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Background Local adaptation drives complex traits in domestic animals, but the roles of positive and balancing selection in Chinese indigenous pig breeds remain unclear. We performed whole-genome resequencing of 79 Yangxin pigs and applied positive and balance selection, integrated findings with PigQTLdb and FarmGTEx. Results In this study, we detected ~ 98 Mb of the genome under adaptive selection, mainly involving non-coding variants. Positive selection signals were concentrated in regulatory regions affected to muscle traits, whereas balancing selection was enriched at loci associated with reproduction. The strongest overlap with regulatory elements was observed in muscle tissue. Additionally, significant enrichment of the Hippo signaling pathway was detected in testis. DNA-level annotation revealed reproductive QTL to be most overrepresented in balancing-selection regions. Notable candidate genes and pathways include VGLL3 and Hippo signaling, and oxytocin, circadian entrainment, vascular smooth muscle contraction, and adrenergic signaling. Conclusion These results underscore a regulatory basis for muscle phenotype variation, and the role of balancing selection in preserving fertility-related diversity. Our findings provide genomic markers for breeding and conservation strategies aimed at enhancing productivity in the Yangxin pig.

Background Vitamin D receptor (VDR) gene polymorphism is reported to be associated with muscle mass and muscle strength. Loss of skeletal muscle mass and decreased muscle strength are the main characteristics of sarcopenia. In this study, the relationship of VDR gene polymorphism with muscle traits (muscle mass, muscle strength, and physical performance) and sarcopenia were studied in Xinjiang, China. Methods Totally, 205 sarcopenia patients were enrolled. Propensity score method was used to match control group. FokI and BsmI polymorphisms were genotyped using improved multiplex ligation detection reaction (iMLDR). Results Fok1, but not Bsm1, polymorphism was significantly associated with sarcopenia. Patients with Fok1 GG genotype were more likely to have sarcopenia. Both Bsm1 and Fok1 polymorphism were related to muscle traits. Patients with Bsm1 CT genotype had lower gait speed (GS) but higher skeletal mass index. Patients with Fok1 GG genotype had lower GS, and female subjects with the Fok1 GG genotype had lower handgrip strength (HS). GS was decreased in Bsm1 CT genotype than CC carriers. HS and GS were decreased in Fok1 GG genotype than AA carriers. Conclusion Fok1, but not Bsm1, polymorphism is associated with sarcopenia. Both Bsm1 and Fok1 polymorphism affect both HS and GS. Fok1 polymorphism affects both handgrip strength and gait speed. Bsm1 polymorphism affects gait speed. But only Fok1 is associated with sarcopenia.

An association between vitamin D level and muscle-related traits has been frequently reported. Vitamin D level is dependent on various factors such as sunlight exposure and nutrition. But also on genetic factors. We, therefore, hypothesize that single nucleotide polymorphisms (SNPs) within the vitamin D pathway-related genes could contribute to muscle mass and function via an impact on vitamin D level. However, the integration of studies investigating these issues is still missing. Therefore, this review aimed to systematically identify and summarize the available evidence on the association between SNPs within vitamin D pathway-related genes and vitamin D status as well as various muscle traits in healthy adults. The review has been registered on PROSPERO and was conducted following PRISMA guidelines. In total, 77 studies investigating 497 SNPs in 13 different genes were included, with significant associations being reported for 59 different SNPs. Variations in GC, CYP2R1, VDR, and CYP24A1 genes were reported most frequently, whereby especially SNPs in the GC (rs2282679, rs4588, rs1155563, rs7041) and CYP2R1 genes (rs10741657, rs10766197, rs2060793) were confirmed to be associated with vitamin D level in more than 50% of the respective studies. Various muscle traits have been investigated only in relation to four different vitamin D receptor (VDR) polymorphisms (rs7975232, rs2228570, rs1544410, and rs731236). Interestingly, all of them showed only very low confirmation rates (6–17% of the studies). In conclusion, this systematic review presents one of the most comprehensive updates of the association of SNPs in vitamin D pathway-related genes with vitamin D status and muscle traits in healthy adults. It might be used for selecting candidate SNPs for further studies, but also for personalized strategies in identifying individuals at risk for vitamin D deficiency and eventually for determining a potential response to vitamin D supplementation.

A genetic linkage map of common carp (Cyprinus carpio L.) was constructed using Type I and Type II microsatellite markers and a pseudo-testcross mapping strategy. The microsatellite markers were isolated from microsatellite-enriched genomic libraries and tested for their segregation in a full-sib mapping panel containing 92 individuals. A total of 161 microsatellite loci were mapped into 54 linkage groups. The total lengths of the female, male and consensus maps were 2,000, 946, and 1,852 cM, with an average marker spacing of approximately 13, 7, and 11 cM, respectively. Muscle fiber-related traits, including muscle fiber cross-section area and muscle fiber density, were mapped to the genetic map. Three QTLs for muscle fiber cross-section area and two QTLs for muscle fiber density were identified when considering both significant and suggestive QTL effects. The QTLs with largest effects for muscle fiber cross-section area and muscle fiber density were 21.9% and 18.9%, and they were located in LG3, respectively.

