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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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Lin Y, Sun L, Lv Y, Liao R, Zhang K, Zhou J, Zhang S, Xu J, He M, Wu C, Zhang D, Shen X, Dai J, Gao J. Transcriptomic and metabolomic dissection of skeletal muscle of crossbred Chongming white goats with different meat production performance. BMC Genomics 2024; 25:443. [PMID: 38704563 PMCID: PMC11069289 DOI: 10.1186/s12864-024-10304-3] [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: 10/07/2023] [Accepted: 04/12/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND The transcriptome and metabolome dissection of the skeletal muscle of high- and low- growing individuals from a crossbred population of the indigenous Chongming white goat and the Boer goat were performed to discover the potential functional differentially expressed genes (DEGs) and differential expression metabolites (DEMs). RESULTS A total of 2812 DEGs were detected in 6 groups at three time stages (3,6,12 Month) in skeletal muscle using the RNA-seq method. A DEGs set containing seven muscle function related genes (TNNT1, TNNC1, TNNI1, MYBPC2, MYL2, MHY7, and CSRP3) was discovered, and their expression tended to increase as goat muscle development progressed. Seven DEGs (TNNT1, FABP3, TPM3, DES, PPP1R27, RCAN1, LMOD2) in the skeletal muscle of goats in the fast-growing and slow-growing groups was verified their expression difference by reverse transcription-quantitative polymerase chain reaction. Further, through the Liquid chromatography-mass spectrometry (LC-MS) approach, a total of 183 DEMs in various groups of the muscle samples and these DEMs such as Queuine and Keto-PGF1α, which demonstrated different abundance between the goat fast-growing group and slow-growing group. Through weighted correlation network analysis (WGCNA), the study correlated the DEGs with the DEMs and identified 4 DEGs modules associated with 18 metabolites. CONCLUSION This study benefits to dissection candidate genes and regulatory networks related to goat meat production performance, and the joint analysis of transcriptomic and metabolomic data provided insights into the study of goat muscle development.
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Affiliation(s)
- Yuexia Lin
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Lingwei Sun
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Yuhua Lv
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Rongrong Liao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Keqing Zhang
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Jinyong Zhou
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Shushan Zhang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Jiehuan Xu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Mengqian He
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Caifeng Wu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Defu Zhang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Xiaohui Shen
- Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
| | - Jianjun Dai
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China.
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China.
| | - Jun Gao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China.
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China.
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Zhao X, Cao Y, Li H, Wu Y, Yao Y, Wang L, Li J, Yao Y. Development of myofibers and muscle transcriptomic analysis in growing Yili geese. Poult Sci 2024; 103:103328. [PMID: 38157792 PMCID: PMC10790089 DOI: 10.1016/j.psj.2023.103328] [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: 09/13/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 01/03/2024] Open
Abstract
In poultries, muscle growth is a quantitative trait controlled by multiple genes. The regulatory mechanisms governing muscle tissue growth and development in poultry, particularly during the early stages of growth, are intricate. Through the examination of leg muscle transcripts from Yili geese during various stages of development, this study offers valuable insights into the molecular mechanisms underlying the growth and development of Yili geese. This study aimed to perform a comparative analysis of the histological characteristics of leg muscles and the mRNA expression profiles of leg muscles in Yili geese at different ages (2, 4, 6, 8, and 10 wk). The objective was to identify differentially expressed genes related to muscle development in Yili geese and utilize bioinformatics to predict the potential biological functions of these genes. Through histological studies on leg muscle tissues, it was discerned that male geese at 4 wk exhibit a significantly reduced muscle fiber density in comparison to females (P < 0.01). In contrast, by the time they reach 6, 8, and 10 wk, their muscle fiber diameter and cross-sectional dimensions significantly outpace the females (P < 0.01). With the advancement in age, muscle fiber density tends to decrease. It is worth noting that 4- and 6-wk-old male geese have a substantially elevated muscle fiber density when matched against females (P < 0.01). Conversely, at the age of 10 wk, their muscle fiber density is notably inferior to the females (P < 0.01). Furthermore, male geese exhibit the most rapid increase in muscle fiber diameter and cross-sectional area between 4 and 6 wk of age. The density of muscle fibers in these geese significantly decreases from 4 to 8 wk. In contrast, female geese show the most pronounced growth in muscle fiber diameter and cross-sectional area between 2 and 6 wk, with a swift decline in density following the 6-wk mark, accompanied by a gradual reduction in the rate of muscle fiber growth. A comprehensive analysis of the leg muscle mRNA expression profiles from 12 Yili geese generated a cumulative total of 502,065,268 valid sequence reads, corresponding to a data volume of 75.30 Gb. In a comparative analysis between 4-wk-old and 2-wk-old groups (T4 vs. T2), 8-wk-old and 2-wk-old groups (T8 vs. T2), and 8-wk-old and 4-wk-old groups (T8 vs. T4), we identified 1,700, 1,583, and 221 differentially expressed genes (DEGs), respectively. Differentially expressed genes were significantly enriched in Gene Ontology (GO) terms such as organelle organization, cytoskeletal protein binding, cation transport, myosin complex, and actin cytoskeleton. Among the significantly enriched signaling pathways, 5 pathways were found to be significantly related to growth and development: adhesion patch, extracellular matrix receptor interaction, tight junction, TGF-β signaling pathway, and MAPK signaling pathway, with a total of 38 differentially differentiated genes contained in these 5 pathways, and it was hypothesized that the above pathways as well as the DEGs in the pathways played an important role in the regulation of early growth and development of the Yili goose. This investigation serves as a foundational reference for elucidating the molecular regulatory mechanisms involved in the development of goose muscle. Furthermore, it contributes to the expansion of the theoretical framework concerning the genetic regulation of muscle growth in geese.
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Affiliation(s)
- Xiaoyu Zhao
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Yan Cao
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China.
| | - Yingping Wu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - YingYing Yao
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Ling Wang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jiahui Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Yang Yao
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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