GSE116951
Identification of candidate genes and regulatory factors underlying intramuscular fat content through longissimus dorsi transcriptome analyses in heavy Iberian pigs
One of the most important determinants of meat quality is the intramuscular fat content (IMF). The development of high-throughput techniques as RNA-seq allows identifying gene pathways and networks with a differential expression (DE) between groups of animals divergent for a particular trait. The Iberian pig is characterized by having an excellent meat quality and a high content of intramuscular fat. The objectives of the current study were to analyze the longissimus dorsi transcriptome of purebred Iberian pigs divergent for IMF breeding value to identify differential expressed genes and regulatory factors affecting gene expression. RNA-seq technique allowed identifying in the samples analyzed around 10,000 of the 25,878 annotated genes. In addition to this, the 42.46% of the identified transcripts corresponded to newly predicted isoforms. The differential expression analyses revealed a total of 221 DE annotated genes and 116 DE newly isoforms. Functional analyses identified an enrichment of overexpressed genes in animals with a higher content of IMF involved in lipid metabolism (FASN, SCD, ELOVL6, DGAT2, PLIN1, CIDEC and ADIPOQ) and an enrichment of overexpressed genes related with myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, FOSB and SEMA4D) in the groups of animals with a lower content of IMF. In addition to this, potential regulatory elements of these DE genes were identified. On the one hand, co-expression networks analyses revealed six lncRNAs (ALDBSSCG0000002079, ALDBSSCG0000002093, ALDBSSCG0000003455, ALDBSSCG0000004244, ALDBSSCG0000005525, ALDBSSCG0000006849) co-expressed with SEMA4D and FOSB genes and one (ALDBSSCG0000004790) with SCD, ELOVL6, DGAT2, PLIN1 and CIDEC. The computation of the regulatory impact factors (RIFs) revealed a total of 301 transcriptionally regulatory factors involved in the expression differences, some of them have a role in adipogenesis (ARID5B, CREB1, VDR, ATF6 and SP1) and other ones take part of myogenesis and development of skeletal muscle (ATF3, KLF11 and MYF6). The results obtained provide a relevant insight about the knowledge of the genetics mechanisms underlying IMF content in purebred Iberian pigs and a set of candidate genes and regulatory factors is proposed for a further identification of polymorphisms susceptible of integrate in a selection program. Overall design: Twelve Iberian individuals with divergent breeding values for intramuscular fat content were selected (six per group), samples of Longissimus dorsi were collected after the slaughter, RNA from these samples was extracted, pair-end libraries we