Gene expression profile analysis of residual feed intake for Isfahan native chickens using RNA-SEQ data
The factors that affect residual feed intake (RFI) of two chicken breeds (Ross as commercial and Isfahan as Iranian local breed with low and high RFI, respectively) were examined. We sequenced their liver transcriptomes using RNA-Seq while focusing on the identification of important candidate genes,...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2019-01-01
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| Series: | Italian Journal of Animal Science |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/1828051X.2018.1507625 |
| _version_ | 1828157106185830400 |
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| author | Hamid Reza Izadnia Mojtaba Tahmoorespur Mohammad Reza Bakhtiarizadeh Mohammadreza Nassiri Saeid Esmaeilkhanien |
| author_facet | Hamid Reza Izadnia Mojtaba Tahmoorespur Mohammad Reza Bakhtiarizadeh Mohammadreza Nassiri Saeid Esmaeilkhanien |
| author_sort | Hamid Reza Izadnia |
| collection | DOAJ |
| description | The factors that affect residual feed intake (RFI) of two chicken breeds (Ross as commercial and Isfahan as Iranian local breed with low and high RFI, respectively) were examined. We sequenced their liver transcriptomes using RNA-Seq while focusing on the identification of important candidate genes, which might influence RFI and growth rate. The differential gene expression analysis revealed that 121 and 279 known genes were significantly up- and down-regulated in the local breed, respectively. QTL enrichment analysis revealed that 63 down-regulated genes in the local breed were enriched in the QTL regions related to feed efficiency traits. Moreover, the functional enrichment analysis showed that the down-regulated genes in the native chickens were mainly involved in the different metabolic processes, such as carboxylic acid metabolic process and response to stress. The Differentially Expressed Genes explored between the chickens of the two breeds led to the identification of some important candidate genes for further breed improvement programmes, including RSAD2, IL15, LIPI, EGR1 and DUSP16. These findings will be a useful resource for the biological investigations of RFI-related genes in Isfahan local chickens and may provide some clues for understanding the molecular genetic mechanisms in other chicken breeds.highlights A global view of transcriptome differences in the liver tissues of commercial and local chicken breeds with different RFI values is obtained. This investigation will contribute to the improvement of chicken genome annotation through the identification of novel transcripts and novel gene. Some important candidate genes related to RFI is obtained. |
| first_indexed | 2024-04-11T23:23:53Z |
| format | Article |
| id | doaj.art-f973800c66724c51b3d62545f0c1d350 |
| institution | Directory Open Access Journal |
| issn | 1828-051X |
| language | English |
| last_indexed | 2024-04-11T23:23:53Z |
| publishDate | 2019-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Italian Journal of Animal Science |
| spelling | doaj.art-f973800c66724c51b3d62545f0c1d3502022-12-22T03:57:24ZengTaylor & Francis GroupItalian Journal of Animal Science1828-051X2019-01-0118124626010.1080/1828051X.2018.15076251507625Gene expression profile analysis of residual feed intake for Isfahan native chickens using RNA-SEQ dataHamid Reza Izadnia0Mojtaba Tahmoorespur1Mohammad Reza Bakhtiarizadeh2Mohammadreza Nassiri3Saeid Esmaeilkhanien4Agricultural and Natural Resources Research and Education CenterFerdowsi University of MashhadCollege of Aburaihan, University of TehranFerdowsi University of MashhadResearch Institute of Animal ScienceThe factors that affect residual feed intake (RFI) of two chicken breeds (Ross as commercial and Isfahan as Iranian local breed with low and high RFI, respectively) were examined. We sequenced their liver transcriptomes using RNA-Seq while focusing on the identification of important candidate genes, which might influence RFI and growth rate. The differential gene expression analysis revealed that 121 and 279 known genes were significantly up- and down-regulated in the local breed, respectively. QTL enrichment analysis revealed that 63 down-regulated genes in the local breed were enriched in the QTL regions related to feed efficiency traits. Moreover, the functional enrichment analysis showed that the down-regulated genes in the native chickens were mainly involved in the different metabolic processes, such as carboxylic acid metabolic process and response to stress. The Differentially Expressed Genes explored between the chickens of the two breeds led to the identification of some important candidate genes for further breed improvement programmes, including RSAD2, IL15, LIPI, EGR1 and DUSP16. These findings will be a useful resource for the biological investigations of RFI-related genes in Isfahan local chickens and may provide some clues for understanding the molecular genetic mechanisms in other chicken breeds.highlights A global view of transcriptome differences in the liver tissues of commercial and local chicken breeds with different RFI values is obtained. This investigation will contribute to the improvement of chicken genome annotation through the identification of novel transcripts and novel gene. Some important candidate genes related to RFI is obtained.http://dx.doi.org/10.1080/1828051X.2018.1507625residual feed intakerna-seqchickenliver transcriptome |
| spellingShingle | Hamid Reza Izadnia Mojtaba Tahmoorespur Mohammad Reza Bakhtiarizadeh Mohammadreza Nassiri Saeid Esmaeilkhanien Gene expression profile analysis of residual feed intake for Isfahan native chickens using RNA-SEQ data Italian Journal of Animal Science residual feed intake rna-seq chicken liver transcriptome |
| title | Gene expression profile analysis of residual feed intake for Isfahan native chickens using RNA-SEQ data |
| title_full | Gene expression profile analysis of residual feed intake for Isfahan native chickens using RNA-SEQ data |
| title_fullStr | Gene expression profile analysis of residual feed intake for Isfahan native chickens using RNA-SEQ data |
| title_full_unstemmed | Gene expression profile analysis of residual feed intake for Isfahan native chickens using RNA-SEQ data |
| title_short | Gene expression profile analysis of residual feed intake for Isfahan native chickens using RNA-SEQ data |
| title_sort | gene expression profile analysis of residual feed intake for isfahan native chickens using rna seq data |
| topic | residual feed intake rna-seq chicken liver transcriptome |
| url | http://dx.doi.org/10.1080/1828051X.2018.1507625 |
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