Transcriptome Analysis Identifies Candidate Genes and Signaling Pathways Associated With Feed Efficiency in Xiayan Chicken
Feed efficiency is an important economic factor in poultry production, and the rate of feed efficiency is generally evaluated using residual feed intake (RFI). The molecular regulatory mechanisms of RFI remain unknown. Therefore, the objective of this study was to identify candidate genes and signal...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-03-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.607719/full |
| _version_ | 1818847105765081088 |
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| author | Cong Xiao Jixian Deng Linghu Zeng Tiantian Sun Zhuliang Yang Xiurong Yang |
| author_facet | Cong Xiao Jixian Deng Linghu Zeng Tiantian Sun Zhuliang Yang Xiurong Yang |
| author_sort | Cong Xiao |
| collection | DOAJ |
| description | Feed efficiency is an important economic factor in poultry production, and the rate of feed efficiency is generally evaluated using residual feed intake (RFI). The molecular regulatory mechanisms of RFI remain unknown. Therefore, the objective of this study was to identify candidate genes and signaling pathways related to RFI using RNA-sequencing for low RFI (LRFI) and high RFI (HRFI) in the Xiayan chicken, a native chicken of the Guangxi province. Chickens were divided into four groups based on FE and sex: LRFI and HRFI for males and females, respectively. We identified a total of 1,015 and 742 differentially expressed genes associated with RFI in males and females, respectively. The 32 and 7 Gene Ontology (GO) enrichment terms, respectively, identified in males and females chiefly involved carbohydrate, amino acid, and energy metabolism. Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 11 and 5 significantly enriched signaling pathways, including those for nutrient metabolism, insulin signaling, and MAPK signaling, respectively. Protein–protein interaction (PPI) network analysis showed that the pathways involving CAT, ACSL1, ECI2, ABCD2, ACOX1, PCK1, HSPA2, and HSP90AA1 may have an effect on feed efficiency, and these genes are mainly involved in the biological processes of fat metabolism and heat stress. Gene set enrichment analysis indicated that the increased expression of genes in LRFI chickens was related to intestinal microvilli structure and function, and to the fat metabolism process in males. In females, the highly expressed set of genes in the LRFI group was primarily associated with nervous system and cell development. Our findings provide further insight into RFI regulation mechanisms in chickens. |
| first_indexed | 2024-12-19T05:56:10Z |
| format | Article |
| id | doaj.art-d4794ee25ac348b19453a94ecd892f2d |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-19T05:56:10Z |
| publishDate | 2021-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-d4794ee25ac348b19453a94ecd892f2d2022-12-21T20:33:26ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-03-011210.3389/fgene.2021.607719607719Transcriptome Analysis Identifies Candidate Genes and Signaling Pathways Associated With Feed Efficiency in Xiayan ChickenCong XiaoJixian DengLinghu ZengTiantian SunZhuliang YangXiurong YangFeed efficiency is an important economic factor in poultry production, and the rate of feed efficiency is generally evaluated using residual feed intake (RFI). The molecular regulatory mechanisms of RFI remain unknown. Therefore, the objective of this study was to identify candidate genes and signaling pathways related to RFI using RNA-sequencing for low RFI (LRFI) and high RFI (HRFI) in the Xiayan chicken, a native chicken of the Guangxi province. Chickens were divided into four groups based on FE and sex: LRFI and HRFI for males and females, respectively. We identified a total of 1,015 and 742 differentially expressed genes associated with RFI in males and females, respectively. The 32 and 7 Gene Ontology (GO) enrichment terms, respectively, identified in males and females chiefly involved carbohydrate, amino acid, and energy metabolism. Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 11 and 5 significantly enriched signaling pathways, including those for nutrient metabolism, insulin signaling, and MAPK signaling, respectively. Protein–protein interaction (PPI) network analysis showed that the pathways involving CAT, ACSL1, ECI2, ABCD2, ACOX1, PCK1, HSPA2, and HSP90AA1 may have an effect on feed efficiency, and these genes are mainly involved in the biological processes of fat metabolism and heat stress. Gene set enrichment analysis indicated that the increased expression of genes in LRFI chickens was related to intestinal microvilli structure and function, and to the fat metabolism process in males. In females, the highly expressed set of genes in the LRFI group was primarily associated with nervous system and cell development. Our findings provide further insight into RFI regulation mechanisms in chickens.https://www.frontiersin.org/articles/10.3389/fgene.2021.607719/fullRNA-seqfeed efficiencycandidate genesprotein–protein interactiongene set enrichment analysis |
| spellingShingle | Cong Xiao Jixian Deng Linghu Zeng Tiantian Sun Zhuliang Yang Xiurong Yang Transcriptome Analysis Identifies Candidate Genes and Signaling Pathways Associated With Feed Efficiency in Xiayan Chicken Frontiers in Genetics RNA-seq feed efficiency candidate genes protein–protein interaction gene set enrichment analysis |
| title | Transcriptome Analysis Identifies Candidate Genes and Signaling Pathways Associated With Feed Efficiency in Xiayan Chicken |
| title_full | Transcriptome Analysis Identifies Candidate Genes and Signaling Pathways Associated With Feed Efficiency in Xiayan Chicken |
| title_fullStr | Transcriptome Analysis Identifies Candidate Genes and Signaling Pathways Associated With Feed Efficiency in Xiayan Chicken |
| title_full_unstemmed | Transcriptome Analysis Identifies Candidate Genes and Signaling Pathways Associated With Feed Efficiency in Xiayan Chicken |
| title_short | Transcriptome Analysis Identifies Candidate Genes and Signaling Pathways Associated With Feed Efficiency in Xiayan Chicken |
| title_sort | transcriptome analysis identifies candidate genes and signaling pathways associated with feed efficiency in xiayan chicken |
| topic | RNA-seq feed efficiency candidate genes protein–protein interaction gene set enrichment analysis |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.607719/full |
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