Identification of SNPs in MYOD gene family and their associations with carcass traits in cattle

Association of variants and expression levels of MYOD1 gene with carcass and muscle characteristic traits in domestic pigeons

This study was to investigate the correlations of myogenic differentiation 1 (MYOD1) gene polymorphisms with carcass traits and its expression with breast muscle development in pigeons. Four SNPs were found in the pigeon MYOD1 gene. Correlation analysis showed that individuals with AA genotype at both SNPs g.2967A > G (p < .01) and g.3044G > A (p < .05) have significantly higher live weight (LW), carcass weight (CW), semi-eviscerated weight (SEW), eviscerated weight (EW) and breast muscle weight (BMW). Moreover, the two SNPs also had the same significant effects on MYOD1 mRNA expression levels in breast muscle of pigeons, ie, the AA genotype showed higher MYOD1 mRNA expression levels. The diameter and cross-section area of muscle fibers continuously increased from 0w to 4w (p < .05), accompanied with the increasing expression of MYOD1 gene, while the density decreased (p < .05) dramatically from 0w to 1w and continuously fell over in the next few weeks (p > .05). What's more, the expression level of MYOD1 gene was positively correlated with a diameter (r = 0.937, p < .05) and cross-sectional area (r = 0.956, p < .01) of myofiber, and negatively correlated with density (r = -0.769, p < .01). The results showed that individuals with AA genotype at both SNPs g.2967A > G and g.3044G > A have showed higher carcass traits (LW, CW, SEW, EW, and BMW) and higher MYOD1 mRNA expression level in breast muscle than AB and BB genotypes. Moreover, the expression level of MYOD1 gene was closely correlated with muscle characteristic traits, indicating variants of MYOD1 gene was closely related to muscle development and could be a potential candidate gene in marker-assisted selection of pigeons.

EEF1A1 transcription cofactor gene polymorphism is associated with muscle gene expression and residual feed intake in Nelore cattle

Cis-acting effects of noncoding variants on gene expression and regulatory molecules constitute a significant factor for phenotypic variation in complex traits. To provide new insights into the impacts of single-nucleotide polymorphisms (SNPs) on transcription factors (TFs) and transcription cofactors (TcoF) coding genes, we carried out a multi-omic analysis to identify cis-regulatory effects of SNPs on these genes' expression in muscle and describe their association with feed efficiency-related traits in Nelore cattle. As a result, we identified one SNP, the rs137256008C > T, predicted to impact the EEF1A1 gene expression (β = 3.02; P-value = 3.51E-03) and the residual feed intake trait (β = - 3.47; P-value = 0.02). This SNP was predicted to modify transcription factor sites and overlaps with several QTL for feed efficiency traits. In addition, co-expression network analyses showed that animals containing the T allele of the rs137256008 SNP may be triggering changes in the gene network. Therefore, our analyses reinforce and contribute to a better understanding of the biological mechanisms underlying gene expression control of feed efficiency traits in bovines. The cis-regulatory SNP can be used as biomarker for feed efficiency in Nelore cattle.

Exploring the effects of different male parent crossings on sheep muscles and related regulatory genes using mRNA-Seq

Objective

With improvements in living standards and increase in population globally, the demand for meat products has been increasing; improved meat production from livestock could effectively meet this demand. In this study, we examined the differences in the muscle traits of different male crossbred sheep and attempted to identify key genes that regulate these traits.

Methods

Dubo sheep × Small-tailed Han sheep (DP×STH) and Suffolk × Small-tailed Han sheep (SFK×STH) were selected to determine meat quality and production performance by Masson staining. Transcriptome sequencing and bioinformatic analysis were performed to identify differentially expressed genes (DEGs) related to meat quality. The presence of DEGs was confirmed by real-time polymerase chain reaction (qPCR).

Results

The production performance of SFK×STH sheep was better than that of DP×STH sheep, but the meat quality of DP×STH sheep was better than that of SFK×STH sheep. The muscle fiber diameter of DP×STH sheep was smaller than that of SFK×STH sheep. Twenty-two DEGs were identified. Among them, four Gene Ontology terms were related to muscle traits, and three DEGs were related to muscle or muscle fibers. There were no significant differences in the number of single nucleotide mutations and mutation sites in the different male parent cross combinations.

Conclusion

This study provides genetic resources for future sheep muscle development and cross-breeding research.

