RESUMO
The aim of this study was to identify mRNA isoforms and small genetic variants that may be affecting marbling and beef color in Nellore cattle. Longissimus thoracis muscle samples from 20 bulls with different phenotypes (out of 80 bulls set) for marbling (moderate (n = 10) and low (n = 10) groups) and beef color (desirable (n = 10) and undesirable (n = 9) group) traits were used to perform transcriptomic analysis using RNA sequencing. Fourteen and 15 mRNA isoforms were detected as differentially expressed (DE) (P-value ≤ 0.001) between divergent groups for marbling and meat color traits, respectively. Some of those DE mRNA isoforms have shown sites of splicing modified by small structural variants as single nucleotide variant (SNV), insertion, and/or deletion. Enrichment analysis identified metabolic pathways, such as O2/CO2 exchange in erythrocytes, tyrosine biosynthesis, and phenylalanine degradation. The results obtained suggest potential key regulatory genes associated with these economically important traits for the beef industry and for the consumer.
Assuntos
Carne , Isoformas de RNA , Animais , Bovinos/genética , Variação Genética , Masculino , Carne/análise , Músculo Esquelético/metabolismo , Fenótipo , Isoformas de RNA/análise , Isoformas de RNA/metabolismo , Análise de Sequência de RNARESUMO
The myofibrillar fragmentation index (MFI) is an indicative trait for meat tenderness. Longissimus thoracis muscle samples from the 20 most extreme bulls (out of 80 bulls set) for MFI (high (n = 10) and low (n = 10) groups) trait were used to perform transcriptomic analysis, using RNA Sequencing (RNA-Seq). An average of 24.616 genes was expressed in the Nellore muscle transcriptome analysis. A total of 96 genes were differentially expressed (p value ≤ 0.001) between the two groups of divergent bulls for MFI. The HEBP2 and BDH1 genes were overexpressed in animals with high MFI. The MYBPH and MYL6, myosin encoders, were identified. The differentially expressed genes were related to increase mitochondria efficiency, especially in cells under oxidative stress conditions, and these also were related to zinc and calcium binding, membrane transport, and muscle constituent proteins, such as actin and myosin. Most of those genes were involved in metabolic pathways of oxidation-reduction, transport of lactate in the plasma membrane, and muscle contraction. This is the first study applying MFI phenotypes in transcriptomic studies to identify and understand differentially expressed genes for beef tenderness. These results suggest that differences detected in gene expression between high and low MFI animals are related to reactive mechanisms and structural components of oxidative fibers under the condition of cellular stress. Some genes may be selected as positional candidate genes to beef tenderness, MYL6, MYBPH, TRIM63, TRIM55, TRIOBP, and CHRNG genes. The use of MFI phenotypes could enhance results of meat tenderness studies.
Assuntos
Bovinos/genética , Músculo Esquelético/metabolismo , Característica Quantitativa Herdável , Carne Vermelha/normas , Transcriptoma , Animais , Bovinos/metabolismo , Proteínas do Citoesqueleto/genética , Proteínas do Citoesqueleto/metabolismo , Perfilação da Expressão Gênica , Proteínas Ligantes de Grupo Heme/genética , Proteínas Ligantes de Grupo Heme/metabolismo , Masculino , Miosinas/genética , Miosinas/metabolismo , Receptores Nicotínicos/genética , Receptores Nicotínicos/metabolismo , Proteínas com Motivo Tripartido/genética , Proteínas com Motivo Tripartido/metabolismoRESUMO
BACKGROUND: The aim of this study was to use transcriptome RNA-Seq data from longissimus thoracis muscle of uncastrated Nelore males to identify hub genes based on co-expression network obtained from differentially expressed genes (DEGs) associated with intramuscular fat content. RESULTS: A total of 30 transcriptomics datasets (RNA-Seq) obtained from longissimus thoracis muscle were selected based on the phenotypic value of divergent intramuscular fat content: 15 with the highest intramuscular fat content (HIF) and 15 with the lowest intramuscular fat content (LIF). The transcriptomics datasets were aligned with a reference genome and 65 differentially expressed genes (DEGs) were identified, including 21 upregulated and 44 downregulated genes in HIF animals. The normalized count data from DEGs was then used for co-expression network construction. From the co-expression network, four modules were identified. The topological properties of the network were analyzed; those genes engaging in the most interactions (maximal clique centrality method) with other DEGs were predicted to be hub genes (PDE4D, KLHL30 and IL1RAP), which consequently may play a role in cellular and/or systemic lipid biology in Nelore cattle. Top modules screened from the gene co-expression network were identify. The two candidate modules had clear associated biological pathways related to fat development, cell adhesion, and muscle differentiation, immune system, among others. The hub genes belonged in top modules and were downregulated in HIF animals. PDE4D and IL1RAP have known effects on lipid metabolism and the immune system through the regulation of cAMP signaling. Given that cAMP is known to play a role in lipid systems, PDE4D and IL1RAP downregulation may contribute to increased levels of intracellular cAMP and thus may have effects on IF content differences in Nelore cattle. KLHL30 may have effects on muscle metabolism. Klhl protein families play a role in protein degradation. However, the downregulation of this gene and its role in lipid metabolism has not yet been clarified. CONCLUSIONS: The results reported in this study indicate candidate genes and molecular mechanisms involved in IF content difference in Nelore cattle.
Assuntos
Tecido Adiposo/metabolismo , Perfilação da Expressão Gênica , Músculo Esquelético/citologia , Animais , Bovinos , Redes Reguladoras de Genes , RNA-SeqRESUMO
The main definition for meat quality should include factors that affect consumer appreciation of the product. Physical laboratory analyses are necessary to identify factors that affect meat quality and specific equipment is used for this purpose, which is expensive and destructive, and the analyses are usually time consuming. An alternative method to performing several beef analyses is near-infrared reflectance spectroscopy (NIRS), which permits to reduce costs and to obtain faster, simpler, and nondestructive measurements. The objective of this study was to evaluate the feasibility of NIRS to predict shear force [Warner-Bratzler shear force (WBSF)], marbling, and color (*a = redness; b* = yellowness; and L* = lightness) in meat samples of uncastrated male Nelore cattle, that were approximately 2-yr-old. Samples of longissimus thoracis (n = 644) were collected and spectra were obtained prior to meat quality analysis. Multivariate calibration was performed by partial least squares regression. Several preprocessing techniques were evaluated alone and in combination: raw data, reduction of spectral range, multiplicative scatter correction, and 1st derivative. Accuracies of the calibration models were evaluated using the root mean square error of calibration (RMSEC), root mean square error of prediction (RMSEP), coefficient of determination in the calibration (R2C), and prediction (R2P) groups. Among the different preprocessing techniques, the reduction of spectral range provided the best prediction accuracy for all traits. The NIRS showed a better performance to predict WBSF (RMSEP = 1.42 kg, R2P = 0.40) and b* color (RMSEP = 1.21, R2P = 0.44), while its ability to accurately predict L* (RMSEP = 1.98, R2P = 0.16) and a* (RMSEP = 1.42, R2P = 0.17) was limited. NIRS was unsuitable to predict subjective meat quality traits such as marbling in Nelore cattle.