CARDOSO, F. F.

GIACHETTO, P. F.

KUSER-FALCÃO, P. R.

NAGAI, L. A. E.

ZERLOTINI, A.

Repository Open Access to Scientific Information from Embrapa

Preliminary analysis  of differentially expressed genes  involved  in  meat tenderness in Angus and Nelore beef cattleAuthors: Luís Augusto Eijy Nagai1,3, Poliana F. Giachetto1, Fernando F. Cardoso2, Adhemar Zerlotini1, Paula R. Kuser-Falcão1Affiliations:  1Laboratório  Multiusuário  de  Bioinformática,  Embrapa  Informática  Agropecuária, Campinas – SP, Brazil. 2Embrapa Pecuária Sul, Bagé, RS - Brazil. 3Univesidade Estadual de Campinas, SP – Brazil.High-throughput  sequencing  technologies  are  responsible  for  great  advances  in  gene  expression research, widening the understanding of the phenotypical characteristics. Over the last years, the data generated through cDNA sequencing (RNA-Seq) have been extensively used. The amount of RNA-Seq data available increased due to improvements in sequencing techniques and low cost, thus becoming an essential tool for transcriptome research. Nevertheless, RNA-Seq experiments must be analyzed with robust,  efficient  and  statistically  grounded  algorithms.  Fortunately,  researchers  and  developers  are further advancing such software tools in order to make it possible to focus on data analyze rather than computational tasks such as software installation and file formats. The Bos taurus genome, published and made available in 2009, has enabled studies on traits of interest. Among them,  meat tenderness is  one of the most important measured attribute.  The zebu breeds, mainly Nelore (Bos indicus), has wide acceptance in the brazilian market, but has lower productivity and meat quality when compared to taurine breeds, such as Angus (Bos taurus). Nowadays, there is a global interest on factors involved with attributes of commercial importance, such as meat tenderness, that justifies the importance of research concerning genetic, molecular and biochemical mechanisms that determine this trait. In  this  study,  we  used  the  open-source  tool  EdgeR  of  the  Bioconductor  R  package  to  identify differentially expressed genes in a cattle Illumina RNA-seq dataset. We used 150Gb of RNA-Seq data from 18 animals (10 from Angus and 8 from Nelore cattle), and compared the process of align trimmed reads  and raw reads   against  Bos  taurus  Genome using  Tophat2.  We also  performed a  functional characterization of such genes in order to identify  gene ontology enrichments, which can be related to genetic factors involved in meat tenderness. Preliminary analysis showed better results from non-trimmed reads alignment. A total of 302 and 449 genes were differentially expressed between tender and tough groups in Angus and Nelore breeds, respectively.  From these,  we found a significant  enrichment  in  genes  related to immune response, skeletal system development, proteolysis, and myoblast cell fate commitment and development. The next step  will be to find a relationship between the trait under study  and the differentially expressed genes that we found, and validate our results by means of RT-qPCR, using a set of 10 randomly chosen genes.

Preliminary analysis of differentially expressed genes involved in meat tenderness in Angus and Nelore beef cattle.

http://www.alice.cnptia.embrapa.br/alice/bitstream/doc/1007513/1/PreliminaryNagai.pdf

Preliminary analysis of differentially expressed genes involved in meat tenderness in Angus and Nelore beef cattle.

Abstract

Similar works

Full text

Available Versions

Repository Open Access to Scientific Information from Embrapa