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.     

Genetic diversity of MYH 3 gene associated with growth and carcass traits in Chinese Qinchuan cattle

MYH₃, whose function is to convert chemical energy to mechanical energy through ATP hydrolysis, is mainly expressed in skeletal muscle at various stages and is indispensable in the procedure of development of skeletal muscle and heart. In the study, genetic variations and genotypes of MYH ₃ gene in a total of 365 Qinchuan cattles were analyzed by polymerase chain reaction-restriction fragment length polymorphism, as well as verified the effect on growth and carcass traits. After PCR products were digested by restriction enzymes, eight SNPs were identified and individuals were genotyped. It showed that the SNPs at nucleotides were all in low linkage disequilibrium, therefore no dominated haplotype was found in the population. The result of statistic analysis indicated seven SNPs were significantly associated with growth and carcass traits (P < 0.05, N = 365) except locus G13791A. To sum up, the result of the study proved that polymorphisms in MYH3 gene are associated with the growth performance of Chinese Qinchuan cattle, so the variations of the gene could be used as possible molecular assisted-makers in the beef cattle breeding program and management.     

Genetic association of <Emphasis Type="Italic">Phosphodiesterase 1B</Emphasis> (PDE1B) with carcass traits in Korean cattle

Quantitative trait loci for fat deposition and carcass traits have been identified in the vicinity of the gene encoding phosphodiesterase 1B (PDE1B) on bovine chromosome 5. Therefore, the PDE1B gene can be considered as a positional and functional candidate gene for carcass traits in beef cattle. This study aimed to identify single nucleotide polymorphisms (SNPs) in the PDE1B gene and to evaluate their associations with carcass traits in Korean cattle. Eight SNPs, g.440T>G, g.17122A>G, g.17507A>C, g.17575A>G, g.17607T>C, g.17609C>A, g.17692C>T, and g.17707C>G, were identified in the region ranged from exon 1 to intron 6. Five of them were used for association analysis because of their availability of restriction fragment length polymorphisms. As a result, g.17122A>G in intron 3 was significantly associated with backfat thickness (BFT), and g.17507A>C in exon 5 was associated with longissimus dorsi muscle area (LMA, P < 0.05). Animals with the AG genotype of g.17122 had thicker BFT than those with the AA genotype. Animals with the AA or AC genotype of g.17507A>C had larger LMA than those with the CC genotype. We suggested the PDE1B gene as a candidate gene for carcass traits of beef cattle. Fine mapping would be required for application to marker-assisted selection.     

The role of BBS2 in regulating adipogenesis and the association of its sequence variants with meat quality in Qinchuan cattle

The BBS2 gene plays a vital role in human obesity and fat deposition. However, little is known about it in beef cattle. Therefore, this study investigates the function of BBS2 in the fat deposition of beef cattle and screens the effective SNPs marker for meat quality traits in cattle breeding. The expression of BBS2 is negatively correlated with marbling ratios of beef cattle. Moreover, the knockdown of BBS2 promoted adipogenesis and lipid accumulation of bovine preadipocytes by stimulating PPARγ, FABP4, and FASN expression (P < 0.01). Four novel SNPs in the exons of BBS2 in Chinese Qinchuan cattle were identified and of which the g.24226239C > T (Q527), g.24223562G > A (V441I), and g.24227851A > G (Q627R) were significantly associated with the meat quality of Qinchuan cattle (P < 0.01, P < 0.05). The findings suggested that BBS2 could be used as a candidate gene for meat quality improvement in Qinchuan cattle. Furthermore, these genotypes can be exploited as molecular markers in future beef breeding projects.     

