Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq

Residual feed intake (RFI) is an important measure of feed efficiency for agricultural animals. Factors associated with cattle RFI include physiology, dietary factors, and the environment. However, a precise genetic mechanism underlying cattle RFI variations in duodenal tissue is currently unavailab...

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Main Authors: Chaoyun Yang, Liyun Han, Peng Li, Yanling Ding, Yun Zhu, Zengwen Huang, Xingang Dan, Yuangang Shi, Xiaolong Kang
Format: Article
Language:English
Published: Frontiers Media S.A. 2021-10-01
Series:Frontiers in Genetics
Subjects:
Online Access:https://www.frontiersin.org/articles/10.3389/fgene.2021.741878/full
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spelling doaj-b7aa594655504175b8ba7ffb4cb41f222021-10-05T10:08:22ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-10-011210.3389/fgene.2021.741878741878Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-SeqChaoyun Yang0Liyun Han1Peng Li2Yanling Ding3Yun Zhu4Zengwen Huang5Xingang Dan6Yuangang Shi7Xiaolong Kang8School of Agriculture, Ningxia University, Yinchuan, ChinaNingxia Agriculture Reclamation Helanshan Diary Co.Ltd., Yinchuan, ChinaSchool of Agriculture, Ningxia University, Yinchuan, ChinaSchool of Agriculture, Ningxia University, Yinchuan, ChinaSchool of Agriculture, Ningxia University, Yinchuan, ChinaSchool of Agriculture, Ningxia University, Yinchuan, ChinaSchool of Agriculture, Ningxia University, Yinchuan, ChinaSchool of Agriculture, Ningxia University, Yinchuan, ChinaSchool of Agriculture, Ningxia University, Yinchuan, ChinaResidual feed intake (RFI) is an important measure of feed efficiency for agricultural animals. Factors associated with cattle RFI include physiology, dietary factors, and the environment. However, a precise genetic mechanism underlying cattle RFI variations in duodenal tissue is currently unavailable. The present study aimed to identify the key genes and functional pathways contributing to variance in cattle RFI phenotypes using RNA sequencing (RNA-seq). Six bulls with extremely high or low RFIs were selected for detecting differentially expressed genes (DEGs) by RNA-seq, followed by conducting GO, KEGG enrichment, protein-protein interaction (PPI), and co-expression network (WGCNA, n = 10) analysis. A total of 380 differentially expressed genes was obtained from high and low RFI groups, including genes related to energy metabolism (ALDOA, HADHB, INPPL1), mitochondrial function (NDUFS1, RFN4, CUL1), and feed intake behavior (CCK). Two key sub-networks and 26 key genes were detected using GO analysis of DEGs and PPI analysis, such as TPM1 and TPM2, which are involved in mitochondrial pathways and protein synthesis. Through WGCNA, a gene network was built, and genes were sorted into 27 modules, among which the blue (r = 0.72, p = 0.03) and salmon modules (r = −0.87, p = 0.002) were most closely related with RFI. DEGs and genes from the main sub-networks and closely related modules were largely involved in metabolism; oxidative phosphorylation; glucagon, ribosome, and N-glycan biosynthesis, and the MAPK and PI3K-Akt signaling pathways. Through WGCNA, five key genes, including FN1 and TPM2, associated with the biological regulation of oxidative processes and skeletal muscle development were identified. Taken together, our data suggest that the duodenum has specific biological functions in regulating feed intake. Our findings provide broad-scale perspectives for identifying potential pathways and key genes involved in the regulation of feed efficiency in beef cattle.https://www.frontiersin.org/articles/10.3389/fgene.2021.741878/fullresidual feed intakefeed efficiencyweighted gene co-expression network analysisbeef cattleduodenal
collection DOAJ
language English
format Article
sources DOAJ
author Chaoyun Yang
Liyun Han
Peng Li
Yanling Ding
Yun Zhu
Zengwen Huang
Xingang Dan
Yuangang Shi
Xiaolong Kang
spellingShingle Chaoyun Yang
Liyun Han
Peng Li
Yanling Ding
Yun Zhu
Zengwen Huang
Xingang Dan
Yuangang Shi
Xiaolong Kang
Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq
Frontiers in Genetics
residual feed intake
feed efficiency
weighted gene co-expression network analysis
beef cattle
duodenal
author_facet Chaoyun Yang
Liyun Han
Peng Li
Yanling Ding
Yun Zhu
Zengwen Huang
Xingang Dan
Yuangang Shi
Xiaolong Kang
author_sort Chaoyun Yang
title Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq
title_short Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq
title_full Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq
title_fullStr Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq
title_full_unstemmed Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq
title_sort characterization and duodenal transcriptome analysis of chinese beef cattle with divergent feed efficiency using rna-seq
publisher Frontiers Media S.A.
series Frontiers in Genetics
issn 1664-8021
publishDate 2021-10-01
description Residual feed intake (RFI) is an important measure of feed efficiency for agricultural animals. Factors associated with cattle RFI include physiology, dietary factors, and the environment. However, a precise genetic mechanism underlying cattle RFI variations in duodenal tissue is currently unavailable. The present study aimed to identify the key genes and functional pathways contributing to variance in cattle RFI phenotypes using RNA sequencing (RNA-seq). Six bulls with extremely high or low RFIs were selected for detecting differentially expressed genes (DEGs) by RNA-seq, followed by conducting GO, KEGG enrichment, protein-protein interaction (PPI), and co-expression network (WGCNA, n = 10) analysis. A total of 380 differentially expressed genes was obtained from high and low RFI groups, including genes related to energy metabolism (ALDOA, HADHB, INPPL1), mitochondrial function (NDUFS1, RFN4, CUL1), and feed intake behavior (CCK). Two key sub-networks and 26 key genes were detected using GO analysis of DEGs and PPI analysis, such as TPM1 and TPM2, which are involved in mitochondrial pathways and protein synthesis. Through WGCNA, a gene network was built, and genes were sorted into 27 modules, among which the blue (r = 0.72, p = 0.03) and salmon modules (r = −0.87, p = 0.002) were most closely related with RFI. DEGs and genes from the main sub-networks and closely related modules were largely involved in metabolism; oxidative phosphorylation; glucagon, ribosome, and N-glycan biosynthesis, and the MAPK and PI3K-Akt signaling pathways. Through WGCNA, five key genes, including FN1 and TPM2, associated with the biological regulation of oxidative processes and skeletal muscle development were identified. Taken together, our data suggest that the duodenum has specific biological functions in regulating feed intake. Our findings provide broad-scale perspectives for identifying potential pathways and key genes involved in the regulation of feed efficiency in beef cattle.
topic residual feed intake
feed efficiency
weighted gene co-expression network analysis
beef cattle
duodenal
url https://www.frontiersin.org/articles/10.3389/fgene.2021.741878/full
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