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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle

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Goncalves, Tassia Mangetti [1] ; de Almeida Regitano, Luciana Correia [2] ; Koltes, James E. [3] ; Mello Cesar, Aline Silva [1] ; da Silva Andrade, Sonia Cristina [1, 4] ; Mourao, Gerson Barreto [1] ; Gasparin, Gustavo [1] ; Monteiro Moreira, Gabriel Costa [1] ; Fritz-Waters, Elyn [3] ; Reecy, James M. [3] ; Coutinho, Luiz Lehmann [1]
Total Authors: 11
[1] Univ Sao Paulo, Dept Anim Sci, Piracicaba - Brazil
[2] Embrapa Southeast Cattle Res Ctr, Sao Carlos, SP - Brazil
[3] Iowa State Univ, Dept Anim Sci, Ames, IA - USA
[4] Univ Sao Paulo, Dept Genet & Evolutionary Biol, Sao Paulo - Brazil
Total Affiliations: 4
Document type: Journal article
Source: FRONTIERS IN GENETICS; v. 9, OCT 5 2018.
Web of Science Citations: 4

Beef tenderness, a complex trait affected by many factors, is economically important to beef quality, industry, and consumer's palatability. In this study, RNA-Seq was used in network analysis to better understand the biological processes that lead to differences in beef tenderness. Skeletal muscle transcriptional profiles from 24 Nellore steers, selected by extreme estimated breeding values (EBVs) for shear force after 14 days of aging, were analyzed and 22 differentially expressed transcripts were identified. Among these were genes encoding ribosomal proteins, glutathione transporter ATP-binding cassette, sub-family C (CFTR/MRP), member 4 (ABCC4), and synaptotagmin IV (SYT4). Complementary co-expression analyses using Partial Correlation with Information Theory (PCIT), Phenotypic Impact Factor (PIF) and the Regulatory Impact Factor (RIF) methods identified candidate regulators and related pathways. The PCIT analysis identified ubiquitin specific peptidase 2 (USP2), growth factor receptor-bound protein 10 (GBR10), anoctamin 1 (ANO1), and transmembrane BAX inhibitor motif containing 4 (TMBIM4) as the most differentially hubbed (DH) transcripts. The transcripts that had a significant correlation with USP2, GBR10, ANO1, and TMBIM4 enriched for proteasome KEGG pathway. RIF analysis identified microRNAs as candidate regulators of variation in tenderness, including bta-mir-133a-2 and bta-mir-22. Both microRNAs have target genes present in the calcium signaling pathway and apoptosis. PIF analysis identified myoglobin (MB), enolase 3 (ENO3), and carbonic anhydrase 3 (CA3) as potentially having fundamental roles in tenderness. Pathways identified in our study impacted in beef tenderness included: calcium signaling, apoptosis, and proteolysis. These findings underscore some of the complex molecular mechanisms that control beef tenderness in Nellore cattle. (AU)

FAPESP's process: 13/26121-9 - Integrative analysis of differential gene expression to elucidate molecular mechanisms that control meat tenderness in Nellore cattle
Grantee:Tassia Mangetti Gonçalves
Support Opportunities: Scholarships abroad - Research Internship - Master's degree
FAPESP's process: 12/23934-6 - Differential expression of genes related with meat tenderness in nelore cattle
Grantee:Tassia Mangetti Gonçalves
Support Opportunities: Scholarships in Brazil - Master