Global muscle gene expression differences in Nelore cattle extremes for meat lipid content

In this work, we identified genes, isoforms and gene's biological function associated with global gene expression in muscle tissue of Nelore cattle extremes for lipid content. Samples of raw meat of 80 animals were used to extract total lipid content using the sodium sulfate method. From those, 20 Nelore animals, extremes for meat lipid content, were selected (10 with high and 10 with low meat lipid content). RNA was extracted from Longissimus dorsi muscle using RNeasy Tissue Mini Kit (Qiagen(R)). Sequencing (RNASeq) was performed with the platform HiSeq 2500 System (Illumina(R)) using 100 bp paired end reads. For data quality control (QC), FASTQ Quality Trimmer and Sickle softwares were used. Data were analyzed with TopHat2, Cufflinks, Cuffmerge, Cuffdiff and cummeRbund softwares. A total of 35 differentially expressed (DE) genes and 32 isoforms were identified. The log2(fold change) indicated 36 DE genes were down-regulated and 9 up-regulated in the LLC (low lipid content) relative to the HLC (high lipid content) group. The expression products of these genes are involved in catalytic activity, in regulation of enzymes and nucleic acids transcription factor. Also, novel protein coding that has not been annotated in bovine and one pseudogene, were found. Using DAVID software, one pathway enrichment (KEGG database) was found for genes DE between the divergent lipid content groups. This pathway was related to Insulin signaling. Insulin regulates the synthesis and degradation of lipids. Three of the DE genes (ACACB and PDK4, up-regulated in animals with HLL; and PPP1R3C, down-regulated in animals with HLL) were interacting in this pathway. Moreover, these genes have actions in the metabolic pathways of fatty acids and on other meat lipid profile pathways. Another important gene is the ARID5B (up-regulated in animals with HLL) which encodes one protein which forms a histone demethylase complex with PHD finger protein 2 and regulates the transcription of target genes involved in adipogenesis and liver development. Our results show genes which act in mechanisms associated with meat lipid content such as the insulin signaling pathway and adipogenesis. These genes can be used as candidates for further association studies with the content of lipids in Nelore cattle meat.