Correction: Corrigendum: Gene expression differences in Longissimus muscle of Nelore steers genetically divergent for residual feed intake

Tizioto, Polyana C.; Coutinho, Luiz Lehmann; Oliveira, P. S. N.; Cesar, Aline Silva Mello; Diniz, Wellison J. S.; Lima, A. O. de; Rocha, M. I. P.; Decker, Jared E.; Schnabel, Robert D.; Mourão, Gérson Barreto; Túllio, R. R.; Zerlotini, Adhemar; Taylor, Jeremy F.; Regitano, Luciana Correia de Almeida

doi:10.1038/srep44345

Cited by 4 publications

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“…As an indicator, RFI is independent of growth traits such as average daily gain (ADG) and body weight (BW) (Baker et al, 2006) and is mainly related to economic traits such as dry matter intake (DMI) and feed conversion efficiency (FCR) (Gomes et al, 2012). Recently, pathways such as adenosine 5′monophosphate (AMP)-activated protein kinase (AMPK) signaling (Karisa et al, 2014), metabolic pathways and oxidative stress (Tizioto et al, 2017), lipid metabolism (Tizioto et al, 2015), and the immune response (Gondret et al, 2017) were reported to be involved in RFI variance. Moreover, genes such as COL14A1 (de Lima et al, 2020), OGN (Vigors et al, 2019), ACE (Yi et al, 2015), and SMCT (de Lima et al, 2020) and quantitative trait loci such as EFEMP1 (de Lima et al, 2020) and SHC3 (Weber et al, 2016) were also identified to be potentially related with RFI.…”

Section: Introductionmentioning

confidence: 99%

“…RNA sequencing (RNA-seq) has previously been used to detect gene expression associated with divergent RFI in cattle. Researchers have identified several RFI-related genes and pathways from cattle liver (Tizioto et al, 2017), skeletal muscle (Khansefid et al, 2017), blood (Xi et al, 2015), adipose tissue (Weber et al, 2016), and rumen epithelium (Kong et al, 2016). However, the reported differentially expressed genes (DEGs) differed significantly among studies, likely due to differences in breeds, age, sex, and tissue.…”

Section: Introductionmentioning

confidence: 99%

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

Yang

Han

et al. 2021

Front. Genet.

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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.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Yang

Han

et al. 2021

Front. Genet.

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“…RFI is a complex quantitative trait controlled by polygenes [ 30 ], and it determines the development of the beef cattle industry. As an important economic trait, researchers have tried to uncover the signaling molecules associated with the trait in different tissues such as liver [ 14 ], skeletal muscle [ 15 ], blood [ 16 ], adipose tissue [ 17 ], rumen epithelium [ 18 ], duodenum [ 2 ]. However, the characteristics and commonalities of RFI in different breeds of beef cattle are not well understood.…”

Section: Discussionmentioning

confidence: 99%

“…Potential mechanisms of phenotypic regulation by specific genes can be revealed using transcriptome sequencing technologies (such as KLF6 [12,13]), but most studies of RFI have focused on gene expression in one or two tissues of a breed [2,[14][15][16][17][18]. In different studies, differences in experimental conditions (e.g.…”

Section: Introductionmentioning

confidence: 99%

Characterization of feed efficiency-related key signatures molecular in different cattle breeds