Polymorphisms in coding and non-coding regions of rabbit (Oryctolagus cuniculus) myogenin (MyoG) gene

In animal breeding, selection based on growth is very often used, as this trait affects the profitability of animal production. Identification of  polymorphisms within the genes affecting the growth process seems to be very important. Therefore, we decided to analyse rabbit myogenin (<em>MyoG</em> gene) for potential polymorphic sites and their association with growth and carcass traits in Termond White (TER), Belgian Giant Grey (BGG) and crossbred New Zealand White×Belgian Giant Grey (NZW×BGG) rabbits. We found three single nucleotide polymorphisms (SNPs) – in 5’ upstream sequence g.68679476 C&gt;T, in exon 1 – silent mutation g.68680096 T&gt;C and g.68680097 G&gt;A resulting in change of GTG triplet (valine) into ATG triplet (methionine). Association analysis showed that GG genotype weaning weight was statistically higher compared to GA in TER population (<em>P</em>=0.005), and that the hind parts for GG genotypes were heavier compared to those of GA (<em>P</em>=0.024), but association analysis of dissectible parts showed this was caused by higher bone weight (<em>P</em>=0.015). For g.68679476 C&gt;T in NZW×BGG population, the CC genotypes for fore (678±35) and hind part (615±29) weights were heavier compared to CT (588±16 and 549±13, respectively); moreover, association analysis of dissectible parts showed that weight of dissectible meat in hind part. Unfortunately, we did not find similar associations for other analysed breeds. For g.68679476 C&gt;T in NZWxBGG musculus longissimus lumborum pH leg after 24 h chilling (pH24L) were statistically lower for CC genotypes compared to CT (<em>P</em>=0.027). For g.68680097 G&gt;A in Termond White population L* value on the hind leg after 24 h chilling (L*24H) was higher for GA genotypes compared to GG (<em>P</em>=0.03), while for g.68679476 C&gt;T for musculus longissimus lumborum L* value after 24 h (L*24L) CC genotypes had higher value compared to CT (<em>P</em>=0.016) in BGG population. Moreover, in BGG population CT genotypes had higher weaning weight compared to CC (<em>P</em>=0.018). Our results show that SNPs within the <em>MyoG </em>gene may influence growth traits in some rabbit breeds, but the evolutionary conserved sequence may not be favourable for changes within coding sequences. For a better understanding thereof, additional analysis is required.

Variants in myostatin and MyoD family genes are associated with meat quality traits in Santa Inês sheep

Myostatin and MyoD family genes play vital roles in myogenesis and this study aimed to identify association of variants in MyoD1, MyoG, MyF5, MyF6, and MSTN genes with meat traits in Santa Inês sheep. A dataset with 44 variants and records of seven meat traits in 192 lambs (pH0, pH24, a*, b*, L*, tenderness assessed by shear force, and water-holding capacity) was used. Single-locus and haplotype association analyses were performed, and the significance threshold was established according to Bonferroni's method. Single-locus analysis revealed two associations at a Bonferroni level, where the variant c.935-185C > G in MyoD1 had an additive effect (-4.31 ± 1.08 N) on tenderness, while the variant c.464 + 185G > A in MyoG had an additive effect (-2.86 ± 0.64) on a*. Additionally, the haplotype replacement GT>AC in MSTN was associated with pH0 (1.26 ± 0.31), pH24 (1.07 ± 0.27), a* (-1.40 ± 0.51), and tenderness (3.83 ± 1.22 N), while the replacement GT > AG in MyoD1 was associated with pH0 (1.43 ± 0.26), pH24 (1.25 ± 0.22), b* (-1.06 ± 0.39), and tenderness (-4.13 ± 1.16 N). Our results have demonstrated that some variants in MyoG, MyF6, MyoD1, and MSTN can be associated with physicochemical meat traits in Santa Inês sheep.