Sequence variants of the <Emphasis Type="Italic">LCORL</Emphasis> gene and its association with growth and carcass traits in Qinchuan cattle in China

Molecular marker-assisted selection is a better way to satisfy the growing customer requirement with the development of beef cattle growth and breeding research. For now, quantitative trait locus (QTL) for cattle growth and carcass traits, just like body height, body length and carcass weight have been detected on bovine chromosome 6. In this study, ligand-dependent nuclear receptor corepressor-like (LCORL) was selected as the potential positional candidate gene located in chromosome 6 which is closely connected with the bovine growth and carcass traits. A total of 450 Qinchuan beef cattle were used to detect mutations in exon and its neighbouring region, and the promoter region of the bovine LCORL gene. The methods for SNPs detection were polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and created restriction site PCR (CRS-PCR), and the results of this study show that there were two variations in intron regions, the other four variations were located in the promoter region. Linkage disequilibrium analysis and haplotype analysis indicated that L78-Q4 had strong linkage disequilibrium, A T G C G C (16.2%) and G C G C A T (16.7%) had higher haplotype frequencies, G C A C A C (0.8%) and G T A C A T (0.7%) had lower haplotype frequencies. Correlation analysis indicated that SNP g. INT + 52098A >G was significantly associated with slaughter weight and carcass weight. Based on the research, we selected LCORL as the candidate gene that can contribute to improved marker-assisted selection for the meat performance of Qinchuan beef cattle.     

Associations between polymorphisms in the NICD domain of bovine <Emphasis Type="Italic">NOTCH1</Emphasis> gene and growth traits in Chinese Qinchuan cattle

NOTCH1 is one of the four mammalian Notch receptors, which is involved in the Notch signaling pathway. Specifically, NOTCH1 promotes the proliferation of myogenic precursor cells, and the NICD domain of NOTCH1 can impair regeneration of skeletal muscles. However, similar research on the bovine NOTCH1 gene is lacking. In this study, we detected the polymorphisms of the bovine NOTCH1 gene in a total of 448 individuals from Chinese Qinchuan cattle with DNA pooling, forced PCR-RFLP, and DNA sequencing methods. Five novel SNPs were identified within the NICD domain, and eight haplotypes comprising combinations of these five SNPs were studied as well. The association analysis of SNPs’ effects with growth traits revealed that g.A48250G was significantly associated with body height, body weight, and height at hip cross, and that g.A49239C only showed significant associations with body height. This suggests that the NOTCH1 gene is a strong candidate gene that could be utilized as a promising marker in beef cattle breeding programs.     

Genetic variations in insulin-like growth factor binding protein acid labile subunit gene associated with growth traits in beef cattle (Bos taurus) in China

The insulin-like growth factor binding protein acid labile subunit (IGFALS) gene encodes a serum protein that binds to IGFs and regulates growth, development, and other physiological processes. We have found that sequencing of the IGFALS gene in Chinese Qinchuan beef cattle (n = 300) revealed four SNP loci in exon two of the gene (g1219: T>C, g1893: T>C, g2612: G>A, and g2696: A>G). The SNP g2696: A>G resulted in a change from asparagine to aspartic acid (p. N574D) in the leucine-rich repeat region in the carboxyl-terminal domain of IGFALS. Four SNPs were in low linkage disequilibrium, and 12 different haplotypes were identified in the population. Association analysis suggested that SNP g1219: T>C had a significant association with hip width (P < 0.05) and SNP g2696: A>G displayed a significant association with stature (P < 0.05). The results from our investigation indicated that polymorphisms in the IGFALS gene were associated with growth traits of bovine, and may serve as a genetic marker for selection of beef cattle for growth traits, including stature.     

Tetra-primer ARMS-PCR identifies the novel genetic variations of bovine HNF-4α gene associating with growth traits

Hepatocyte nuclear factor-4α (HNF-4α), a member of the hepatocyte nuclear factor family, plays an important role in regulating the expression of genes involved in the development, differentiation and normal function of liver and pancreatic β cells, as well as the maintenance of glucose homeostasis. Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) is a new method offering fast detection and extreme simplicity at a negligible cost for SNP genotyping. In this paper, we characterize the polymorphisms of the bovine HNF-4α gene in three Chinese indigenous cattle breeds (n = 660). Six novel SNPs were identified including 1 mutation in the coding region and others in introns. The statistical analyses indicated that 4 SNPs (g.T53729C, g.A53861G, g.A65188C and g.T65444C) affected growth traits markedly (P < 0.05) in Qinchuan cattle (2 years after birth). Besides, haplotypes involving these 4 SNP sites in the bovine HNF-4α gene were identified and their effects on growth traits were also analyzed. The results showed that haplotypes 2, 7, 9 and 11 were predominant and accounted for 73.2%, 59.6%, and 67.1% in Qinchuan, Nanyang and Jiaxian cattle breeds, respectively. Hap9 (TAAT) was extremely predominant in all test populations, which suggested that individuals with Hap9 were more adapted to the environment. Furthermore, 4 combined haplotypes were constructed to guarantee the reliability of analysis results in Qinchuan cattle. There were also significant differences in body length (P < 0.05). These findings will benefit for the application of DNA marker related to the growth traits on marker-assisted selection (MAS), and improve the performance of beef cattle.     

