A second mutant allele (V199I) at the PRKAG3 (RN) locus—II. Effect on colour characteristics of pork loin

Genome-Wide Association Study and FST Analysis Reveal Four Quantitative Trait Loci and Six Candidate Genes for Meat Color in Pigs

Meat color is the primary criterion by which consumers evaluate meat quality. However, there are a few candidate genes and molecular markers of meat color that were reported for pig molecular breeding. The purpose of the present study is to identify the candidate genes affecting meat color and provide the theoretical basis for meat color molecular breeding. A total of 306 Suhuai pigs were slaughtered, and meat color was evaluated at 45 min and 24 h after slaughter by CIELAB color space. All individuals were genotyped using GeneSeek GGP-Porcine 80K SNP BeadChip. The genomic estimated breeding values (GEBVs), heritability, and genetic correlation of meat color were calculated by DMU software. The genome-wide association studies (GWASs) and the fixation index (F_ST) tests were performed to identify SNPs related to meat color, and the candidate genes within 1 Mb upstream and downstream of significant SNPs were screened by functional enrichment analysis. The heritability of L* 45 min, L* 24 h, a* 45 min, a* 24 h, b* 45 min, and b* 24 h was 0.20, 0.16, 0.30, 0.13, 0.29, and 0.22, respectively. The genetic correlation between a* (a* 45 min and a* 24 h) and L* (L* 45 min and L* 24 h) is strong, whereas the genetic correlation between b* 45 min and b* 24 h is weak. Forty-nine significant SNPs associated with meat color were identified through GWAS and F_ST tests. Among these SNPs, 34 SNPs were associated with L* 45 min within a 5-Mb region on Sus scrofa chromosome 11 (SSC11); 22 SNPs were associated with a* 45 min within a 14.72-Mb region on SSC16; six SNPs were associated with b* 45 min within a 4.22-Mb region on SSC13; 11 SNPs were associated with b* 24 h within a 2.12-Mb region on SSC3. These regions did not overlap with meat color–associated QTLs reported previously. Moreover, six candidate genes (HOMER1, PIK3CG, PIK3CA, VCAN, FABP3, and FKBP1B), functionally related to muscle development, phosphatidylinositol phosphorylation, and lipid binding, were detected around these significant SNPs. Taken together, our results provide a set of potential molecular markers for the genetic improvement of meat color in pigs.

Understanding the role of myoglobin content in Iberian pigs fattened in an extensive system through analysis of the transcriptome profile

Meat color is the first perceived sensory feature and one of the most important quality traits. Myoglobin is the main pigment in meat, giving meat its characteristic cherry‐red color, highly appreciated by the consumers. In the current study, we used the RNA‐seq technique to characterize the longissimus dorsi muscle transcriptome in two groups of Iberian pigs with divergent breeding values for myoglobin content. As a result, we identified 57 differentially expressed genes and transcripts (DEGs). Moreover, we have validated the RNA‐seq expression of a set of genes by quantitative PCR (qPCR). Functional analyses revealed an enrichment of DEGs in biological processes related to oxidation (HBA1), lipid metabolism (ECH1, PLA2G10, PLD2), inflammation (CHST1, CD209, PLA2G10), and immune system (CD209, MX2, LGALS3, LGALS9). The upstream analysis showed a total of five transcriptional regulatory factors and eight master regulators that could moderate the expression of some DEGs, highlighting SPI1 and MAPK1, since they regulate the expression of DEGs involved in immune defense and inflammatory processes. Iberian pigs with high myoglobin content also showed higher expression of the HBA1 gene and both molecules, myoglobin and hemoglobin, have been described as having a protective effect against oxidative and inflammatory processes. Therefore, the HBA1 gene is a very promising candidate gene to harbor polymorphisms underlying myoglobin content, whereby further studies should be carried out for its potential use in an Iberian pig selection program.

Effects of single nucleotide polymorphisms and haplotypes of the protein kinase AMP-activated non-catalytic subunit gamma 3 (PRKAG3) gene on production, meat quality and carcass traits in Italian Large White pigs

PRKAG3 is a major gene for meat quality and production in pigs. In this study, we investigated two single nucleotide polymorphisms (SNPs) of the PRKAG3 promoter region (g.-995A>G and g.-311A>G) in 381 pigs of different breeds. Association between these SNPs and three major haplotypes, constructed including other three substitutions (c.89C>A, c.154A>G and c.595G>A) and different traits (meat quality parameters: pH_2h, pH_u, glycogen and lactate content, glycolytic potential and cathepsin B activity of Semimembranosus muscle; estimated breeding values and random residuals for growth performances and carcass traits) were analysed in 271 Italian Large White performance tested pigs. A significant effect (P=0.043) of the g.-995A>G SNP on cathepsin B activity and a suggestive effect (P=0.067) of the g.-311A>G SNP on pH_u were found. The haplotype [g.-995G:g.-311G:c.89A:c.154G:c.595G] was associated with pH_u (P=0.024), glycolytic potential (P=0.040) and cathepsin B activity (P=0.086). This study on haplotypes, including promoter region SNPs, contribute to explain the effect of this gene on meat quality traits in pigs.