Genetic variants in MYF5 affected growth traits and beef quality traits in Chinese Qinchuan cattle

Myogenic factor 5 plays actively roles in the regulation of myogenesis. The aims of this study are to identify the evolution information of MYF5 protein among 10 domestic and mammalian animals, to uncover the expression patterns of MYF5 gene in calves and adults of Qinchuan cattle, and to expose the genetic variants of the MYF5 gene and explore its effect on cattle growth traits and beef quality traits in Qinchuan cattle. The bioinformatics results showed that the MYF5 proteins highly conserved in different mammalian or domestic animals apart from chicken. The expression level of MYF5 gene in the heart, muscle, lung, large intestine and liver was greater than that of other tissues. PCR amplicons sequencing identified four novel SNPs at g.5738A>G, g.5785C>T and g.5816A>G in the 3rd exon region and g.6535A>G in the 3' UTR. Genotypic frequencies of g.5785C>T was harshly deviated from the HWE (P < .05). Genetic diversity was low or intermediate for the four SNPs and those SNPs were in the weak linkage disequilibrium. Association analysis results indicated g.5785C>T, g.5816A>G and g.6535A>G significant effect on growth performance and beef quality traits of Qinchuan cattle. H1H3 diplotype had greater body size and better beef quality. All the results implicate that the MYF5 gene might be applied as a promising candidate gene in Qinchuan cattle breeding.

Gene Expression and Fatty Acid Profiling in Longissimus thoracis Muscle, Subcutaneous Fat, and Liver of Light Lambs in Response to Concentrate or Alfalfa Grazing

A better understanding of gene expression and metabolic pathways in response to a feeding system is critical for identifying key physiological processes and genes associated with polyunsaturated fatty acid (PUFA) content in lamb meat. The main objective of this study was to investigate transcriptional changes in L. thoracis (LT) muscle, liver, and subcutaneous fat (SF) of lambs that grazed alfalfa (ALF) and concentrate-fed (CON) slaughtered at 23 kg and using the Affymetrix Ovine Gene 1.1 ST whole-genome array. The study also evaluated the relationship between meat traits in LT muscle, including color, pigments and lipid oxidation during 7 days of display, α-tocopherol content, intramuscular fat (IMF) content and the fatty acid (FA) profile. Lambs that grazed on alfalfa had a greater α-tocopherol concentration in plasma than CON lambs (P < 0.05). The treatment did not affect the IMF content, meat color or pigments (P > 0.05). Grazing increased the α-tocopherol content (P < 0.001) and decreased lipid oxidation on day 7 of display (P < 0.05) in LT muscle. The ALF group contained a greater amount of conjugated linoleic acid (CLA), C18:3 n−3, C20:5 n−3, C22:5 n−3, and C22:6 n−3 than did the CON group (P < 0.05). We identified 41, 96 and four genes differentially expressed in LT muscle, liver, and subcutaneous fat, respectively. The most enriched biological processes in LT muscle were skeletal muscle tissue development, being the genes related to catabolic and lipid processes downregulated, except for CPT1B, which was upregulated in the ALF lambs. Animals grazing alfalfa had lower expression of desaturase enzymes in the liver (FADS1 and FADS2), which regulate unsaturation of fatty acids and are directly involved in the metabolism of n−3 PUFA series. The results found in the current study showed that ingesting diets richer in n−3 PUFA might have negative effects on the de novo synthesis of n−3 PUFA by downregulating the FADS1 and FADS2 expression. However, feeding diets poorer in n−3 PUFA can promote fatty acid desaturation, which makes these two genes attractive candidates for altering the content of PUFAs in meat.

Variation in the ovine MYF5 gene and its effect on carcass lean meat yield in New Zealand Romney sheep

Myogenic factor 5 (MYF5) plays an important role in regulating skeletal muscle, but to date there have been no reports on whether the gene is variable and whether this variation is associated with meat yield in sheep. In this study, four variants (A to D) of ovine MYF5 containing two Single Nucleotide Polymorphisms (SNPs) and one basepair (bp) insertion/deletion were detected by Polymerase Chain Reaction - Single Stranded Conformational Polymorphism (PCR-SSCP) analysis. Breed differences in variant frequencies were observed. The effect of variation in ovine MYF5 on lean meat yield, predicted using VIAScan® technology, was investigated in 388 male NZ Romney lambs. Only genotypes AA and AB were found in these lambs. Lambs with genotype AA had a higher leg yield (P=0.044), loin yield (P=0.002) and total yield (P=0.012) than those with genotype AB. No association with shoulder yield was detected. These results suggest that ovine MYF5 may be a valuable genetic marker for improved lean meat yield.