Yang,

Huang,

Pan

et al. 2023

PLoS ONE

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Feed efficiency is a major constraint in the beef industry and has a significant negative correlation with residual feed intake (RFI). RFI is widely used as a measure of feed efficiency in beef cattle and is independent of economic traits such as body weight and average daily gain. However, key traits with commonality or specificity among beef cattle breeds at the same level of RFI have not been reported. Accordingly, the present study hypothesized that signatures associated with feed efficiency would have commonality or specificity in the liver of cattle breeds at the same RFI level. By comparing and integrating liver transcriptome data, we investigated the critical signatures closely associated with RFI in beef cattle using weighted co-expression network analysis, consensus module analysis, functional enrichment analysis and protein network interaction analysis. The results showed that the consensus modules in Angus and Charolais cattle were negatively correlated, and four (turquoise, red, tan, yellow) were significantly positively correlated in Angus liver, while (turquoise, red) were significantly negatively correlated in Charolais liver. These consensus modules were found to be primarily involved in biological processes such as substance metabolism, energy metabolism and gene transcription, which may be one of the possible explanations for the difference in feed efficiency between the two beef breeds. This research also identified five key candidate genes, PLA2G12B, LCAT, MTTP, LCAT, ABCA1 and FADS1, which are closely associated with hepatic lipid metabolism. The present study has identified some modules, genes and pathways that may be the major contributors to the variation in feed efficiency among different cattle breeds, providing a new perspective on the molecular mechanisms of feed efficiency in beef cattle and a research basis for investigating molecular markers associated with feed efficiency in beef cattle.

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“…However, the specific mechanisms underlying the biology of RFI are still underdeveloped. Plenty of experimenters have endeavored to elucidate RFI variation in terms of gene expression from a single tissue [e.g., liver ( 23 ), skeletal muscle ( 24 ), blood ( 25 ), adipose tissue ( 26 ), rumen epithelium ( 27 ), duodenum ( 5 )]. As each study has focused on only individual tissue, it is highly variable and couldn't acquire a coherent conclusion ( 28 ).…”

Section: Introductionmentioning

confidence: 99%

Multi-transcriptomics reveals RLMF axis-mediated signaling molecules associated with bovine feed efficiency

et al. 2023

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The regulatory axis plays a vital role in interpreting the information exchange and interactions among mammal organs. In this study on feed efficiency, it was hypothesized that a rumen-liver-muscle-fat (RLMF) regulatory axis exists and scrutinized the flow of energy along the RLMF axis employing consensus network analysis from a spatial transcriptomic standpoint. Based on enrichment analysis and protein-protein interaction analysis of the consensus network and tissue-specific genes, it was discovered that carbohydrate metabolism, energy metabolism, immune and inflammatory responses were likely to be the biological processes that contribute most to feed efficiency variation on the RLMF regulatory axis. In addition, clusters of genes related to the electron respiratory chain, including ND (2,3,4,4L,5,6), NDUF (A13, A7, S6, B3, B6), COX (1,3), CYTB, UQCR11, ATP (6,8), clusters of genes related to fatty acid metabolism including APO (A1, A2, A4, B, C3), ALB, FG (A, G), as well as clusters of the ribosomal-related gene including RPL (8,18A,18,15,13, P1), the RPS (23,27A,3A,4X), and the PSM (A1-A7, B6, C1, C3, D2-D4, D8 D9, E1) could be the primary effector genes responsible for feed efficiency variation. The findings demonstrate that high feed efficiency cattle, through the synergistic action of the regulatory axis RLMF, may improve the efficiency of biological processes (carbohydrate metabolism, protein ubiquitination, and energy metabolism). Meanwhile, high feed efficiency cattle might enhance the ability to respond to immunity and inflammation, allowing nutrients to be efficiently distributed across these organs associated with digestion and absorption, energy-producing, and energy-storing organs. Elucidating the distribution of nutrients on the RLMF regulatory axis could facilitate an understanding of feed efficiency variation and achieve the study on its molecular regulation.

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Correction: Corrigendum: Gene expression differences in Longissimus muscle of Nelore steers genetically divergent for residual feed intake

Abstract: Scientific Reports 6: Article number: 39493; published online: 22 December 2016; updated: 05 April 2017 This Article contains an error in the order of the Figures, where Figures 2 and 3 were inverted. The correct Figures 2 and 3 appear below:

Cited by 4 publications

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

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

Characterization of feed efficiency-related key signatures molecular in different cattle breeds

Multi-transcriptomics reveals RLMF axis-mediated signaling molecules associated with bovine feed efficiency

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