The genetic factors determining the phenotypic variation of porcine fatness phenotypes are still largely unknown. We investigated whether the polymorphism of eight genes (
MIGA2
,
CRY2
,
NPAS2
,
CIART
,
ARNTL2
,
PER1
,
PER2
and
PCK1
), which display differential expression in the skeletal muscle of fasted and fed sows, is associated with the variation of lipid and mRNA expression phenotypes in Duroc pigs. The performance of an association analysis with the GEMMA software demonstrated that the rs330779504 SNP in the
MIGA2
gene is associated with LDL concentration at 190 days (LDL
2
, corrected
P
-value = 0.057). Moreover, the rs320439526 SNP of the
CRY2
gene displayed a significant association with stearic acid content in the
longissimus dorsi
muscle (LD C18:0, corrected
P
-value = 0.015). Both SNPs were also associated with the mRNA levels of the corresponding genes in the
gluteus medius
skeletal muscle. From a biological perspective these results are meaningful because
MIGA2
protein plays an essential role in mitochondrial fusion, a process tightly connected with the energy status of the cell, while
CRY2
is a fundamental component of the circadian clock. However, inclusion of these two SNPs in chromosome-wide association analyses demonstrated that they are not located at the peaks of significance for the two traits under study (LDL
2
for rs330779504 and LD C18:0 for rs320439526), thus implying that these two SNPs do not have causal effects.