Expression analysis, single nucleotide polymorphisms and combined genotypes in candidate genes and their associations with growth and carcass traits in Qinchuan cattle

The apolipoprotein E (ApoE) gene is an important component of plasma lipoprotein, and Fas apoptosis inhibitory molecule (FAIM) is a novel anti-apoptotic gene. In this study, we researched and discussed seven genes in eight different tissues in Qinchuan cattle by quantitative Real-time PCR. The result of analysis showed that ApoE and FAIM ₂ genes had a correlation with muscle and fat. PCR–RFLP was applied to analyze the genetic variations of the ApoE and FAIM ₂ genes and verify the effect on growth and carcass traits in a total of 365 Qinchuan cattles. The result of haplotype analysis showed that nine different haplotypes were identified among the four SNPs in ApoE and FAIM ₂ genes. The statistical analyses indicated that the four SNPs were significant association with growth and carcass traits (P < 0.05, N = 365); and the four SNPs were significant association between nine combined genotypes of candidate genes and growth and carcass traits. Taken together, our results provide the evidence that polymorphisms in candidate genes are associated with growth and carcass traits in Qinchuan cattle, and may be used as a possible candidate for marker-assisted selection and management in beef cattle breeding program.     

Effects of DGAT1 gene on meat and carcass fatness quality in Chinese commercial cattle

This study was designed to investigate the candidate single nucleotide polymorphisms (SNPs) in the exon’s region of bovine diacylglycerol O-acyltransferase (DGAT1) gene using bioinformatics and experimental methods. A total of 17 SNPs were screened from public data resources and DNA sequencing. Three SNPs (c.572A>G, c.1241C>T and c.1416T>G) of these candidate SNPs were genotyped by created restriction site-polymerase chain reaction (CRS-PCR) methods. The gene-specific SNP markers and their effects on meat and carcass fatness quality traits were evaluated in Chinese commercial cattle. The c.572A>G and c.1416T>G significantly effected on backfat thickness, longissimus muscle area, marbling score, fat color and Warner-Bratzler shear force. No significant association was detected between the c.1241C>T and measured traits. Results from this study suggested that the SNP markers may be effective for the marker-assisted selection of meat and carcass fatness quality traits, and added new evidence that DGAT1 gene is an important candidate gene for the improvement of meat and carcass fatness quality in beef cattle industry.     

DEFB1 polymorphisms are involved in susceptibility to human papillomavirus infection in Brazilian gynaecological patients

The human beta defensin 1 (hBD-1) antimicrobial peptide is a member of the innate immune system known to act in the first line of defence against microorganisms, including viruses such as human papillomavirus (HPV). In this study, five functional polymorphisms (namely g-52G>A, g-44C>G and g-20G>A in the 5’UTR and c.*5G>A and c.*87A>G in the 3’UTR) in the DEFB1 gene encoding for hBD-1 were analysed to investigate the possible involvement of these genetic variants in susceptibility to HPV infection and in the development of HPV-associated lesions in a population of Brazilian women. The DEFB1 g-52G>A and c.*5G>A single-nucleotide polymorphisms (SNPs) and the GCAAA haplotype showed associations with HPV-negative status; in particular, the c.*5G>A SNP was significantly associated after multiple test corrections. These findings suggest a possible role for the constitutively expressed beta defensin-1 peptide as a natural defence against HPV in the genital tract mucosa.     

