Identification of single nucleotide polymorphisms (SNPs) potentially associated with residual feed intake in Qinchuan beef cattle by hypothalamus and duodenum RNA-Seq data
The regulation of residual feed intake (RFI) in beef cattle involves brain-gut mechanisms due to the interaction between neural signals in the brain and hunger or satiety in the gut. RNA-Seq data contain an extensive resource of untapped SNPs. Therefore, hypothalamic and duodenal tissues from ten ex...
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2025-04-01
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| author | Zonghua Su Chenglong Li Chaoyun Yang YanLing Ding Xiaonan Zhou Junjie Xu Chang Qu Yuangang Shi Cong-Jun Li Xiaolong Kang |
| author_facet | Zonghua Su Chenglong Li Chaoyun Yang YanLing Ding Xiaonan Zhou Junjie Xu Chang Qu Yuangang Shi Cong-Jun Li Xiaolong Kang |
| author_sort | Zonghua Su |
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| description | The regulation of residual feed intake (RFI) in beef cattle involves brain-gut mechanisms due to the interaction between neural signals in the brain and hunger or satiety in the gut. RNA-Seq data contain an extensive resource of untapped SNPs. Therefore, hypothalamic and duodenal tissues from ten extreme RFI individuals were collected, and transcriptome sequenced in this study. All the alignment data were combined according to RFI, and the SNPs in the same group were identified. A total of 270,410 SNPs were found in the high RFI group, and 255,120 SNPs were found in the low RFI group. Most SNPs were detected in the intronic region, followed by the intergenic region, and the exon region accounts for 1.11% and 1.38% in the high and low RFI groups, respectively. Prediction of high-impact SNPs and annotation of the genes in which they are located yielded 83 and 97 genes in the high-RFI and low-RFI groups, respectively. GO enrichment analysis of these genes revealed multiple NADH/NADPH-related pathways, with ND4, ND5, and ND6 significantly enriched as core subunits of NADH dehydrogenase (complex I), and is closely related to mitochondrial function. KEGG enrichment analysis of ND4, ND5, and ND6 genes was enriched in the thermogenic pathway. Multiple genes, such as ATP1A2, SLC9A4, and PLA2G5, were reported to be associated with RFI energy metabolism in the concurrent enrichment analysis. Protein-protein interaction analysis identified multiple potential candidate genes related to energy metabolism that were hypothesized to be potentially associated with the RFI phenotype. The results of this study will help to increase our understanding of identifying SNPs with significant genetic effects and their potential biological functions. |
| format | Article |
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| institution | DOAJ |
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| language | English |
| publishDate | 2025-04-01 |
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| spelling | doaj-art-474355b3e2634b7e85f603db182e718a2025-08-20T03:18:52ZengPeerJ Inc.PeerJ2167-83592025-04-0113e1927010.7717/peerj.19270Identification of single nucleotide polymorphisms (SNPs) potentially associated with residual feed intake in Qinchuan beef cattle by hypothalamus and duodenum RNA-Seq dataZonghua Su0Chenglong Li1Chaoyun Yang2YanLing Ding3Xiaonan Zhou4Junjie Xu5Chang Qu6Yuangang Shi7Cong-Jun Li8Xiaolong Kang9Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, ChinaKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, ChinaKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, ChinaKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, ChinaKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, ChinaKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, ChinaKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, ChinaKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, ChinaAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agricultural, Beltsville, MD, United StatesKey Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, ChinaThe regulation of residual feed intake (RFI) in beef cattle involves brain-gut mechanisms due to the interaction between neural signals in the brain and hunger or satiety in the gut. RNA-Seq data contain an extensive resource of untapped SNPs. Therefore, hypothalamic and duodenal tissues from ten extreme RFI individuals were collected, and transcriptome sequenced in this study. All the alignment data were combined according to RFI, and the SNPs in the same group were identified. A total of 270,410 SNPs were found in the high RFI group, and 255,120 SNPs were found in the low RFI group. Most SNPs were detected in the intronic region, followed by the intergenic region, and the exon region accounts for 1.11% and 1.38% in the high and low RFI groups, respectively. Prediction of high-impact SNPs and annotation of the genes in which they are located yielded 83 and 97 genes in the high-RFI and low-RFI groups, respectively. GO enrichment analysis of these genes revealed multiple NADH/NADPH-related pathways, with ND4, ND5, and ND6 significantly enriched as core subunits of NADH dehydrogenase (complex I), and is closely related to mitochondrial function. KEGG enrichment analysis of ND4, ND5, and ND6 genes was enriched in the thermogenic pathway. Multiple genes, such as ATP1A2, SLC9A4, and PLA2G5, were reported to be associated with RFI energy metabolism in the concurrent enrichment analysis. Protein-protein interaction analysis identified multiple potential candidate genes related to energy metabolism that were hypothesized to be potentially associated with the RFI phenotype. The results of this study will help to increase our understanding of identifying SNPs with significant genetic effects and their potential biological functions.https://peerj.com/articles/19270.pdfRNA-SeqSingle nucleotide polymorphismsBeef cattleHypothalamusDuodenum |
| spellingShingle | Zonghua Su Chenglong Li Chaoyun Yang YanLing Ding Xiaonan Zhou Junjie Xu Chang Qu Yuangang Shi Cong-Jun Li Xiaolong Kang Identification of single nucleotide polymorphisms (SNPs) potentially associated with residual feed intake in Qinchuan beef cattle by hypothalamus and duodenum RNA-Seq data PeerJ RNA-Seq Single nucleotide polymorphisms Beef cattle Hypothalamus Duodenum |
| title | Identification of single nucleotide polymorphisms (SNPs) potentially associated with residual feed intake in Qinchuan beef cattle by hypothalamus and duodenum RNA-Seq data |
| title_full | Identification of single nucleotide polymorphisms (SNPs) potentially associated with residual feed intake in Qinchuan beef cattle by hypothalamus and duodenum RNA-Seq data |
| title_fullStr | Identification of single nucleotide polymorphisms (SNPs) potentially associated with residual feed intake in Qinchuan beef cattle by hypothalamus and duodenum RNA-Seq data |
| title_full_unstemmed | Identification of single nucleotide polymorphisms (SNPs) potentially associated with residual feed intake in Qinchuan beef cattle by hypothalamus and duodenum RNA-Seq data |
| title_short | Identification of single nucleotide polymorphisms (SNPs) potentially associated with residual feed intake in Qinchuan beef cattle by hypothalamus and duodenum RNA-Seq data |
| title_sort | identification of single nucleotide polymorphisms snps potentially associated with residual feed intake in qinchuan beef cattle by hypothalamus and duodenum rna seq data |
| topic | RNA-Seq Single nucleotide polymorphisms Beef cattle Hypothalamus Duodenum |
| url | https://peerj.com/articles/19270.pdf |
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