Changes in physicochemical and microbiological properties of isoflavone-treated dry-cured sausage from sulfur-fed pork during storage

This study was performed to investigate the physicochemical and microbiological properties of isoflavone-treated dry cured sausage from sulfur fed pork (0.3%) during storage at 15°C for 45 days. Groups were divided into three treatments: dry-cured sausages produced with pork fed general diet as the control group (CON), sulfur-fed pork (SUL) and isoflavone-(0.25%) treated sulfur-fed pork (ISO). Moisture content in all groups decreased dramatically from 55–57% to 10–11% during storage, whereas crude protein, crude fat, and ash content increased (P < 0.05). The ISO group showed excellent antioxidant effect compared to CON during storage. Redness and lightness of ISO was higher than that of CON during storage. VBN in the ISO group was significantly lower than that in the CON and SUL treatments during 30 and 45 days of storage (P < 0.05). A total plate count of ISO was significantly lower than that of CON at 45 days (P < 0.05). In this study, adding isoflavone to meat products indicated prevention of lipid oxidation and improved color stability in meat products.

Current research in meat color

This review surveyed recent literature focused on factors that affect myoglobin chemistry, meat color, pigment redox stability, and methodology used to evaluate these properties. The appearance of meat and meat products is a complex topic involving animal genetics, ante- and postmortem conditions, fundamental muscle chemistry, and many factors related to meat processing, packaging, distribution, storage, display, and final preparation for consumption. These factors vary globally, but the variables that affect basic pigment chemistry are reasonably consistent between countries. Essential for maximizing meat color life is an understanding of the combined effects of two fundamental muscle traits, oxygen consumption and metmyoglobin reduction. In the antemortem sector of research, meat color is being related to genomic quantitative loci, numerous pre-harvest nutritional regimens, and housing and harvest environment. Our knowledge of postmortem chilling and pH effects, atmospheres used for packaging, antimicrobial interventions, and quality and safety of cooked color are now more clearly defined. The etiology of bone discoloration is now available. New color measurement methodology, especially digital imaging techniques, and improved modifications to existing methodology are now available. Nevertheless, unanswered questions regarding meat color remain. Meat scientists should continue to develop novel ways of improving muscle color and color stability while also focusing on the basic principles of myoglobin chemistry.

SNP variation in the promoter of the PRKAG3 gene and association with meat quality traits in pig

Background

The PRKAG3 gene encodes the γ3 subunit of adenosine monophosphate activated protein kinase (AMPK), a protein that plays a key role in energy metabolism in skeletal muscle. Non-synonymous single nucleotide polymorphisms (SNPs) in this gene such as I199V are associated with important pork quality traits. The objective of this study was to investigate the relationship between gene expression of the PRKAG3 gene, SNP variation in the PRKAG3 promoter and meat quality phenotypes in pork.

Results

PRKAG3 gene expression was found to correlate with a number of traits relating to glycolytic potential (GP) and intramuscular fat (IMF) in three phenotypically diverse F1 crosses comprising of 31 Large White, 23 Duroc and 32 Pietrain sire breeds. The majority of associations were observed in the Large White cross. There was a significant association between genotype at the g.-311A>G locus and PRKAG3 gene expression in the Large White cross. In the same population, ten novel SNPs were identified within a 1.3 kb region spanning the promoter and from this three major haplotypes were inferred. Two tagging SNPs (g.-995A>G and g.-311A>G) characterised the haplotypes within the promoter region being studied. These two SNPs were subsequently genotyped in larger populations consisting of Large White (n = 98), Duroc (n = 99) and Pietrain (n = 98) purebreds. Four major haplotypes including promoter SNP’s g.-995A>G and g.-311A>G and I199V were inferred. In the Large White breed, HAP1 was associated with IMF% in the M. longissmus thoracis et lumborum (LTL) and driploss%. HAP2 was associated with IMFL% GP-influenced traits pH at 24 hr in LTL (pHULT), pH at 45 min in LTL (pH₄₅LT) and pH at 45 min in the M. semimembranosus muscle (pH₄₅SM). HAP3 was associated with driploss%, pHULT pH₄₅LT and b* Minolta. In the Duroc breed, associations were observed between HAP1 and driploss% and pHUSM. No associations were observed with the remaining haplotypes (HAP2, HAP3 and HAP4) in the Duroc breed. The Pietrain breed was monomorphic in the promoter region. The I199V locus was associated with several GP-influenced traits across all three breeds and IMF% in the Large White and Pietrain breed. No significant difference in promoter function was observed for the three main promoter haplotypes when tested in vitro.

