10.3389/fgene.2018.00608.s003
María Muñoz
María
Muñoz
Juan María García-Casco
Juan María
García-Casco
Carmen Caraballo
Carmen
Caraballo
Miguel Ángel Fernández-Barroso
Miguel Ángel
Fernández-Barroso
Fernando Sánchez-Esquiliche
Fernando
Sánchez-Esquiliche
Fernando Gómez
Fernando
Gómez
María del Carmen Rodríguez
María
del Carmen Rodríguez
Luis Silió
Luis
Silió
Image_2_Identification of Candidate Genes and Regulatory Factors Underlying Intramuscular Fat Content Through Longissimus Dorsi Transcriptome Analyses in Heavy Iberian Pigs.TIF
Frontiers
2018
transcriptome
longissimus dorsi muscle
intramuscular fat
Iberian pigs
RNA-seq
2018-12-04 04:36:05
Figure
https://frontiersin.figshare.com/articles/figure/Image_2_Identification_of_Candidate_Genes_and_Regulatory_Factors_Underlying_Intramuscular_Fat_Content_Through_Longissimus_Dorsi_Transcriptome_Analyses_in_Heavy_Iberian_Pigs_TIF/7414121
<p>One of the most important determinants of meat quality is the intramuscular fat (IMF) content. 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 present study were to analyze the longissimus dorsi transcriptome of purebred Iberian pigs divergent for their IMF breeding value to identify differential expressed genes and regulatory factors affecting gene expression. RNA-seq allowed identifying ∼10,000 of the 25,878 annotated genes in the analyzed samples. In addition to this, 42.46% of the identified transcripts corresponded to newly predicted isoforms. Differential expression analyses revealed a total of 221 DE annotated genes and 116 DE new isoforms. Functional analyses identified an enrichment of overexpressed genes involved in lipid metabolism (FASN, SCD, ELOVL6, DGAT2, PLIN1, CIDEC, and ADIPOQ) in animals with a higher content of IMF and an enrichment of overexpressed genes related with myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, FOSB, and SEMA4D) in the animals with a lower content of IMF. In addition to this, potential regulatory elements of these DE genes were identified. Co-expression networks analyses revealed six long non-coding RNAs (lncRNAs) (ALDBSSCG0000002079, ALDBSSCG0000002093, ALDBSSCG0000003455, ALDBSSCG0000004244, ALDBSSCG0000005525, and ALDBSSCG0000006849) co-expressed with SEMA4D and FOSB genes and one (ALDBSSCG0000004790) with SCD, ELOVL6, DGAT2, PLIN1, and CIDEC. Analyses of the regulatory impact factors (RIFs) revealed 301 transcriptionally regulatory factors involved in expression differences, with five of them involved in adipogenesis (ARID5B, CREB1, VDR, ATF6, and SP1) and other three taking part of myogenesis and development of skeletal muscle (ATF3, KLF11, and MYF6). The results obtained provide relevant insights about the genetic mechanisms underlying IMF content in purebred Iberian pigs and a set of candidate genes and regulatory factors for further identification of polymorphisms susceptible of being incorporated in a selection program.</p>