Genetic Variants in SDC3 Gene are Significantly Associated with Growth Traits in Two Chinese Beef Cattle Breeds

Identification of the genes and polymorphisms underlying quantitative traits, and understanding these genes and polymorphisms affect economic growth traits, are important for successful marker-assisted selection and more efficient management strategies in commercial cattle (Bos taurus) population. Syndecan-3 (SDC3), a member of the syndecan family of type I transmembrane heparan sulfate proteoglycans is a novel regulator of feeding behavior and body weight. The aim of this study is to examine the association of the SDC3 polymorphism with growth traits in Chinese Jiaxian and Qinchuan cattle breeds (). Four single nucleotide polymorphisms (SNPs: 1–4) were detected in 555 cows from three Chinese native cattle breeds by means of sequencing pooled DNA samples and polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) methods. We found one SNP (g.28362A > G) in intron and three SNPs (g.30742T > G, g.30821C > T and 33418 A > G) in exons. The statistical analyses indicated that these SNPs of SDC3 gene were associated with bovine body height, body length, chest circumference, and circumference of cannon bone (P < 0.05). The mutant-type variant was superior for growth traits; the heterozygote was associated with higher growth traits compared to wild-type homozygote. Our result confirms the polymorphisms in the SDC3 gene are associated with growth traits that may be used for marker-assisted selection in beef cattle breeding programs.     

Molecular Factors Underlying the Deposition of Intramuscular Fat and Collagen in Skeletal Muscle of Nellore and Angus Cattle

Studies have shown that intramuscular adipogenesis and fibrogenesis may concomitantly occur in skeletal muscle of beef cattle. Thus, we hypothesized that the discrepancy of intramuscular fat content in beef from Nellore and Angus was associated with differences in intramuscular adipogenesis and fibrogenesis during the finishing phase. To test our hypothesis, longissimus muscle samples of Nellore (n = 6; BW = 372.5 ± 37.3 kg) and Angus (n = 6; BW = 382.8 ± 23.9 kg) cattle were collected for analysis of gene and protein expression, and quantification of intramuscular fat and collagen. Least-squares means were estimated for the effect of Breed and differences were considered at P ≤ 0.05. A greater intramuscular fat content was observed in skeletal muscle of Angus compared to Nellore cattle (P≤0.05). No differences were observed for mRNA expression of lipogenic and lipolytic markers ACC, FAS, FABP4, SERBP–1, CPT–2, LPL, and ACOX (P > 0.05) in skeletal muscle of Nellore and Angus cattle. Similarly, no differences were observed in mRNA expression of adipogenic markers Zfp423, PPARγ, and C/EBPα (P>0.05) However, a greater PPARγ protein content was observed in skeletal muscle of Angus compared to Nellore cattle (P≤0.05). A greater abundance of adipo/fibrogenic cells, evaluated by the PDGFRα content, was observed in skeletal muscle of Angus than Nellore cattle (P≤0.05). No differences in fibrogenesis were observed in skeletal muscle of Angus and Nellore cattle, which is in accordance with the lack of differences in intramuscular collagen content in beef from both breeds (P>0.05). These findings demonstrate that difference in intramuscular fat content is associated with a slightly enhanced adipogenesis in skeletal muscle of Angus compared to Nellore cattle, while no difference in fibrogenesis.     

SNP and haplotype analysis reveal IGF2 variants associated with growth traits in Chinese Qinchuan cattle

Insulin-like growth factor 2 (IGF2) is a potent cell growth and differentiation factor and is implicated in mammals’ growth and development. The objective of this study was to evaluate the effects of the mutations in the bovine IGF2 with growth traits in Chinese Qinchuan cattle. Four single nucleotide polymorphisms (SNPs) were detected of the bovine IGF2 by DNA pool sequencing and forced polymerase chain reaction–restriction fragment length polymorphism (forced PCR–RFLP) methods. We also investigated haplotype structure and linkage disequilibrium (LD) coefficients for four SNPs in 817 individuals representing two main cattle breeds from China. The result of haplotype analysis showed eight different haplotypes and 27 combined genotypes within the study population. The statistical analyses indicated that the four SNPs, combined genotypes and haplotypes are associated with the withers height, body length, chest breadth, chest depth and body weight in Qinchuan cattle population (P < 0.05 or <0.01). The mutant-type variants and mutant haplotype (Hap 8: ATGG; likely to be the beneficial QTN allele) was superior for growth traits; the heterozygote diplotype was associated with higher growth traits compared to wild-type homozygote. Our results provide evidence that polymorphisms in the IGF2 gene are associated with growth traits, and may be used for marker-assisted selection in beef cattle breeding program.