Gonçalves Tássia Mangetti, de Almeida Regitano Luciana Correia, Koltes James E, Cesar Aline Silva Mello, da Silva Andrade Sónia Cristina, Mourão Gerson Barreto, Gasparin Gustavo, Moreira Gabriel Costa Monteiro, Fritz-Waters Elyn, Reecy James M, Coutinho Luiz Lehmann
Department of Animal Science, University of São Paulo, Piracicaba, Brazil.
Embrapa Southeast-Cattle Research Center, São Carlos, Brazil.
Front Genet. 2018 Oct 5;9:441. doi: 10.3389/fgene.2018.00441. eCollection 2018.
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 (), and synaptotagmin IV (). 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 (), growth factor receptor-bound protein 10 (), anoctamin 1 (), and transmembrane BAX inhibitor motif containing 4 () as the most differentially hubbed (DH) transcripts. The transcripts that had a significant correlation with , , , and enriched for proteasome KEGG pathway. RIF analysis identified microRNAs as candidate regulators of variation in tenderness, including and . Both microRNAs have target genes present in the calcium signaling pathway and apoptosis. PIF analysis identified myoglobin (), enolase 3 (), and carbonic anhydrase 3 () 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.
牛肉嫩度是一个受多种因素影响的复杂性状，对牛肉品质、产业及消费者的适口性具有重要经济意义。在本研究中，利用RNA测序进行网络分析，以更好地理解导致牛肉嫩度差异的生物学过程。分析了24头内洛尔阉牛的骨骼肌转录谱，这些阉牛是根据14天成熟后剪切力的极端估计育种值（EBV）挑选出来的，共鉴定出22个差异表达的转录本。其中包括编码核糖体蛋白、谷胱甘肽转运体ATP结合盒亚家族C（CFTR/MRP）成员4以及突触结合蛋白IV的基因。使用基于信息论的偏相关（PCIT）、表型影响因子（PIF）和调控影响因子（RIF）方法进行的互补共表达分析确定了候选调控因子和相关途径。PCIT分析确定泛素特异性肽酶2、生长因子受体结合蛋白10、八聚体膜蛋白1和含跨膜BAX抑制基序4为差异最大的中枢（DH）转录本。与、、和显著相关的转录本在蛋白酶体KEGG途径中富集。RIF分析确定微小RNA为嫩度变异的候选调控因子，包括和。这两种微小RNA都有存在于钙信号通路和凋亡中的靶基因。PIF分析确定肌红蛋白、烯醇化酶3和碳酸酐酶3可能在嫩度中起重要作用。我们研究中确定的影响牛肉嫩度的途径包括：钙信号传导、凋亡和蛋白水解。这些发现强调了一些控制内洛尔牛牛肉嫩度的复杂分子机制。
