Characterization of novel lncRNA muscle expression profiles associated with meat quality in beef cattle

Author(s)

Magalhaes Muniz, Maria Malane ; Simielli Fonseca, Larissa Fernanda ; Becker Scalez, Daiane Cristina ; Vega, Aroa Suarez ; dos Santos Silva, Danielly Beraldo ; Ferro, Jesus Aparecido ; Chardulo, Artur Loyola ; Baldi, Fernando ; Canovas, Angela ; de Albuquerque, Lucia Galvao

• Document type: Journal article
• Source: EVOLUTIONARY APPLICATIONS; v. 15, n. 4, p. 13-pg., 2022-03-25.

Abstract

The aim of this study was to identify novel lncRNA differentially expressed (DE) between divergent animals for beef tenderness and marbling traits in Nellore cattle. Longissimus thoracis muscle samples from the 20 most extreme bulls (of 80 bulls set) for tenderness, tender (n = 10) and tough (n = 10) groups, and marbling trait, high (n = 10) and low (n = 10) groups were used to perform transcriptomic analysis using RNA-Sequencing. For tenderness, 29 lncRNA were DE (p-value <= 0.01) in tough beef animals in relation to tender beef animals. We observed that genic lncRNAs, for example, lncRNA_595.1, were overlapping exonic part of the PICK gene, while lncRNA_3097.2 and lncRNA_3129.5 overlapped intronic part of the genes GADL1 and PSMD6. The lncRNA associated with PICK1, GADL1, and PMD6 genes were enriched in the pathways associated with the ionotropic glutamate receptor, gamma-aminobutyric acid synthesis, and the ubiquitin-proteasome pathway. For marbling, 50 lncRNA were DE (p-value <= 0.01) in high marbling group compared with low marbling animals. The genic lncRNAs, such as lncRNA_3191.1, were overlapped exonic part of the ITGAL gene, and the lncRNA_512.1, lncRNA_3721.1, and lncRNA_41.4 overlapped intronic parts of the KRAS and MASP1 genes. The KRAS and ITGAL genes were enriched in pathways associated with integrin signaling, which is involved in intracellular signals in response to the extracellular matrix, including cell form, mobility, and mediates progression through the cell cycle. In addition, the lincRNAs identified to marbling trait were associated with several genes related to calcium binding, muscle hypertrophy, skeletal muscle, lipase, and oxidative stress response pathways that seem to play a role important in the physiological processes related to meat quality. These findings bring new insights to better understand the biology mechanisms involved in the gene regulation of these traits, which will be valuable for a further investigation of the interactions between lncRNA and mRNAs, and of how these interactions may affect meat quality traits. (AU)

• FAPESP's process: 18/11154-2 - Identification of co-expression genes in Nellore cattle muscle tissue with divergent marbling and myofibrilar fragmentation index phenotypes, using RNA-Seq data
• Grantee: Maria Malane Magalhães Muniz
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• FAPESP's process: 18/20026-8 - Multi-user equipment approved in grant 2017/10630-2: server
• Grantee: Lucia Galvão de Albuquerque
• Support Opportunities: Multi-user Equipment Program
• FAPESP's process: 09/16118-5 - Genomic tools to genetic improvement of direct economic important traits in Nelore cattle
• Grantee: Lucia Galvão de Albuquerque
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 17/10630-2 - Genetic aspects of meat production quality, efficiency and sustainability in Nelore breed animals
• Grantee: Lucia Galvão de Albuquerque
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 11/21241-0 - Study of the genetic variability of meat fatty acid profile in Nelore cattle finished in feedlot
• Grantee: Fernando Sebastián Baldi Rey
• Support Opportunities: Research Grants - Young Investigators Grants