Association of MYF5 and KLF15 gene polymorphisms with carcass traits in domestic pigeons (Columba livia)

Single nucleotide polymorphisms (SNPs) in the exons of the myogenic factor 5 (MYF5) and Kruppel-like factor 15 (KLF15) genes were identified and analysed by using DNA sequencing methods in 60 female domestic pigeons (Columba livia). Five SNPs (T5067A, C5084T, C5101T, T5127A and C5154G) were detected in exon 3 of MYF5 and 6 SNPs (C1398T, C1464T, G1542A, C1929T, G1965A and A2355G) were found in exon 2 of KLF15, respectively. The analysis revealed three genotypes, in which the AA genotype was dominant and the A allele showed a dominant advantage. For the MYF5 gene, the C5084T and T5127A SNP genotypes were significantly associated with carcass traits of pigeons. Within those two SNPs, the BB genotype showed relatively higher trait association values than those of AA or AB genotypes. No significant association was observed between the KLF15 SNP genotypes and carcass traits. These results indicated that the MYF5 gene is a potential major gene affecting carcass traits in domestic pigeons. The BB genotype of the C5084T and T5127A SNPs could be a potential candidate genetic marker for marker-assisted selection in pigeon.

Identification of Gene Networks for Residual Feed Intake in Angus Cattle Using Genomic Prediction and RNA-seq

Improvement in feed conversion efficiency can improve the sustainability of beef cattle production, but genomic selection for feed efficiency affects many underlying molecular networks and physiological traits. This study describes the differences between steer progeny of two influential Angus bulls with divergent genomic predictions for residual feed intake (RFI). Eight steer progeny of each sire were phenotyped for growth and feed intake from 8 mo. of age (average BW 254 kg, with a mean difference between sire groups of 4.8 kg) until slaughter at 14-16 mo. of age (average BW 534 kg, sire group difference of 28.8 kg). Terminal samples from pituitary gland, skeletal muscle, liver, adipose, and duodenum were collected from each steer for transcriptome sequencing. Gene expression networks were derived using partial correlation and information theory (PCIT), including differentially expressed (DE) genes, tissue specific (TS) genes, transcription factors (TF), and genes associated with RFI from a genome-wide association study (GWAS). Relative to progeny of the high RFI sire, progeny of the low RFI sire had -0.56 kg/d finishing period RFI (P = 0.05), -1.08 finishing period feed conversion ratio (P = 0.01), +3.3 kg^0.75 finishing period metabolic mid-weight (MMW; P = 0.04), +28.8 kg final body weight (P = 0.01), -12.9 feed bunk visits per day (P = 0.02) with +0.60 min/visit duration (P = 0.01), and +0.0045 carcass specific gravity (weight in air/weight in air-weight in water, a predictor of carcass fat content; P = 0.03). RNA-seq identified 633 DE genes between sire groups among 17,016 expressed genes. PCIT analysis identified >115,000 significant co-expression correlations between genes and 25 TF hubs, i.e. controllers of clusters of DE, TS, and GWAS SNP genes. Pathway analysis suggests low RFI bull progeny possess heightened gut inflammation and reduced fat deposition. This multi-omics analysis shows how differences in RFI genomic breeding values can impact other traits and gene co-expression networks.

Expression profiles and association analysis with growth traits of the MyoG and Myf5 genes in the Jinghai yellow chicken

In order to analyze the association of single nucleotide polymorphisms (SNPs) in the MyoG and Myf5 genes with chicken growth traits, PCR-SSCP approach was used to detect the (SNPs). The general linear model was used to analyze gene interaction and genetic effects between different genotypes and growth traits of the Jinghai yellow chicken. For the MyoG gene, three genotypes (AA, AB and BB) were detected in the Jinghai yellow chicken population. Gene sequencing revealed one mutation (T36C) in the genotype BB in comparison to the genotype AA. For the Myf5 gene, three genotypes (CC, CD and DD) were detected in the Jinghai yellow chicken population. Gene sequencing revealed one mutation (A1313G) in the genotype DD in comparison to the genotype CC. Gene interaction effect has significant influence on 6, 8-week-weight and 300-day-weight. The least square analysis showed that individuals with BB genotype of the MyoG gene had higher bodyweight at 2, 4, 10, 12, 14 and 16 weeks compared to individuals with AA and AB genotypes. Individuals with CD genotype of the Myf5 gene had higher birth weight than individuals with CC genotype (P < 0.05). The interactive genotype AB*DD performs well at 6, 8 weeks and 300 days bodyweight. The results suggested that SNPs of the MyoG and Myf5 genes had certain effects on growth traits of the Jinghai yellow chicken.