A total of 120 crossbred [synthetic line x (Large White x Landrace)] pigs (castrated males and females) were used to evaluate the influence of rearing conditions for growing-finishing pigs on growth performance, carcass, stress reactions at slaughter, and meat eating quality. At approximately 35 kg of live weight (LW), littermates were allocated to either a conventional (fully slatted floor, 0.65 m²/pig, considered as control, CON) or an alternative (sawdust bedding with free access to an outdoor area, 2.4 m²/pig, OUT) system, until slaughter at approximately 110 kg of LW. Pigs had free access to standard growing and finishing diets. The trials were conducted in spring, summer, and winter, with each season involving 2 pens of 10 pigs in each system. Compared with the CON, the OUT pigs exhibited a greater growth rate (+10%, P < 0.001) due to their greater feed intake (+0.23 kg/d, P < 0.01), resulting in a greater body weight at slaughter (+7 kg, P < 0.001). The OUT pigs had thicker backfat (+2.4 mm, P < 0.01) and lower lean meat content (- 2.0% points, P < 0.001) than the CON pigs. The OUT system did not (P > 0.10) influence the behavioral activities of pigs during lairage at the slaughterhouse, or the urinary levels of catecholamines and cortisol, and plasma levels of ACTH, cortisol, lactate, creatine kinase, and FFA immediately after slaughter. The OUT pigs had similar (P > 0.10) pH values 30 min postmortem (pH₁) in the LM, biceps femoris (BF), and semimembranosus (SM) muscles, similar ultimate pH (pHu) in LM, but lower pHu in SM (- 0.07 unit, P < 0.001) and in BF (- 0.03 unit, P = 0.029). Despite nonsignificant effects of production system on stress reactions at slaughter, assessed by urine and plasma indicators and muscle metabolism at 30 min postmortem, meat from OUT pigs had more LM drip loss after 2 (+1.0%, P = 0.003) and 4 (+1.1%, P = 0.010) d than did meat from the CON pigs. The OUT system slightly increased meat yellowness (b* value) in the LM (+0.7 unit, P = 0.001), BF (+0.5 unit, P = 0.014), and SM (+0.5, unit P = 0.041), whereas redness (a*) and lightness (L*) of the 3 muscles were unaffected (P > 0.07). Intramuscular fat content was greater in the LM (+17%, P = 0.001), BF (+14%, P = 0.004), and SM (+17%, P = 0.003) of the OUT pigs. Outdoor rearing during summer and winter improved meat juiciness, whereas odor, flavor, and tenderness were unaffected (P > 0.10). Influence of rearing conditions on all the other traits studied did not depend on the season.

The traditional beef production in the South of Portugal is based on a discontinuous growth (DG) system that requires lower external inputs and could enhance meat quality and financial returns to cattle producers. This system allows farmers to take advantage of the bull’s compensatory growth when the pasture is abundant and finishes the cattle on concentrates for 2 to 3 months before slaughter. The fast gain rate before slaughter could be a valuable strategy to improve tenderness and to reduce its inconsistency in beef production. Therefore, the aim of this study was to evaluate the effects of production system (continuous growth (CG) v. DG) on longissimus thoracis muscle properties from Alentejana bulls. In total, 40 Alentejana male calves were allocated to two distinct feeding regimes: in the CG system, animals were fed concentrate plus hay and slaughtered at 18 months of age, whereas in the DG system, animals were fed on hay until 15 months of age and then fed the same diet provided to the CG group until 24 months of age. The DG system had a positive impact on meat tenderness (P<0.001) and global acceptability (P<0.001). DG bulls had greater fibre cross-sectional area (CSA) of glycolytic fibres (P<0.05) and relative area of the muscle (RA) occupied by type IIX fibres (P<0.01) and greater levels of α-actinin (P<0.05) and myosin light chain 2 (P<0.01) proteins, and pH24h (P<0.01) than CG bulls. The latter had greater CSA of type I (P<0.05) and type IIA (P<0.01) and greater RA of type IIA (P<0.05) and oxidative (P<0.05) than CG bulls. The compensatory growth production system had a positive impact on meat tenderness and global acceptability, overcoming the negative effects of slaughter of the bulls at a later age. The DG beef system could be a worthwhile strategy of beef production in Mediterranean areas due to the low-quality pasture in summer.

