 COPS8, SAP18, IGF2R, PARL, SNRNP200, ACTG1, CLTA, GANAB, GABARAP, PCBP2, CTSB, and CD151) selected based on previous transcriptome data as new candidate reference genes, 3 (PFDN5, CTNNB1, and EIF3M) recommended in previous studies, and 2 traditional reference genes (ACTB and GAPDH) was evaluated. Real-time quantitative PCR (RT-qPCR) technology was used to detect the expression level of candidate reference genes during goat BAT "whiting". Four algorithms: Normfinder, geNorm, ΔCt method, and BestKeeper, and two comprehensive algorithms: ComprFinder and RefFinder, were used to analyze the stability of each candidate reference genes. GABARAP, CLTA, GAPDH, and ACTB were identified as the most stable reference genes, while CTNNB1, CTSB, and EIF3M were the least stable. Moreover, two randomly selected target genes IDH2 and RBP4, were effectively normalized using the selected most stable reference genes. These findings collectively suggest that GABARAP, CLTA, GAPDH, and ACTB are relatively stable reference genes that can potentially be used for the development of perirenal fat in goats.
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Gebeyew K, Jiang C, Gao Q, Zhang L, Zhu H, Tian Y, Wang Q, Wei Y, Tan Z, Han X. Cadmium Accumulation in the Goat Liver and Kidney Is Partially Promoted by the Upregulation of Metal Transporter Genes. Animals (Basel) 2022; 12:ani12111408. [PMID: 35681874 PMCID: PMC9179383 DOI: 10.3390/ani12111408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/16/2022] Open
Abstract
Metal transporters, including divalent metal-ion transporter-1 (DMT1), Zrt-/Irt-like protein 8 and 14 (ZIP8 and ZIP14), and ferroportin-1 (FPN1), reportedly participate in cellular cadmium (Cd) uptake, but those in farm animals remain unclarified. This study aimed to examine the growth, plasma biochemical indices, Cd accumulation, and expression of metal transporter genes in the liver, kidney, and muscle of goats exposed to rice paddies contaminated with different levels of Cd. Twenty-four goats were randomly assigned across three dietary treatments: 0.23, 0.63, and 1.07 mg of Cd/kg of dry matter (DM) for 60 days. The results showed that dietary Cd exposure increased (p < 0.05) both Cd accumulation and the mRNA expressions of metal transporter genes (DMT1, ZIP, and FPN1) in the liver and kidney but not in the muscle, suggesting dietary Cd exhibited different deposition rates between goat liver, kidney, and muscle. These outcomes suggest that high levels of dietary Cd stimulated the expression of metal transporter genes and thereby enhanced the uptake and accumulation of Cd in the goat liver and kidney. As such, higher Cd concentrations in the liver and kidney observed with Cd diets could be partly explained by upregulation of metal transport genes expression.
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Affiliation(s)
- Kefyalew Gebeyew
- Key Laboratory of Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science, Tarim University, Alar 843300, China; (K.G.); (C.J.); (Q.G.)
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (L.Z.); (H.Z.); (Y.T.); (Q.W.); (Y.W.); (Z.T.)
| | - Chunyu Jiang
- Key Laboratory of Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science, Tarim University, Alar 843300, China; (K.G.); (C.J.); (Q.G.)
| | - Qinghua Gao
- Key Laboratory of Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science, Tarim University, Alar 843300, China; (K.G.); (C.J.); (Q.G.)
| | - Liping Zhang
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (L.Z.); (H.Z.); (Y.T.); (Q.W.); (Y.W.); (Z.T.)
| | - Hanhua Zhu
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (L.Z.); (H.Z.); (Y.T.); (Q.W.); (Y.W.); (Z.T.)
| | - Yushi Tian
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (L.Z.); (H.Z.); (Y.T.); (Q.W.); (Y.W.); (Z.T.)
| | - Qi Wang
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (L.Z.); (H.Z.); (Y.T.); (Q.W.); (Y.W.); (Z.T.)
| | - Yuqing Wei
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (L.Z.); (H.Z.); (Y.T.); (Q.W.); (Y.W.); (Z.T.)
| | - Zhiliang Tan
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (L.Z.); (H.Z.); (Y.T.); (Q.W.); (Y.W.); (Z.T.)
| | - Xuefeng Han
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (L.Z.); (H.Z.); (Y.T.); (Q.W.); (Y.W.); (Z.T.)
- Correspondence: ; Tel.: +86-731-84615218; Fax: +86-731-84612685
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