Conclusion

Gene expression levels of the porcine PRKAG3 are associated with meat quality phenotypes relating to glycolytic potential and IMF% in the Large White breed, while SNP variation in the promoter region of the gene is associated with PRKAG3 gene expression and meat quality phenotypes.

Investigation of candidate genes for glycolytic potential of porcine skeletal muscle: Association with meat quality and production traits in Italian Large White pigs

The objective of this study was to investigate the association of DNA markers in candidate genes for glycolytic potential on meat quality parameters (pH(1), pH(u), glycogen and lactate content and glycolytic potential of semimembranosus muscle) and estimated breeding values (EBVs) for average daily gain, lean cuts, back fat thickness, ham weight, and feed:gain ratio in 272 Italian Large White pigs. Three mutations in the PRKAG3 gene (T30N, G52S and I199V) were investigated as well as single nucleotide polymorphisms in two other skeletal muscle genes (PGAM2 and PKM2) involved in the glycolytic pathway. Association analysis with the PRKAG3 markers showed significant results (P<0.05) only for pH(1) (I199V, with significant additive effect) and lactate content (T30N), confirming, at least in part, the effects of this gene on meat quality traits. Significant association (P<0.05) was also observed for PGAM2 and ham weight EBV with significant additive and dominance effects. PKM2 was associated with average daily gain, lean cuts (P<0.001), back fat thickness and feed:gain ratio (P<0.05), with significant additive and/or dominance effects on these traits. PKM2 encodes for a key enzyme of the muscle glycolytic pathway and maps on porcine chromosome 7 where other studies have reported important QTL for the same traits. These data might suggest an important function of this gene in the mechanisms that produce the observed effects. The results will be important to evaluate the inclusion of some of these DNA polymorphisms in marker assisted selection programs.

Genome-wide identification of quantitative trait loci in a cross between Hampshire and Landrace II: meat quality traits

Background

Meat quality traits are important in pig breeding programs, but they are difficult to include in a traditional selection program. Marker assisted selection (MAS) of meat quality traits is therefore of interest in breeding programs and a Quantitative Trait Locus (QTL) analysis is the key to identifying markers that can be used in MAS. In this study, Landrace and Hampshire intercross and backcross families were used to investigate meat quality traits. Hampshire pigs are commonly used as the sire line in commercial pig breeding. This is the first time a pedigree including Hampshire pigs has been used for a QTL analysis of meat quality traits.

Results

In total, we analyzed 39 meat quality traits and identified eight genome-wide significant QTL peaks in four regions: one on chromosome 3, two on chromosome 6 and one on chromosome 16. At least two of the QTLs do not appear to have been detected in previous studies. On chromosome 6 we identified QTLs for water content in M. longissimus dorsi (LD), drip loss in LD and post mortem pH decline in LD. On chromosomes 3 and 16 we identified previously undetected QTLs for protein content in LD and for freezing and cooking loss respectively.

Conclusion

We identified at least two new meat quality trait QTLs at the genome-wide significance level. We detected two QTLs on chromosome 6 that possibly coincide with QTLs detected in other studies. We were also able to exclude the C1843T mutation in the ryanodine receptor (RYR1) as a causative mutation for one of the chromosome 6 QTLs in this cross.

Impact of RN genotype and ageing time on colour characteristics of the pork muscles longissimus dorsi and semimembranosus

The effect of RN genotype on pH decline, ultimate pH, pigment content, blooming and colour stability during 6 days of display at 5°C was studied in two pig muscles, M. longissimus dorsi (LD) and M. semimembranosus (SM), and furthermore the effect of anaerobic storage time (2 days vs. 9 days of ageing) on the same parameters was examined. The postmortem pH decline was faster and the ultimate pH lower in LD and SM of the RN(-) genotype compared with corresponding muscles from the rn(+) genotype. Pork of the RN(-) genotype was initially lighter and more red and yellow than pork of the rn(+) genotype due to a higher degree of blooming, which might be explained by the faster pH decline and/or lower ultimate pH. The level of oxymyoglobin (MbO(2)) was decisive for the redness of both muscles during display in air despite a higher presence of metmyoglobin (MetMb). Pork of the RN(-) genotype was thus redder than that of the rn(+) genotype throughout display in air despite higher oxidation to MetMb. Ageing for 9 days in chill improved the blooming potential in pork of both genotypes compared with 2 days of ageing, resulting in superior meat colour. However, only in pork from the RN(-) genotype, the colour was not negatively affected by ageing time upon display in air.