Genome‐wide study on intramuscular fat in Italian Large White pig breed using the PorcineSNP60 BeadChip

Abstract

Genome-wide association study results are presented for intramuscular fat in Italian Large White pig breed. A total of 886 individuals were genotyped with PorcineSNP60 BeadChip. After quality control performed with plink software and in R environment, 49 208 markers remained for the association analysis. The genome-wide association studies was conducted using linear mixed model implemented in GenABEL. We detected seven new SNPs of genes till now not found associated to intramuscular fat (IMF). Three markers map in a wide intergenic region rich of QTL linked to fat traits, one map 388 kb upstream the gene SDK1, one map inside PPP3CA gene, one inside SCPEP1 gene and the last is not mapped in the porcine genome yet. Associations here presented indicate a moderate effect of these genes on IMF. In particular, PPP3CA, that is involved in the oxidative metabolism of skeletal muscle, could be considerated as an interesting candidate gene for IMF content in pigs. However, further studies are needed to clarify the role of these genes on the physiological processes involved in IMF regulation. These results may be useful to control this trait that is important in terms of nutritional, technological and organoleptic characteristics of fresh meat and processed products.

RNA-seq based detection of differentially expressed genes in the skeletal muscle of Duroc pigs with distinct lipid profiles

“…Two of the genes listed in Table 1 might be related with meat quality i.e. RNF181 , which encodes a E3 ubiquitin-protein ligase that participates in the degradation of muscle proteins through the ubiquitin-proteasome system 13 , and SDK1 , which has been associated with intramuscular fat (IMF) content in Large White pigs 14 .…”

Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed—The Ramo Grande Cattle from the Azores

“…The p-values were then corrected by multiplying observed p-values by the deflation factor λ obtained in GWAS [29]. We used the two higher level genome-wide significance thresholds defined by Teyssedre et al (2012) [30] and used by [14,29,31]. The used thresholds were 5 × 10 −6 and 5 × 10 −5 , where the first corresponds to 10,000 independent Bonferroni corrected tests and the second was proposed as the threshold allowing the detection of moderate associations [30].…”

miR-34a regulates adipogenesis in porcine intramuscular adipocytes by targeting ACSL4

“…High-throughput methods, such as genome-wide association studies and transcriptome expression profiling, have been used to search for genes that potentially affect fat deposition in swine. Many genes associated with an extreme capacity for IMF deposition have been identified [3][4][5][6][7][8][9]. In addition to the multiple genes that influence adipogenesis, IMF is also likely to be under the control of posttranscriptional regulatory factors such as microRNAs.…”