Potential Biomarkers for Feed Efficiency-Related Traits in Nelore Cattle Identified by Co-expression Network and Integrative Genomics Analyses

Abstract The goal of this study was to evaluate the performance and the carcass traits of Nelore cattle progenies from bulls selected by contrasting traits for precocity, growth and muscularity, through the Expected Progeny Difference (EPD). One hundred and five Nelore bulls (initial weight of 350kg±15kg) and 20 months of age were confined and fed with same diet (73% of concentrate). Thirty-two animals were selected to create the contrasting groups for precocity, growth and muscularity (16 animals assigned as a low EPD group - LEPD and 16 animals assigned as a high EPD group - HEPD), based on the EPD of their parents. The ribeye area and backfat thickness were performed by ultrasonography of 12–13th rib fat thickness and longissimus muscle area (LMA), as well as rump fat thickness (RF) measurements. Animals were harvested after 100 days and during the deboning, meat cuts were weight for cutting yield. The animals selected for the HEPD group had greater average daily gain (P = 0.006), which can be explained by the higher feed intake (P = 0.006). However, there are no difference between groups for the final body weight (P = 0.254) and feed efficiency (P = 0.715). The LEPD group presented higher dressing percentage (P = 0.028). Although the groups evaluated did not presented difference in LMA (P = 0.329) and weight of longissimus muscle (P = 0.480), the weight of rump displayed heaviest in the HEPD (P = 0.037). There was no difference between groups for RF (P = 0.086). Nevertheless, backfat thickness was higher in HEPD group (P = 0.006). The present study indicates that Nelore cattle progenies, with parents displaying higher potential for precocity, growth, and muscularity, show greater backfat thickness and weightiest of rump than the other genetic backgrounds. Thanks to FAPESP for the scholarship (Grant # 2017/02349–1).

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Identification of genomic regions associated with feed efficiency in Nelore cattle

BMC Genetics ◽

10.1186/s12863-014-0100-0 ◽

2014 ◽

Vol 15 (1) ◽

Cited By ~ 41

Author(s):

Priscila SN de Oliveira ◽

Aline SM Cesar ◽

Michele L do Nascimento ◽

Amália S Chaves ◽

Polyana C Tizioto ◽

...

Keyword(s):

Feed Efficiency ◽

Genomic Regions ◽

Nelore Cattle

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Genome regulation and gene interaction networks inferred from muscle transcriptome underlying feed efficiency in Pigs

10.1101/2020.03.20.998203 ◽

2020 ◽

Cited By ~ 2

Author(s):

Victor AO. Carmelo ◽

Haja N. Kadarmideen

Keyword(s):

Network Analysis ◽

Feed Efficiency ◽

Differential Expression Analysis ◽

Gene Interaction ◽

Mitochondrial Genes ◽

Pathway Enrichment Analysis ◽

Mitochondrial Translation ◽

Pathway Enrichment ◽

Genome Regulation ◽

Potential Biomarkers

AbstractImprovement of feed efficiency (FE) is key for sustainability and cost reduction in pig production. Our aim was to characterize the muscle transcriptomic profiles in Danbred Duroc (Duroc) and Danbred Landrace (Landrace), in relation to FE for identifying potential biomarkers. RNA-seq data was analyzed employing differential gene expression methods, gene-gene interaction and network analysis, including pathway and functional analysis. We compared the results with genome regulation in human exercise data. In the differential expression analysis, 13 genes were differentially expressed, including: MRPS11, MTRF1, TRIM63, MGAT4A, KLH30. Based on a novel gene selection method, the divergent count, we performed pathway enrichment analysis. We found 5 significantly enriched pathways related to feed conversion ratio (FCR). These pathways were mainly mitochondrial, and summarized in the mitochondrial translation elongation (MTR) pathway. In the gene interaction analysis, highlights include the mitochondrial genes: PPIF, MRPL35, NDUFS4and the fat metabolism and obesity genes: AACS, SMPDL3B, CTNNBL1, NDUFS4 and LIMD2. In the network analysis, we identified two modules significantly correlated with FCR. Pathway enrichment of modules identified MTR, electron transport chain and DNA repair as enriched pathways. In the network analysis, the mitochondrial gene group NDUF was a key hub group, showing potential as biomarkers. Comparing with human transcriptomic exercise studies, genes related to exercise displayed enrichment in our FCR related genes. We conclude that mitochondrial activity is a driver for FCR in muscle tissue, and mitochondrial genes could be potential biomarkers for FCR in pigs. We hypothesize that increased FE mimics processes triggered in exercised muscle.

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Differentially Expressed Genes in Blood from Young Pigs between Two Swine Lines Divergently Selected for Feed Efficiency: Potential Biomarkers for Improving Feed Efficiency

10.31274/ans_air-180814-1331 ◽

2015 ◽

Author(s):

Haibo Liu ◽

Yet T. Nguyen ◽

Daniel S. Nettleton ◽

Jack C. M. Dekkers ◽

Christopher K. Tuggle

Keyword(s):

Differentially Expressed Genes ◽

Feed Efficiency ◽

Differentially Expressed ◽

Young Pigs ◽

Potential Biomarkers

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144 Rumen Fluid Metabolites as Potential Biomarkers of Feed Efficiency in Angus Steers

Journal of Animal Science ◽

10.1093/jas/skz397.118 ◽

2020 ◽

Vol 98 (Supplement_2) ◽

pp. 51-52

Author(s):

Brooke A Clemmons ◽

Joshua B Powers ◽

Shawn R Campagna ◽

Taylor B Ault ◽

Mallory M Embree ◽

...

