Identification of Important Proteins and Pathways Affecting Feed Efficiency in DLY Pigs by iTRAQ-Based Proteomic Analysis
Feed efficiency is an economically important trait controlled by multiple genes in pigs. The small intestine is the main organ of digestion and nutrient absorption. To explore the biological processes by which small intestine proteomics affects feed efficiency (FE), we investigated the small intesti...
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| Format: | Article |
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MDPI AG
2020-01-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/10/2/189 |
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| author | Jie Wu Xingwang Wang Rongrong Ding Jianping Quan Yong Ye Ting Gu Zheng Xu Enqin Zheng Gengyuan Cai Zhenfang Wu Ming Yang Jie Yang |
| author_facet | Jie Wu Xingwang Wang Rongrong Ding Jianping Quan Yong Ye Ting Gu Zheng Xu Enqin Zheng Gengyuan Cai Zhenfang Wu Ming Yang Jie Yang |
| author_sort | Jie Wu |
| collection | DOAJ |
| description | Feed efficiency is an economically important trait controlled by multiple genes in pigs. The small intestine is the main organ of digestion and nutrient absorption. To explore the biological processes by which small intestine proteomics affects feed efficiency (FE), we investigated the small intestinal tissue proteomes of high-FE and low-FE pigs by the isobaric tag for relative and absolute quantification (iTRAQ) method. In this study, a total of 225 Duroc × (Landrace × Yorkshire) (DLY) commercial pigs were ranked according to feed efficiency, which ranged from 30 kg to 100 kg, and six pigs with extreme phenotypes were selected, three in each of the high and low groups. A total of 1219 differentially expressed proteins (DEPs) were identified between the high-FE and low-FE groups (fold change ≥1.2 or ≤0.84; <i>p</i> ≤ 0.05), of which 785 were upregulated, and 484 were downregulated. Enrichment analysis indicated that the DEPs were mainly enriched in actin filament formation, microvilli formation, and small intestinal movement pathways. Protein functional analysis and protein interaction networks indicated that RHOA, HCLS1, EZR, CDC42, and RAC1 were important proteins that regulate FE in pigs. This study provided new insights into the important pathways and proteins involved in feed efficiency in pigs. |
| first_indexed | 2024-12-20T18:30:49Z |
| format | Article |
| id | doaj.art-fc57e334d8304fcc898b4ce239b3990e |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-12-20T18:30:49Z |
| publishDate | 2020-01-01 |
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| record_format | Article |
| series | Animals |
| spelling | doaj.art-fc57e334d8304fcc898b4ce239b3990e2022-12-21T19:30:04ZengMDPI AGAnimals2076-26152020-01-0110218910.3390/ani10020189ani10020189Identification of Important Proteins and Pathways Affecting Feed Efficiency in DLY Pigs by iTRAQ-Based Proteomic AnalysisJie Wu0Xingwang Wang1Rongrong Ding2Jianping Quan3Yong Ye4Ting Gu5Zheng Xu6Enqin Zheng7Gengyuan Cai8Zhenfang Wu9Ming Yang10Jie Yang11National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaCollege of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaFeed efficiency is an economically important trait controlled by multiple genes in pigs. The small intestine is the main organ of digestion and nutrient absorption. To explore the biological processes by which small intestine proteomics affects feed efficiency (FE), we investigated the small intestinal tissue proteomes of high-FE and low-FE pigs by the isobaric tag for relative and absolute quantification (iTRAQ) method. In this study, a total of 225 Duroc × (Landrace × Yorkshire) (DLY) commercial pigs were ranked according to feed efficiency, which ranged from 30 kg to 100 kg, and six pigs with extreme phenotypes were selected, three in each of the high and low groups. A total of 1219 differentially expressed proteins (DEPs) were identified between the high-FE and low-FE groups (fold change ≥1.2 or ≤0.84; <i>p</i> ≤ 0.05), of which 785 were upregulated, and 484 were downregulated. Enrichment analysis indicated that the DEPs were mainly enriched in actin filament formation, microvilli formation, and small intestinal movement pathways. Protein functional analysis and protein interaction networks indicated that RHOA, HCLS1, EZR, CDC42, and RAC1 were important proteins that regulate FE in pigs. This study provided new insights into the important pathways and proteins involved in feed efficiency in pigs.https://www.mdpi.com/2076-2615/10/2/189feed efficiencyitraqsmall intestinedly pig |
| spellingShingle | Jie Wu Xingwang Wang Rongrong Ding Jianping Quan Yong Ye Ting Gu Zheng Xu Enqin Zheng Gengyuan Cai Zhenfang Wu Ming Yang Jie Yang Identification of Important Proteins and Pathways Affecting Feed Efficiency in DLY Pigs by iTRAQ-Based Proteomic Analysis Animals feed efficiency itraq small intestine dly pig |
| title | Identification of Important Proteins and Pathways Affecting Feed Efficiency in DLY Pigs by iTRAQ-Based Proteomic Analysis |
| title_full | Identification of Important Proteins and Pathways Affecting Feed Efficiency in DLY Pigs by iTRAQ-Based Proteomic Analysis |
| title_fullStr | Identification of Important Proteins and Pathways Affecting Feed Efficiency in DLY Pigs by iTRAQ-Based Proteomic Analysis |
| title_full_unstemmed | Identification of Important Proteins and Pathways Affecting Feed Efficiency in DLY Pigs by iTRAQ-Based Proteomic Analysis |
| title_short | Identification of Important Proteins and Pathways Affecting Feed Efficiency in DLY Pigs by iTRAQ-Based Proteomic Analysis |
| title_sort | identification of important proteins and pathways affecting feed efficiency in dly pigs by itraq based proteomic analysis |
| topic | feed efficiency itraq small intestine dly pig |
| url | https://www.mdpi.com/2076-2615/10/2/189 |
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