scholarly journals Systems biology reveals NR2F6 and TGFB1 as key regulators of feed efficiency in beef cattle

2018 ◽  
Author(s):  
Pâmela A. Alexandre ◽  
Marina Naval-Sanchez ◽  
Laercio R. Porto-Neto ◽  
José Bento S. Ferraz ◽  
Antonio Reverter ◽  
...  
Keyword(s):  
Systems Biology ◽  
Beef Cattle ◽  
Feed Efficiency ◽  
Motif Discovery ◽  
Bos Indicus ◽  
Hormonal Control ◽  
Biological Processes ◽  
Tissue Specific ◽  
Complex Phenotypes ◽  
Important Trait

AbstractSystems biology approaches are used as strategy to uncover tissue-specific perturbations and regulatory genes related to complex phenotypes. We applied this approach to study feed efficiency (FE) in beef cattle, an important trait both economically and environmentally. Poly-A selected RNA of five tissues (adrenal gland, hypothalamus, liver, skeletal muscle and pituitary) of eighteen young bulls, selected for high and low FE, were sequenced (100bp, pared-end). From the 17,354 expressed genes, 1,317 were prioritized by five selection categories (differentially expressed, harbouring SNPs associated with FE, tissue-specific, secreted in plasma and key regulators) and used for network construction. NR2F6 and TGFB were identified and validated by motif discovery as key regulators of hepatic inflammatory response and muscle tissue development, respectively, two biological processes demonstrated to be associated to FE. Moreover, we indicated potential biomarkers of FE which are related to hormonal control of metabolism and sexual maturity. By using robust methodologies and validation strategies, we confirmed main biological processes related to FE in Bos indicus and indicated candidate genes as regulators or biomarkers of superior animals.

scholarly journals Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 997
Author(s):  
Pâmela A. Alexandre ◽  
Antonio Reverter ◽  
Roberta B. Berezin ◽  
Laercio R. Porto-Neto ◽  
Gabriela Ribeiro ◽  
...  
Keyword(s):  
Feed Efficiency ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Rna Seq ◽  
Complex Phenotypes ◽  
Non Coding Rna ◽  
Genomic Location ◽  
Regulatory Potential ◽  
Long Non Coding Rna ◽  
Pituitary Adrenal Axis

Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from the liver, muscle, hypothalamus, pituitary gland and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management.

scholarly journals Exploring regulation in tissues with eQTL networks

2017 ◽  
Vol 114 (37) ◽  
pp. E7841-E7850 ◽  
Author(s):  
Maud Fagny ◽  
Joseph N. Paulson ◽  
Marieke L. Kuijjer ◽  
Abhijeet R. Sonawane ◽  
Cho-Yi Chen ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Regulatory Function ◽  
Biological Processes ◽  
Bipartite Networks ◽  
Tissue Specific ◽  
Complex Phenotypes ◽  
Regulatory Impact ◽  
Regulatory Potential ◽  
Trait Locus ◽  
Gene Expression Levels

Characterizing the collective regulatory impact of genetic variants on complex phenotypes is a major challenge in developing a genotype to phenotype map. Using expression quantitative trait locus (eQTL) analyses, we constructed bipartite networks in which edges represent significant associations between genetic variants and gene expression levels and found that the network structure informs regulatory function. We show, in 13 tissues, that these eQTL networks are organized into dense, highly modular communities grouping genes often involved in coherent biological processes. We find communities representing shared processes across tissues, as well as communities associated with tissue-specific processes that coalesce around variants in tissue-specific active chromatin regions. Node centrality is also highly informative, with the global and community hubs differing in regulatory potential and likelihood of being disease associated.

758 Understanding the nature of complex phenotypes in beef cattle using systems biology

2017 ◽  
Vol 95 (suppl_4) ◽  
pp. 367-367
Author(s):  
A. Canovas ◽  
M. G. Thomas ◽  
J. Casellas ◽  
J. F. Medrano
Keyword(s):  
Systems Biology ◽  
Beef Cattle ◽  
Complex Phenotypes

scholarly journals Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle

2020 ◽  
Author(s):  
Pamela A. Alexandre ◽  
Antonio Reverter ◽  
Laercio R. Porto-Neto ◽  
Roberta B. Berezin ◽  
Gabriela Ribeiro ◽  
...  
Keyword(s):  
Feed Efficiency ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Rna Seq ◽  
Complex Phenotypes ◽  
Non Coding Rna ◽  
Genomic Location ◽  
Regulatory Potential ◽  
Long Non Coding Rna ◽  
Pituitary Adrenal Axis

Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from liver, muscle, hypothalamus, pituitary and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management.

