Abstract
Transcript data obtained by RNA-Seq were used to identify differentially expressed alternatively spliced genes in ribeye muscle tissue between Nelore cattle that differed in their ribeye area (REA) or intramuscular fat content (IF). A total of 166 alternatively spliced transcripts from 125 genes were significantly differentially expressed in ribeye muscle between the highest and lowest REA groups (p ≤ 0.05). For animals selected on their IF content, 269 alternatively spliced transcripts from 219 genes were differentially expressed in ribeye muscle between the highest and lowest IF animals. Cassette exons and alternative 3′ splice sites were the most frequently found alternatively spliced transcripts for REA and IF content. For both traits, some differentially expressed alternatively spliced transcripts belonged to myosin and myotilin gene families. The hub transcripts were identified for REA (LRRFIP1, RCAN1 and RHOBTB1) and IF (TRIP12, HSPE1 and MAP2K6) have an important role to play in muscle cell degradation, development and motility. In general, transcripts were found for both traits with biological process GO terms that were involved in pathways related to protein ubiquitination, muscle differentiation, lipids and hormonal systems. Our results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the whole cell muscle mRNA of Nelore cattle.
Highlights
Transcript data obtained by RNA sequencing (RNA-Seq) were used to identify differentially expressed alternatively spliced genes in ribeye muscle tissue between Nelore cattle that differed in their ribeye area (REA) or intramuscular fat content (IF)
Regulator of Calcineurin 1 (RCAN1) has two known transcript variants annotated in cattle, we found one RCAN1 produce transcript that differ by known alternative first exons, which were more abundant in the low ribeye muscle area (LREA) animals
RNA-Seq was used to identify candidate genes that encode alternatively spliced transcripts that were associated with REA and IF content in Nelore bulls
Summary
Transcript data obtained by RNA-Seq were used to identify differentially expressed alternatively spliced genes in ribeye muscle tissue between Nelore cattle that differed in their ribeye area (REA) or intramuscular fat content (IF). Cassette exons and alternative 3′ splice sites were the most frequently found alternatively spliced transcripts for REA and IF content. For both traits, some differentially expressed alternatively spliced transcripts belonged to myosin and myotilin gene families. RNA sequencing (RNA-Seq), is an accurate method for measuring gene expression and can measure all genes in the transcriptome at the same time This technology could be used to screen the expression of functional candidate genes and identifying essential molecular processes creating a diversity in pathways leading to different tissue phenotypes. Knowledge concerning the molecular mechanisms regulated by alternative splicing events, especially in the context of individual differences in carcass and meat traits in bovine, is limited
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
