Muscle development and lipid accumulation in muscle critically affect meat quality of livestock. However, the genetic factors underlying myofiber-type specification and intramuscular fat (IMF) accumulation remain to be elucidated. Using two independent intercrosses between Western commercial breeds and Korean native pigs (KNPs) and a joint linkage-linkage disequilibrium analysis, we identified a 488.1-kb region on porcine chromosome 12 that affects both reddish meat color (a*) and IMF. In this critical region, only the MYH3 gene, encoding myosin heavy chain 3, was found to be preferentially overexpressed in the skeletal muscle of KNPs. Subsequently, MYH3-transgenic mice demonstrated that this gene controls both myofiber-type specification and adipogenesis in skeletal muscle. We discovered a structural variant in the promotor/regulatory region of MYH3 for which Q allele carriers exhibited significantly higher values of a* and IMF than q allele carriers. Furthermore, chromatin immunoprecipitation and cotransfection assays showed that the structural variant in the 5′-flanking region of MYH3 abrogated the binding of the myogenic regulatory factors (MYF5, MYOD, MYOG, and MRF4). The allele distribution of MYH3 among pig populations worldwide indicated that the MYH3 Q allele is of Asian origin and likely predates domestication. In conclusion, we identified a functional regulatory sequence variant in porcine MYH3 that provides novel insights into the genetic basis of the regulation of myofiber type ratios and associated changes in IMF in pigs. The MYH3 variant can play an important role in improving pork quality in current breeding programs. Local native livestock breeds, such as pigs and cattle, are important reservoirs of genetic variation, because they have adapted to local conditions and have not been as strongly selected as commercial livestock breeds. Therefore, the study of local native breeds is of utmost interest to identify causative mutations for traits in which large differences exist between local native breeds and breeds used internationally for meat production. Herein, we apply these principles to meat quality related traits in pigs. A combined linkage-linkage disequilibrium analysis identified the MYH3 gene on pig chromosome 12, which encodes myosin heavy chain 3 protein. Subsequently, we discovered a regulatory mutation in MYH3, which occurs at high frequency in Korean Native Pigs compared to the frequency at which it occurs in Western pig breeds. We confirmed the effect of MYH3 on muscle fiber-type composition and intramuscular fat content using transgenic mice and transfection assays in porcine fibroblast cells. This is the first causal mutation identified in livestock for these traits and the result is immediately applicable for the genetic improvement of pork quality. These results also enhance our understanding of the genetic basis regarding the regulation of myofiber type ratios and associated changes in intramuscular fat contents in pigs and mammals in general.

Myosin heavy chain (MyHC) isoforms consist of Myh7, Myh2, Myh1, and Myh4, which are expressed in skeletal muscle tissues during postnatal development. These genes influence the contraction–relaxation activity in skeletal muscles and are involved in determining muscle composition such as the proportion of fast-to-slow and/or slow-to-fast fiber types. Among them, Myh1 is associated with skeletal muscle contraction and is involved in both slow-to-fast and fast-to-slow transition. However, the muscle transition mechanism is not well understood. For this study, we first produced porcine Myh1 transgenic (TG) mice to study whether the ectopic expressed porcine Myh1 gene had any effects on muscle composition, especially on slow-type muscle components. Our results showed that the factors associated with slow muscles, such as Myh7, Myoglobin, Troponin (slow-type units), and cytochrome C, were highly expressed in the quadriceps muscles of Myh1 transgenic mice. Furthermore, the ectopic porcine MYH1 protein was located only in the slow-type muscle fibers of the quadriceps muscles in Myh1 transgenic mice. In physical endurance tests, Myh1 transgenic mice ran longer and further on a treadmill than wild-type (WT) mice. These data fully supported our hypothesis that Myh1 is associated with slow muscle composition, with overexpression of Myh1 in muscle tissues possibly being a new key in modulating muscle fiber types. Our study provides a better understanding of muscle composition metabolism, physical mobility, and genetic factors in muscle fatigue.