Identification of KCNJ11 as a functional candidate gene for bovine meat tenderness

The potassium inwardly rectifying channel, subfamily J, member 11 (KCNJ11) gene was investigated as a candidate for meat tenderness based on the effects reported on muscle for KCNJ11 gene knockout in rat models and its position in a quantitative trait locus (QTL) for meat tenderness in the bovine genome. Sequence variations in the KCNJ11 gene were described by sequencing six amplified fragments, covering almost the entire gene. We identified single nucleotide polymorphisms (SNP) and validated them by different approaches, taking advantage of simultaneous projects that are being developed with the same Nelore population. By sequencing the KCNJ11 in Nelore steers representing extreme phenotypes for Warner-Bratzler shear force (WBSF), it was possible to identify 22 SNPs. We validated two of the identified markers by genotyping the whole population (n = 460). Analysis of association between genotypes and WBSF values revealed a significant additive effect of a SNP at different meat aging times (P ≤ 0.05). In addition, an association between the expression levels of KCNJ11 and WBSF was found, with lower expression levels of KCNJ11 associated with more tender meat (P ≤ 0.05). The results showed that the KCNJ11 gene is a candidate mapped to a QTL for meat tenderness previously identified on BTA15 and may be useful to identify animals with genetic potential to produce tender meat. The effect of KCNJ11 observed on muscle is potentially due to changes in activity of KATP channels, which in turn influence the flow of potassium in the intracellular space, allowing establishment of the membrane potential necessary for muscle contraction.

SNPs of bovine HGF gene and their association with growth traits in Nanyang cattle

Hepatocyte growth factor (HGF) is one of the multifunctional cell factors that regulates cellular proliferation, motility and morphogenesis in mammalians. And its medical research has deep significance. In this paper, polymorphisms of HGF gene were investigated in 1433 health and irrelated Chinese cattle by PCR-RFLP and DNA sequencing approach. Ten novel Single nucleotide polymorphisms (SNPs) were identified, which included one missense mutation, g.72801G>A in the coding region, and the others in the intron. Association analysis between four of them, g.288T>C, g.72801G>A, g.77172G>T, and g.77408T>G, and growth traits in Nanyang, were performed. The results indicated that SNPs within bovine HGF gene were significantly associated with growth traits. Phylogenetic analysis showed that the genetic background of Caoyuan Red cattle was different from the others in the tested breeds. The findings will provide a background for application of bovine HGF gene in the selection program in Chinese cattle.

An SNP in the MyoD1 gene intron 2 associated with growth and carcass traits in three duck populations

Myogenic differentiation 1 (MyoD1) genes belong to the MyoD gene family and play key roles in growth and muscle development. This study was designed to investigate the effects of variants in the MyoD1 gene on duck growth and carcass traits. Three duck populations (Cherry Valley, Jingjiang, and Muscovy) were sampled, their growth and carcass traits were measured, and they were genotyped using the PCR-RFLP method. The results showed one novel polymorphism, an alteration in intron 2 of the MyoD1 gene (A to T). It was associated with the traits of weight at 8 weeks, carcass weight, breast muscle weight, leg muscle weight, eviscerated percentage, percentage of leg muscle weight, dressing percentage, and lean meat percentage. This alteration in intron 2 of MyoD1 may be linked with potential major loci or genes affecting some growth and carcass traits.

A novel polymorphism of the myogenin gene is associated with body measurement traits in native Chinese breeds

Using PCR-SSCP and DNA sequencing technology, we examined the association of single nucleotide polymorphisms (SNPs) in the bovine MyoG gene with body measurement traits in 779 individuals of six native Chinese cattle breeds, namely Luxi, Luxi × Simmental crossbred, Nanyang, Xia'nan, Jiaxian red, and Qinchuan. A novel SNP, T314C, was detected. Allelic frequencies of MyoG-T/C in the six breeds were 0.8308/0.1692, 0.8774/0.1226, 0.8021/0.1979, 0.8209/0.1791, 0.8630/0.1370, 0.8044/0.1956, respectively. Least squares analysis revealed a significant (P < 0.05) association of the MyoG SNP with rump length in four breeds (Luxi, Xia'nan, Jiaxian red, and Qinchuan), with hucklebone width in three breeds (Luxi × Simmental crossbred, Nanyang and Xia'nan), with waist height in two breeds (Luxi × Simmental crossbred and Nanyang) and with body length in the Luxi breed. We conclude that the MyoG SNP has potential as a genetic marker for economically relevant body measurement traits in native Chinese cattle breeds.