Systems Biology Application in Feed Efficiency in Beef Cattle

2016 ◽  
pp. 79-95
Author(s):  
Heidge Fukumasu ◽  
Miguel Henrique Santana ◽  
Pamela Almeida Alexandre ◽  
José Bento Sterman Ferraz
Keyword(s):  
Systems Biology ◽  
Beef Cattle ◽  
Feed Efficiency

scholarly journals 415 More efficient steers on good diets are not the most efficient ones on limiting diets

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 168-169
Author(s):  
Peter Carmona ◽  
Luis Silva ◽  
Diogo Fleury Azevedo Costa ◽  
Lais Lima
Keyword(s):  
Beef Cattle ◽  
Feed Efficiency ◽  
Block Design ◽  
Average Daily Gain ◽  
Bos Indicus ◽  
Economic Benefits ◽  
Experimental Unit ◽  
Protein Requirements ◽  
Low Protein ◽  
Randomized Block Design

Abstract Nutrition for a positive growth path represents the major cost of any beef cattle enterprise. Improvements on feed efficiency (FE) can lead to significant economic benefits and reduce the environmental footprint. Usually, animals selected for FE on high-protein (HP) diets are expected to perform as efficiently on low-protein (LP) diets. This experiment used 30 Bos indicus steers (398 ± 24 kg BW) to determine the agreement between FE rankings of beef cattle fed a LP or a HP diet. As hypothesis, it was suggested that the agreement would be high. A completely randomized block design was used, where each steer represented an experimental unit. Steers were fed in individual pens for two periods of 70 days, including an adaptation of 10 days, with diets supplying either 70% or 100% of their rumen degradable protein requirements. Average daily gain (ADG) and dry matter intake (DMI) were measured, while residual feed intake (RFI) and residual gain (RG) were calculated. Kappa analysis was used to determine the agreement between FE of both diets. In the LP diet, ADG was 0.93 kg/d (0.38 to 1.47), DMI averaged 9.67 kg/d (7.9 to 12.1), RFI varied between -1.55 and 1.84, and RG from -0.61 to 0.53. In the HP diet, ADG was 1.16 kg/d (0.77 to 1.57) and DMI averaged 9.87 kg/d (4.79 to 11.87). RFI varied between -2.53 and 1.61 and RG from -0.34 to 0.33. Chance-corrected analysis of the ranking between diets showed no agreement for RFI (Kappa=5.6%, P = 0.68) nor for RG (Kappa=9.1%, P = 0.44). These results suggest that different physiological mechanisms are responsible for FE regulation in both diets; thus, appropriate diets targeting each scenario must be used when selecting animals for feed efficiency.

scholarly journals Erratum to: Liver transcriptomic networks reveal main biological processes associated with feed efficiency in beef cattle

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Pamela A. Alexandre ◽  
Lisette J. A. Kogelman ◽  
Miguel H. A. Santana ◽  
Danielle Passarelli ◽  
Lidia H. Pulz ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Feed Efficiency ◽  
Biological Processes

scholarly journals Liver transcriptomic networks reveal main biological processes associated with feed efficiency in beef cattle

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Pamela A. Alexandre ◽  
Lisette J. A. Kogelman ◽  
Miguel H. A. Santana ◽  
Danielle Passarelli ◽  
Lidia H. Pulz ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Feed Efficiency ◽  
Biological Processes

scholarly journals Systems Biology Reveals NR2F6 and TGFB1 as Key Regulators of Feed Efficiency in Beef Cattle

2019 ◽  
Vol 10 ◽  
Author(s):  
Pâmela A. Alexandre ◽  
Marina Naval-Sanchez ◽  
Laercio R. Porto-Neto ◽  
José Bento S. Ferraz ◽  
Antonio Reverter ◽  
...  
Keyword(s):  
Systems Biology ◽  
Beef Cattle ◽  
Feed Efficiency

scholarly journals Identification of Important Proteins and Pathways Affecting Feed Efficiency in DLY Pigs by iTRAQ-Based Proteomic Analysis

Animals ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 189 ◽  
Author(s):  
Jie Wu ◽  
Xingwang Wang ◽  
Rongrong Ding ◽  
Jianping Quan ◽  
Yong Ye ◽  
...  
Keyword(s):  
Small Intestine ◽  
Feed Efficiency ◽  
Enrichment Analysis ◽  
Absolute Quantification ◽  
Biological Processes ◽  
Intestinal Movement ◽  
Extreme Phenotypes ◽  
Isobaric Tag ◽  
Important Trait ◽  
Small Intestinal

Feed efficiency is an economically important trait controlled by multiple genes in pigs. The small intestine is the main organ of digestion and nutrient absorption. To explore the biological processes by which small intestine proteomics affects feed efficiency (FE), we investigated the small intestinal tissue proteomes of high-FE and low-FE pigs by the isobaric tag for relative and absolute quantification (iTRAQ) method. In this study, a total of 225 Duroc × (Landrace × Yorkshire) (DLY) commercial pigs were ranked according to feed efficiency, which ranged from 30 kg to 100 kg, and six pigs with extreme phenotypes were selected, three in each of the high and low groups. A total of 1219 differentially expressed proteins (DEPs) were identified between the high-FE and low-FE groups (fold change ≥1.2 or ≤0.84; p ≤ 0.05), of which 785 were upregulated, and 484 were downregulated. Enrichment analysis indicated that the DEPs were mainly enriched in actin filament formation, microvilli formation, and small intestinal movement pathways. Protein functional analysis and protein interaction networks indicated that RHOA, HCLS1, EZR, CDC42, and RAC1 were important proteins that regulate FE in pigs. This study provided new insights into the important pathways and proteins involved in feed efficiency in pigs.

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