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Transcriptome study of muscle tissue in nellore cattle divergent for beef quality

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Author(s):
Maria Malane Magalhães Muniz
Total Authors: 1
Document type: Doctoral Thesis
Press: Jaboticabal. 2020-06-08.
Institution: Universidade Estadual Paulista (Unesp). Faculdade de Ciências Agrárias e Veterinárias. Jaboticabal
Defense date:
Advisor: Lucia Galvão de Albuquerque
Abstract

The measurement of meat quality traits are costly, because of that it is rarely included in breeding programs. However, it is necessary to know about the genes and the molecular mechanisms that control these traits, this may help in the evaluation of animals at an early stage.Thus, the identification of mRNA isoforms and the associated splice variants affecting meat quality traits in Nellore cattle could allow to better understanding the genetic architecture of these complex traits. The objective of this study was to identify and analyze genes and mRNA isoforms differentially expressed in the Longissimus thoracis muscle tissue of Nellore cattle, phenotypically divergent for meat color, marbling and meat tenderness (evaluated using WBSF and MFI methodologies) traits, using RNA-Seq data. In addition, to identify structural variants affecting splice sites of differencially expressed mRNA isoforms for marbling and meat color traits. An average of 37 thousand transcripts were detected in the Nellore muscle transcriptomic analysis. A total of 40 and 28 mRNA isoforms (p-value |<| 0.001) were differentially expressed between divergent groups for WBSF and MFI phenotypes, respectively. The differentially expressed mRNA isoforms [WBSF(MYL1, MYL3, MYH1 and MYBPC2) and MFI (MYL6) traits], which are myosin encoders, was the family with most abundantly number of mRNA isoforms detected as diferencially expressed. In addition, we identified as DE [WBSF (SYNPO-201 isoform) and for MFI (ANKRD23-202 isoform) traits], and other mRNA isoforms related with genes affecting the speed fibers degradation during the meat aging process, such as [for WBSF (MYOT, CASQ1, TPM2, MB and SYNM) and for MFI (FGFRL1 and NEB)]. The DE mRNA isoforms are transcripted by genes with biological functions related to oxidative process, energy production, striated muscle contraction, HIF-1 signaling pathway and metabolism of amino acids and derivatives. A total of 14 and 15 mRNA isoforms were differentially expressed (DE) (p-value ≤0.001) between the two groups of divergent bulls for marbling and color of meat traits, respectively. The DE mRNA for marbling trait (COL4A2-202, RPL30-203, MAPKAPK2-204 and NEURL1-201) and color trait (SCL16A6-201 and JSP.1-204) shown sites of splicing modified by structural variants as Single Nucleotide Variant (SNV), insertion or deletion (Indels). Enrichment analysis using the list of significant differentially expressed mRNA isoforms identified common metabolic pathways, such as O2/CO2 exchange in erythrocytes, tyrosine biosynthesis and phenylalanine degradation. The interaction mechanism among them, suggested that, mitochondrial lipid oxidation was closely related to ferric myoglobin formation, molecule important for maintaining fresh red meat color. The results obtained suggest potential key regulatory genes associated with economically important traits for the beef industry and for the consumer. (AU)

FAPESP's process: 17/04270-3 - STUDY OF TRANSCRIPTOMA OF MUSCULAR TISSUE OF NELORE BREED BOVINE DIVERGENS FOR MEAT QUALITY
Grantee:Maria Malane Magalhães Muniz
Support Opportunities: Scholarships in Brazil - Doctorate