Identification of strong candidate genes for backfat and intramuscular fatty acid composition in three crosses based on the Iberian pig

Abstract

Meat quality has an important genetic component and can be modified by the fatty acid (FA) composition and the amount of fat contained in adipose tissue and muscle. The present study aimed to find genomic regions associated with the FA composition in backfat and muscle (longissimus dorsi) in 439 pigs with three different genetic backgrounds but having the Iberian breed in common. Genome-wide association studies (GWAS) were performed between 38,424 single-nucleotide polymorphisms (SNPs) covering the pig genome and 60 phenotypic traits related to backfat and muscle FA composition. Nine significant associated regions were found in backfat on the Sus scrofa chromosomes (SSC): SSC1, SSC2, SSC4, SSC6, SSC8, SSC10, SSC12, and SSC16. For the intramuscular fat, six significant associated regions were identified on SSC4, SSC13, SSC14, and SSC17. A total of 52 candidate genes were proposed to explain the variation in backfat and muscle FA composition traits. GWAS were also reanalysed including SNPs on five candidate genes (ELOVL6, ELOVL7, FADS2, FASN, and SCD). Regions and molecular markers described in our study may be useful for meat quality selection of commercial pig breeds, although several polymorphisms were breed-specific, and further analysis would be needed to evaluate possible causal mutations. Meat quality depends on the consumer's perception, which is subjected to the socio-demographic backgrounds of the consumer 1 , and is based on factors such as the nutritional value and the organoleptic properties of meat 2. These factors can be modified by the fatty acid (FA) composition and the amount of fat that is contained in adipose tissue and muscle 3. In addition, the consumer is becoming more concerned about the healthfulness of meat 1. Certain saturated FAs (SFAs) raise the cholesterol and low-density lipoprotein (LDL) levels in blood, which increase the risk of suffering a cardiovascular disease 4,5 ; whereas monounsaturated FAs (MUFAs) reduce plasma total LDL-cholesterol without affecting high-density lipoprotein (HDL) levels, which have an anti-atherogenic effect 4,5. Polyunsaturated FAs (PUFAs), especially long-chain omega-3 fatty acids, also reduce LDL-cholesterol levels and the risk of cardiovascular disease 6 , but high amount of PUFAs in meat increase its susceptibility to oxidation, producing meat with undesirable sensory properties 3. In contrast, a high concentration of MUFAs improve meat flavour 7. The Iberian pig is a breed characterized by its great meat quality, due to its high intramuscular fat (IMF) content with an increased proportion of MUFAs (mostly oleic acid) and a reduced quantity of PUFAs 8,9. Conversely, other commercial breeds such as Pietrain and Landrace produce lean meat with a lower proportion of fat,

Tracing selection signatures in the pig genome gives evidence for selective pressures on a unique curly hair phenotype in Mangalitza

“…On the one hand, it is known as a fat type pig, producing fine quality meat as a delicacy with a considerably high proportion of intramuscular fat and a high amount of unsaturated fatty acids compared to other pig breeds 47 . In that respect, it was no surprise that we identified several genes in Mangalitza consensus ROHR, which were proposed to have an impact on fat metabolism including lipase I (LIPI) and phospholipase A2 group IID (PLA2G2D) influencing fatty acid composition of meat 48 , 49 or phospholipase A2 group V ( PLA2G5), hydroxysteroid 11-beta dehydrogenase 1 (HSD11B1) and diacylglycerol kinase delta (DGKD) , which have a crucial role in insulin resistance and the susceptibility for obesity 50 – 52 .…”

Evidence Against the Causal Relationship Between a Putative Cis-Regulatory Variant of MYH3 and Intramuscular Fat Content in Pigs

“…In fact, a large number of quantitative trait loci (QTL) or candidate genes for IMF have been identified by linkage and genomewide association (GWA) studies. However, despite the progress achieved in this field in recent years, molecular mechanisms behind IMF trait remains elusive, as few causative genes or causative mutations affecting IMF content of pork have been determined (6)(7)(8)(9)(10).…”

Association of IFNA16 and TNFRSF19 Polymorphisms with Intramuscular Fat Content and Fatty Acid Composition in Pigs

“…This result agreed with previous studies, which indicated that stearic acid had a positive phenotypic and genetic correlation with arachidic acid levels in the backfat tissue of pigs [ 49 , 50 ]. Moreover, numerous previous studies have proposed the elongation of long-chain fatty acid family number 7 ( ELOVL7) as a strong candidate gene that is indicative of the GWAS signals associated with arachidic acid levels and the metabolic indexes of arachidic to stearic acid or the ratios of eicosenoic to arachidic acid levels [ 9 , 10 , 51 , 52 ]. The evidence presented above indicates that the TNFRSF19 gene may have a relationship with arachidic acid levels and may be related to the genes that regulate FA metabolism in muscle tissues.…”