Thirty single nucleotide polymorphisms (SNP) and one 6-bp insertion-deletion (indel) from 8 genes of somatotropic axis were used to study the association with chicken fatness and muscle fibers. The allele frequency difference between Xinghua and White Plymouth Rock chickens was observed, and their effects on fatness and muscle fiber traits were also evaluated by linkage analyses. The G143831A (G+1705A) SNP of the growth hormone (GH) gene was related to fat width, and the G144762A (G+119A) SNP of the GH gene was significantly associated with abdominal fat pad weight, abdominal fat pad ratio, and crude fatty content of the breast muscle. The 6-bp indel of the growth hormone secretagogue receptor (GHSR) gene was significantly linked with the fat traits. The C51978309T SNP of the insulin-like factor-I (IGF-I) gene was significantly linked with the transversal area of the leg muscle fiber and transversal area of the breast muscle fiber. There was significant linkage between the insulin (INS) gene and 2 traits of the transversal area of transversal area of the leg muscle fiber and transversal area of the breast muscle fiber. Association of 30 SNP and one 6-bp indel from 8 genes of somatotropic axis with chicken fatness and muscle fiber traits was analyzed in the present study. The GH, GHSR, and leptin receptor genes were significantly related to chicken fatness. The INS and IGF-I genes were linked with muscle fiber density. Therefore, the genes of somatotropic axis not only affected chicken growth and body composition but also were associated with fatness and muscle fiber traits.

We integrate comeasured gene expression and DNA methylation (DNAme) in 265 human skeletal muscle biopsies from the FUSION study with >7 million genetic variants and eight physiological traits: height,waist,weight,waist–hip ratio, body mass index, fasting serum insulin, fasting plasma glucose, and type 2 diabetes. We find hundreds of genes and DNAme sites associated with fasting insulin, waist, and body mass index, as well as thousands of DNAme sites associated with gene expression (eQTM). We find that controlling for heterogeneity in tissue/muscle fiber type reduces the number of physiological trait associations, and that long-range eQTMs (>1 Mb) are reduced when controlling for tissue/muscle fiber type or latent factors. We map genetic regulators (quantitative trait loci; QTLs) of expression (eQTLs) and DNAme (mQTLs). Using Mendelian randomization (MR) and mediation techniques, we leverage these genetic maps to predict 213 causal relationships between expression and DNAme, approximately two-thirds of which predict methylation to causally influence expression. We use MR to integrate FUSION mQTLs, FUSION eQTLs, and GTEx eQTLs for 48 tissues with genetic associations for 534 diseases and quantitative traits. We identify hundreds of genes and thousands of DNAme sites that may drive the reported disease/quantitative trait genetic associations. We identify 300 gene expression MR associations that are present in both FUSION and GTEx skeletal muscle and that show stronger evidence of MR association in skeletal muscle than other tissues, which may partially reflect differences in power across tissues. As one example, we find that increased RXRA muscle expression may decrease lean tissue mass.

Forty-eight Duroc x Landrace x Large White gilts were used to determine the relationship between proteome changes of longissimus muscle and intramuscular fat (IMF) content in arginine-supplemented pigs. Beginning at 60 kg BW, pigs were fed a corn- and soybean meal-based diet supplemented or not with 1% L-arginine until they reached a BW of 100 kg. Supplementation with 1% L-arginine did not affect the growth performance or carcass traits, while it increased IMF content by 32% (P < 0.01), it also decreased the drip loss at 48 h post-mortem and the b* meat color value at 24 h post-mortem; supplementation with 1% dietary L-arginine did not change the proportion of SFA and MUFA in muscle lipids. The proteome changes in longissimus muscle between the control and supplemented pigs showed that L-arginine significantly influenced the abundance of proteins related to energy metabolism, fiber type and structure. The increase in IMF content was positively correlated with the increased abundance of slow twitch troponin I (TNNI1) protein and negatively correlated with myosin heavy chain IIb (MyHC IIb) protein content. It is suggested that the proteome changes in longissimus muscle contributed to the greater IMF content in L-arginine supplemented pigs.

The heart muscle diseases hypertrophic (HCM) and dilated (DCM) cardiomyopathies are leading causes of sudden death and heart failure in young, otherwise healthy, individuals. We conducted genome-wide association studies and multi-trait analyses in HCM (1,733 cases), DCM (5,521 cases) and nine left ventricular (LV) traits (19,260 UK Biobank participants with structurally normal hearts). We identified 16 loci associated with HCM, 13 with DCM and 23 with LV traits. We show strong genetic correlations between LV traits and cardiomyopathies, with opposing effects in HCM and DCM. Two-sample Mendelian randomization supports a causal association linking increased LV contractility with HCM risk. A polygenic risk score explains a significant portion of phenotypic variability in carriers of HCM-causing rare variants. Our findings thus provide evidence that polygenic risk score may account for variability in Mendelian diseases. More broadly, we provide insights into how genetic pathways may lead to distinct disorders through opposing genetic effects. Genome-wide analyses identify multiple loci associated with hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM) and left ventricular (LV) traits. Cardiomyopathies exhibit strong genetic correlations with LV traits, with opposing effects in HCM and DCM.