Differentially expressed genes and alternative splicing related to carcass and meat traits of the Nelore cattle

Author(s)

Danielly Beraldo dos Santos Silva

• Document type: Doctoral Thesis
• Press: Jaboticabal. 2019-02-08.
• Institution: Universidade Estadual Paulista (Unesp). Faculdade de Ciências Agrárias e Veterinárias. Jaboticabal
• Defense date: 2019-01-25
• Advisor: Lucia Galvão de Albuquerque

Abstract

RNA sequencing (RNA-Seq) is an approach for screening the expression of functional candidate genes and identifying important molecular mechanisms creating variation in pathways that result in different tissue phenotypes. Since ribeye muscle area (REA) and intramuscular fat content (IF) are polygenic traits, many genes and mechanisms that induce differences in muscle growth and development, as well as IF content of the Nelore cattle still unknown. The aim was to study the muscle transcriptome of the Nelore cattle with the purpose of identifying differentially expressed genes (DEGs) and differentially expressed alternative splicing events (DAS) associated with the carcass (REA) and meat (IF) traits, through of the RNA-seq approach. Therefore, a total of 80 animals were sequenced and phenotyped for REA and IF contet (measured by the chemical method - which evaluate total lipids). The results were presented in chapters 2, 3 and 4. In chapter 2, 15 animals with highest REA and 15 animals with lowest REA were selected for differential expression analysis. Upon analysis, 289 DEGs were identified (q-value ≤0.05): 183 upregulated and 106 downregulated in the highest REA group. Genes belonging to important families, such as actin, myosin, collagen, integrin, solute carrier, ubiquitin, and kelch-like, were among the DEGs. Gene set enrichment analysis showed that many of the significantly enriched gene ontology (GO) terms are closely associated with muscle development, growth, and degradation. Through co-expression network analysis, we predicted three hub genes (PPP3R1, FAM129B and UBE2G1). These genes are involved in muscle growth and proteolysis. In chapter 3, 15 animals with highest and 15 animals with lowest IF content were selected for differential expression analysis. Upon analysis, 65 DEGs were identified, including 21 upregulated and 44 downregulated genes in highest IF content animals. Gene set enrichment analysis was performed and showed that the GO terms were closely associated with lipid and muscle metabolism, as well as genes related to the immune system. Gene co-expression network analysis showed three hub genes (PDE4D, KLHL30, and IL1RAP) that may play a role in cellular and/or systemic lipid biology in Nelore cattle. In Chapter 4, differentially expressed alternative splicing events (DAS), and their associated genes, were identified in the same groups of animals selected in Chapter 2 (phenotypically divergent for REA) and Chapter 3 (phenotypically divergent for IF content). The DAS events were identified from the exon-centric approach. The results showed 166 and 269 DAS events (p-value ≤ 0,05), respectively, for REA and IF. The exon cassette and alternative 3' splice site were the most frequently found events for both traits. The DAS found were transcribed for 125 and 219 genes, respectively for REA and for IF. The genes found in chapter 4, in general, play a role in muscle metabolism and systemic lipid biology. The results reported in this tese show possible candidate genes and provide a theoretical basis for a better understanding of the molecular mechanism of REA development and growth as well as the deposition of IF in Nelore cattle. (AU)

• FAPESP's process: 15/16850-9 - Differential gene expression associated with traits of carcass and meat in Nelore cattle
• Grantee: Danielly Beraldo dos Santos Silva
• Support Opportunities: Scholarships in Brazil - Doctorate