Transcript level of the porcine ME1 gene is affected by SNP in its 3′UTR, which is also associated with subcutaneous fat thickness

Abstract

Pork quality depends on multiple factors, including fatty acid composition in muscle and fat tissues. The ME1 gene is a strong candidate for fat accumulation, as it encodes the malic enzyme, which is required for fatty acid synthesis. We identified seven new polymorphisms in 3'UTR of the ME1 gene and moreover confirmed the presence of 4 polymorphisms detected previously. Interestingly, the studied Duroc pigs were monomorphic at all these polymorphic sites, while in 3 other breeds (Pietrain, Polish Landrace and Polish Large White), the polymorphisms were unevenly distributed. One of the novel SNPs (c.*488A>G) was found in the Polish Large White and the Polish Landrace only, and the association studies revealed that it was significantly associated with backfat thickness and average daily weight gain in the Polish Landrace (N = 207) and the Polish Large White (N = 157). This SNP was differently associated with ME1 transcript level in muscle and backfat. The in silico analysis of another novel SNP (c.*548C>T) indicated that it is located within a binding sequence conserved among vertebrates for the miR-30 family in 3'UTR of the ME1. It was shown that in the longissimus muscle, but not in adipose tissue, CT gilts compared with CC ones had significantly lower levels of the ME1 transcript. This polymorphism, however, was not associated with production traits. Additionally, we observed that transcript level of the ME1 was significantly higher in subcutaneous fat than in the longissimus muscle, as well as both investigated tissues of the Polish Landrace when compared to the other breeds. However, no association was found between this polymorphism and fatty acid profiles. We conclude that the ME1 gene polymorphism (c.*488A>G) is a potential marker for porcine backfat thickness.

Polymorphism of the porcine miR-30d is associated with adipose tissue accumulation, its fatty acid profile and the ME1 gene expression

“…FA profile in the LD muscle is less influenced by the breed effect than in backfat or visceral fat (KlensporfPawlik et al, 2012). Recently, it was reported that the miR-30d target transcript of the ME1 gene has a much lower level in IMF than in subcutaneous fat (Bartz et al, 2014).…”

“…The statistical linear model for ME1 transcript level included the fixed effect of the SNP (rs340704946, 3 levels: AA, AG, GG) and also the effect of the SNP c.*488A4G in the pig ME1 gene (3'UTR, 2 levels: AA and AG). The SNP c.*488A4G was considered in the model because it was found to be significantly associated with the porcine ME1 transcript level in LD and backfat (subcutaneous fat) in our earlier study (Bartz et al, 2014). The relative transcript level of ME1 was analyzed in a log scale to reduce skewness.…”

“…Sequencing procedure described earlier by Bartz et al (2014) was applied. Six primer pairs were designed using the Primer3Plus tool (http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3-plus.cgi) to cover fragments of all miR-30 genes in the pig genome (Supplementary Table 1).…”

“…Moreover, two performance traits were considered: post-weaning average daily gain (calculated for the fattening period from 25 to 100 kg live weight) and feed conversion ratio (calculated as a ratio of the consumed feed and gain during the fattening period). Data on the FA profiles in subcutaneous fat, visceral fat and the LD muscle for this pig population were derived from our earlier studies (Bartz et al, 2014;KlensporfPawlik et al, 2012). The study was accepted by a local Bioethical Commission for Animal Care and Use in Poznan (Poland).…”

“…Deep sequencing demonstrated co-expression of the miR-30 and ME1 genes in porcine adipose and muscle tissues (Nielsen et al, 2010;Li et al, 2012). It was also reported that a polymorphism within the 3'UTR of the ME1 gene may alter ME1 transcript level (Bartz et al, 2014).…”