Keyword(s):

United States ◽

Beef Cattle ◽

Feed Efficiency ◽

Rumen Fluid ◽

The United States ◽

Cattle Industry ◽

Total Input ◽

Cattle Herds ◽

Syringe Filter ◽

Potential Biomarkers

Abstract Beef cattle is the most consumed red meat in the United States, and the United States is the largest producer and consumer of beef cattle globally. Feed is one of the largest input costs for the beef cattle industry, accounting for 40–60% of the total input costs. Identifying methods for improving feed efficiency in beef cattle herds could result in decreased cost to both producers and consumers, as well as increased animal protein available for global consumption. Identification of feed efficiency biomarkers could aid in the selection of more feed-efficient animals. To identify potential biomarkers of feed efficiency, rumen fluid was collected from low- (n = 14) and high-RFI (n = 15) Angus steers based on RFI ± 0.5 SD around the mean following a 70d feed efficiency trial to determine rumen metabolites associated with variations in feed efficiency. Steers were 7 months of age, weighing 264±2.7 kg. Rumen fluid was collected via gastric tubing, filtered through a 0.22 µM syringe filter, extracted for metabolomic analysis using 0.1% formic acid in acetonitrile:water:methanol (2:2:1), and injected into the Dionex UltiMate 3000 UHPLC system with an Exactive Plus Orbitrap MS. Peaks for known metabolites were identified using MAVEN and analyzed using MetaboAnalyst 4.0 and SAS. Significance was determined using an α ≤ 0.05. Based on fold change (high/low RFI), eight metabolites were greater in low-RFI steers compared to high-RFI steers, including 3,4-dihydroxyphenylacetate, 4-pyridoxate, citraconate, hypoxanthine, succinate/methylmalonate, thymine, uracil, and xylose (P ≤ 0.05), while 12 metabolites differed by ≥ 2-fold. These metabolites were predominantly involved in amino acid and lipid metabolism. Rumen fluid metabolomes differed in steers of varying feed efficiencies. These metabolites may be used as biomarkers of feed efficiency and may provide insight as to factors contributing to differences in feed efficiency that may be exploited to improve feed efficiency in beef cattle herds.

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143 Rumen Fluid Metabolites as Potential Biomarkers of Feed Efficiency in Angus Steers

Journal of Animal Science ◽

10.1093/jas/skz397.037 ◽

2020 ◽

Vol 98 (Supplement_2) ◽

pp. 17-17

Author(s):

Brooke A Clemmons ◽

Joshua B Powers ◽

Shawn R Campagna ◽

Taylor B Ault ◽

Mallory M Embree ◽

...

Keyword(s):

United States ◽

Beef Cattle ◽

Feed Efficiency ◽

Rumen Fluid ◽

The United States ◽

Cattle Industry ◽

Total Input ◽

Cattle Herds ◽

Syringe Filter ◽

Potential Biomarkers

Abstract Beef cattle is the most consumed red meat in the United States, and the United States is the largest producer and consumer of beef cattle globally. Feed is one of the largest input costs for the beef cattle industry, accounting for 40–60% of the total input costs. Identifying methods for improving feed efficiency in beef cattle herds could result in decreased cost to both producers and consumers, as well as increased animal protein available for global consumption. Identification of feed efficiency biomarkers could aid in the selection of more feed-efficient animals. To identify potential biomarkers of feed efficiency, rumen fluid was collected from low- (n = 14) and high-RFI (n = 15) Angus steers based on RFI ± 0.5 SD around the mean following a 70-d feed efficiency trial to determine rumen metabolites associated with variations in feed efficiency. Steers were 7 mo of age, weighing 264±2.7 kg. Rumen fluid was collected via gastric tubing, filtered through a 0.22 µM syringe filter, extracted for metabolomic analysis using 0.1% formic acid in acetonitrile:water:methanol (2:2:1), and injected into the Dionex UltiMate 3000 UHPLC system with an Exactive Plus Orbitrap MS. Peaks for known metabolites were identified using MAVEN and analyzed using MetaboAnalyst 4.0 and SAS. Significance was determined using an α ≤ 0.05. Based on fold change (high/low RFI), eight metabolites were greater in low-RFI steers compared to high-RFI steers, including 3,4-dihydroxyphenylacetate, 4-pyridoxate, citraconate, hypoxanthine, succinate/methylmalonate, thymine, uracil, and xylose (P ≤ 0.05), while 12 metabolites differed by ≥ 2-fold. These metabolites were predominantly involved in amino acid and lipid metabolism. Rumen fluid metabolomes differed in steers of varying feed efficiencies. These metabolites may be used as biomarkers of feed efficiency and may provide insight as to factors contributing to differences in feed efficiency that may be exploited to improve feed efficiency in beef cattle herds.

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