We conducted a genome-wide linkage analysis to identify quantitative trait loci (QTL) that influence meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs. Thirteen meat quality-related traits of the m. longissimus lumborum et thoracis were measured in more than 830 F2 progeny. All these animals were genotyped with 173 microsatellite markers located throughout the pig genome, and the GridQTL program based on the least squares regression model was used to perform the QTL analysis. We identified 23 genome-wide significant QTL in eight chromosome regions (SSC1, 2, 6, 7, 9, 12, 13, and 16) (SSC for Sus Scrofa) and detected 51 suggestive QTL in the 17 chromosome regions. QTL that affect 10 meat quality traits were detected on SSC12 and were highly significant at the genome-wide level. In particular, the QTL with the largest effect affected crude fat percentage and explained 22.5% of the phenotypic variance (F-ratio = 278.0 under the additive model, nominal P = 5.5 × 10−55). Interestingly, the QTL on SSC12 that influenced meat quality traits showed an obvious trend for co-localization. Our results confirm several previously reported QTL. In addition, we identified novel QTL for meat quality traits, which together with the associated positional candidate genes improve the knowledge on the genetic structure that underlies genetic variation for meat quality traits in pigs.

Number of vertebrae is associated with body size and meat productivity in pigs. The aim of this study was to identify QTL and associated positional candidate genes affecting the number of thoracic vertebrae (THO). A genomewide association study was conducted in a large resource population derived from an F₂ intercross between Landrace and Korean native pigs using the Porcine SNP 60K BeadChip and the genomewide complex trait analysis (GCTA) program based on a linear mixed-effects model. A total of 38,385 SNP markers from 1,105 F₂ progeny were analyzed for the THO trait after filtering for quality control. A total of 90 genomewide significant SNP markers (P < 1.30 × 10⁻⁶) on SSC 7 covering a 20-Mb region were identified for THO in this study. Several previous studies also mapped QTL for vertebral numbers in this region. The strongest association signals were detected at ASGA0035500 (P-value = 4.46 × 10⁻⁴⁰; 103,574,383 bp) and DIAS0000795 (P-value = 4.46 × 10⁻⁴⁰; 103,594,753 bp). The QTL region on SSC 7 for THO encompasses VRTN and LTBP2, which are previously described candidate genes for vertebral number variation. To refine the QTL region, a haplotype-based linkage and linkage disequilibrium (LALD) analysis using the DualPHASE program was applied because subsequent conditional association and haplotype block analyses could not resolve the region that contains the 2 loci. The LALD analysis refined the critical region to a 533.9-kb region including LTBP2; VRTN was located outside the critical region. The LTBP2 gene encoding latent transforming growth factor beta binding protein 2 is involved in bone metabolisms. Based on these data, we propose LTBP2 as a positional candidate gene for THO in pigs. After further functional studies and verification of the association in other independent populations, these results could be useful for optimizing breeding programs that improve THO and other economically important traits in pigs.

In mammals, imprinted genes often exist in the form of clusters in specific chromosome regions. However, in pigs, genomic imprinting of a relatively few genes and clusters has been identified, and genes within or adjacent to putative imprinted clusters need to be investigated including those at the SGCE/PEG10 locus. The objective of this study was to, using porcine parthenogenetic embryos, investigate imprinting status of genes within the genomic region spans between the COL1A2 and ASB4 genes in chromosome 9. Whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) were conducted with normal and parthenogenetic embryos, and methylome and transcriptome were analyzed. As a result, differentially methylated regions (DMRs) between the embryos were identified, and parental allele-specific expressions of the SGCE and PEG10 genes were verified. The pig imprinted interval was limited between SGCE and PEG10, since both the COL1A2 and CASD1 genes at the centromere-proximal region and the genes between PPP1R9A and ASB4 toward the telomere were non-imprinted and biallelically expressed. Consequently, our combining analyses of methylome, transcriptome, and informative polymorphisms revealed the boundary of imprinting cluster at the SGCE/PEG10 locus in pig chromosome 9 and consolidated the landscape of genomic imprinting in pigs.