Abstract
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.
Highlights
Intramuscular fat content (IMF) plays a major role in the determination of meat quality since it influences technological and sensorial features such as flavor, tenderness, and juiciness (Verbeke et al, 1999; Wood et al, 2008)
The percentage of potentially new isoforms predicted represents the 42.46% of the transcripts detected. This could be due to an incomplete porcine genome annotation which that still does not gather all the isoforms expressed in longissimus dorsi (LD) or to an incorrect assembly of the full-length transcript caused
Lipid metabolism genes (FASN, stearoyl-CoA desaturase (SCD), ELOVL6, Diacylglycerol O-acyltransferase 2 (DGAT2), perilipin 1 (PLIN1), Cell death inducing DFFA like effector c (CIDEC), and ADIPOQ) were clearly overexpressed in animals with higher estimate breeding values (EBVs) for intramuscular fat (IMF) (H group), whereas genes involved in myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, Factor Subunit (FOSB), and SEMA4D) were overexpressed in animals with a lower content in IMF
Summary
Intramuscular fat content (IMF) plays a major role in the determination of meat quality since it influences technological and sensorial features such as flavor, tenderness, and juiciness (Verbeke et al, 1999; Wood et al, 2008). Understanding of the genetic and physiological mechanisms affecting IMF, as well as different gene expression patterns along development has become one of the main challenges in meat science (Hocquette et al, 2010). The number (hyperplasia) and size (hypertrophia) of adipocytes within the muscle are some of the main determinants of IMF (Shi-Zheng and Su-Mei, 2009). The increase in adipose cell number and size continues along after the birth and is maintained during all the development of the individual (Lee and Kauffman, 1974). The hypertrophy process is caused by the accumulation of triglycerides in mature adipocytes, which is determined by the ratio between lipogenesis and lipolysis
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