Comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in pork
Abstract Background Drip loss is a key aspect of meat quality. Transcriptome profiles of muscle with divergent drip loss would offer important insight into the genetic factors responsible for the trait. In this study, drip loss and other meat quality traits of 28 purebred Duroc pigs were measured, m...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-12-01
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| Series: | BMC Genetics |
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| Online Access: | https://doi.org/10.1186/s12863-019-0794-0 |
| _version_ | 1828220413865361408 |
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| author | Xueyan Zhao Cheng Wang Yanping Wang Haichao Lin Huaizhong Wang Hongmei Hu Jiying Wang |
| author_facet | Xueyan Zhao Cheng Wang Yanping Wang Haichao Lin Huaizhong Wang Hongmei Hu Jiying Wang |
| author_sort | Xueyan Zhao |
| collection | DOAJ |
| description | Abstract Background Drip loss is a key aspect of meat quality. Transcriptome profiles of muscle with divergent drip loss would offer important insight into the genetic factors responsible for the trait. In this study, drip loss and other meat quality traits of 28 purebred Duroc pigs were measured, muscles of these individuals were RNA sequenced, and eight individuals with extremely low and high drip loss were selected for analyzing their transcriptome differences and identifying potential candidate genes affecting drip loss. Results As a result, 363 differentially expressed (DE) genes were detected in the comparative gene expression analysis, of which 239 were up-regulated and 124 were down-regulated in the low drip loss group. The DE genes were further filtered by correlation analysis between their expression and drip loss values in the 28 Duroc pigs measured and comparison of them with QTLs affecting drip loss. Consequently, of the 363 DE genes, 100 were identified as critical DE genes for drip loss. Functional analysis of these critical DE genes revealed some GO terms (extracellular matrix, cell adhesion mediated by integrin, heterotypic cell-cell adhesion), pathway (ECM-receptor interaction), and new potential candidate genes (TNC, ITGA5, ITGA11, THBS3 and CD44) which played an important role in regulating the variation of drip loss, and deserved to carry further studies to unravel their specific mechanism on drip loss. Conclusions Our study revealed some GO terms, pathways and potential candidate genes affecting drip loss. It provides crucial information to understand the molecular mechanism of drip loss, and would be of help for improving meat quality of pigs. |
| first_indexed | 2024-04-12T16:26:49Z |
| format | Article |
| id | doaj.art-b204d16080694682876efc7c40cf125d |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-04-12T16:26:49Z |
| publishDate | 2019-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genetics |
| spelling | doaj.art-b204d16080694682876efc7c40cf125d2022-12-22T03:25:22ZengBMCBMC Genetics1471-21562019-12-012011910.1186/s12863-019-0794-0Comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in porkXueyan Zhao0Cheng Wang1Yanping Wang2Haichao Lin3Huaizhong Wang4Hongmei Hu5Jiying Wang6Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural SciencesAbstract Background Drip loss is a key aspect of meat quality. Transcriptome profiles of muscle with divergent drip loss would offer important insight into the genetic factors responsible for the trait. In this study, drip loss and other meat quality traits of 28 purebred Duroc pigs were measured, muscles of these individuals were RNA sequenced, and eight individuals with extremely low and high drip loss were selected for analyzing their transcriptome differences and identifying potential candidate genes affecting drip loss. Results As a result, 363 differentially expressed (DE) genes were detected in the comparative gene expression analysis, of which 239 were up-regulated and 124 were down-regulated in the low drip loss group. The DE genes were further filtered by correlation analysis between their expression and drip loss values in the 28 Duroc pigs measured and comparison of them with QTLs affecting drip loss. Consequently, of the 363 DE genes, 100 were identified as critical DE genes for drip loss. Functional analysis of these critical DE genes revealed some GO terms (extracellular matrix, cell adhesion mediated by integrin, heterotypic cell-cell adhesion), pathway (ECM-receptor interaction), and new potential candidate genes (TNC, ITGA5, ITGA11, THBS3 and CD44) which played an important role in regulating the variation of drip loss, and deserved to carry further studies to unravel their specific mechanism on drip loss. Conclusions Our study revealed some GO terms, pathways and potential candidate genes affecting drip loss. It provides crucial information to understand the molecular mechanism of drip loss, and would be of help for improving meat quality of pigs.https://doi.org/10.1186/s12863-019-0794-0PigMeat qualityRNA sequencingDifferentially expressed genes |
| spellingShingle | Xueyan Zhao Cheng Wang Yanping Wang Haichao Lin Huaizhong Wang Hongmei Hu Jiying Wang Comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in pork BMC Genetics Pig Meat quality RNA sequencing Differentially expressed genes |
| title | Comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in pork |
| title_full | Comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in pork |
| title_fullStr | Comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in pork |
| title_full_unstemmed | Comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in pork |
| title_short | Comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in pork |
| title_sort | comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in pork |
| topic | Pig Meat quality RNA sequencing Differentially expressed genes |
| url | https://doi.org/10.1186/s12863-019-0794-0 |
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