A large indel mutation of the bovine ADD1/SREBP1c gene and its effects on growth traits in some native cattle breeds from China

Adipocyte determination and differentiation-dependent factor 1/sterol regulatory element-binding protein-1c (ADD1/SREBP1c) is a major determinant of tissue differential lipogenic capacity in mammalian and avian species. The objectives of the present study were to focus on insertion-deletion polymorphism (indel) in the bovine ADD1/SREBP1c gene, and analyzing its effect on growth traits in a sample of 1035 cattle belonging to four Chinese cattle breeds. PCR-SSCP, DNA sequencing and agarose electrophoresis methods were used. The 778 bp PCR products of ADD1/SREBP1c gene exhibited three genotypes and two alleles were revealed: W and D. Frequencies of the W allele varied from 0.8651 to 1.000. The associations of the 84 bp indel mutation of ADD1/SREBP1c gene with growth traits of 265 Nanyang cows were analyzed. The animals with genotype WD had significantly higher birth weight, body weight, average daily gain than those with genotype WW at birth, 6-, 12-, 18-, and 24-month old (P < 0.05 or P < 0.01). These results suggest that the indel mutation of bovine ADD1/SREBP1c gene may influence the growth traits in cattle.     

Effect of Genetic Variations of the POU1F1 Gene on Growth Traits of Nanyang Cattle

PCR-RFLP was applied to analyze the effect of the genetic variations of the POU1F1 gene on growth traits of 100 Nanyang cattle. The results showed that the 451 bp PCR product digested with Hinf I demonstrated polymorphism in the population, which was at Hardy-Weinberg equilibrium. Moreover, the frequencies of alleles A/B in the Nanyang population were 0.465/0.535. The association of the variations of the POU1F1 gene with the growth traits in the population was analyzed. The following parameters were greater in individuals with a genotype BB than in those with an genotype AB: birth weight, average weight increase before ablactation, body height at 12 months, body weight, body length, and chest girth at 6 months and 12 months (P<0.05). The body weight at 12 months was higher in the BB individuals than in the AA individuals (P <0.05). The body weight and body sizes also showed a trend of allele B> allele A in the other age groups. Therefore, the genotype BB maybe a dominant genotype and the allele B may be a dominant allele. These results imply that the allele B of the POU1F1 gene is likely to positively affect the growth traits.     

Novel 35-bp insertion in Visfatin Gene in Chinese cattle

Visfatin is a protein that is preferentially produced in visceral adipose tissue. Both its tissue expression and secreted plasma levels increase in parallel with obesity. Therefore, the present study is focused on detecting insertion in bovine visfatin gene and analyzing its effect on growth traits in four Chinese cattle breeds (Nangyang, Qinchuan, Jiaxian, and Chinese Holstein) using PCR-SSCP, DNA sequencing and agarose electrophoresis methods. For the first time, a 35-bp insertion was described in the gene and two alleles were revealed: W and I. The x ²-test analysis demonstrated that all breeds were in agreement with Hardy-Weinberg equilibrium (P > 0.05). The associations of the novel 35 bp-insertion of visfatin gene with growth traits of Nanyang cattle at 6, 12, 18, and 24 months old were analyzed: 6 month-old cows with genotype WW had greater birth weight than cows with genotype II and WI (P < 0.01 or P < 0.05). These results suggest that the presence of 35 bpinsertion in visfatin gene may influence the birth weight and bodyweight in 6 month-old cows.     

Associations of polymorphism within the GHSR gene with growth traits in Nanyang cattle

GH secretagogue receptor (ghrelin receptor, GHSR) is known to be involved in the control of GH release by mediating the strong stimulatory effect of the endogenous ligand, ghrelin, on GH secretion. Associations between the GHSR gene polymorphism and the growth traits were revealed in Nanyang cattle. The mutations at nt456(G > A) and nt667(C > T) were complete linkage and located in exon 1 of the coding region of the GHSR gene. Least squares analysis revealed a significant statistical effect (P < 0.05) of the GHSR gene different genotypes on body weight and average daily gain at 6 months of age in Nanyang cattle. Individuals with GHSR-MM genotype showed higher body weight and average daily gain than individuals with GHSR-MN genotype.     

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.     

mRNA expression pattern and association study with growth traits of bovine vaspin gene

Visceral adipose tissue-derived serine protease inhibitor (vaspin) is an interesting novel adipocytokine with insulin-sensitizing effects. Some studies have suggested that vaspin could play an important role in the development of obesity and metabolic disorders. However, the tissue expression patterns in cattle and impact of vaspin gene variants on the growth traits has not been determined yet. Herein, we firstly investigated the tissue expression patterns of vaspin gene in new born and adult cattle. The results showed that vaspin was ubiquitously expressed in most tissues and strongly expressed in the heart, skeletal muscle and fat. Then, genetic variants within bovine vaspin gene were screened in 1235 individuals from five Chinese indigenous cattle breeds. Two novel mutations in coding region (NW_001494061: g.1124477 G>A and g.1118561 T>C) of bovine vaspin gene were identified using MspI PCR–RFLP and HhaI ACRS PCR–RFLP detection. Association analysis revealed both two mutations were significantly associated with bodyweight and chest girth at 24 months in cattle (P < 0.05). Therefore, the MspI and HhaI genetic variants of bovine vaspin gene were recommended as DNA markers related to growth traits through marker-assisted selection for genetics and breeding in cattle.     

Two Novel Coding SNPs of SREBP1c Gene are Associated with Body Weight and Average Daily Gain in Bovine

It is known that the SREBP1c gene is an important gene responsible for adipogenesis and regulation of the expression of genes controlling fatty acid biosynthesis. Its expression levels increase in parallel with obesity. Therefore, the present study focused on screening the genetic variation within bovine SREBP1c gene and analyzing its effect on growth traits in 1035 individuals belonging to four Chinese cattle breeds (QC, NY, JX, CH) using PCR-SSCP, DNA sequencing, and forced PCR-RFLP methods. The results revealed two novel mutations: NC_007317: g. 10781 C > A (457aa), 10914 G > A (502aa). Association analysis with growth traits in the Nangyang breed indicated that: The SNPs in the bovine SREBP1c gene had significant effects on body weight and average daily gain at birth, 6 and 12 months old (P < 0.05 or P < 0.01). Therefore, these results suggest that the SREBP1c gene is a strong candidate gene that affects growth traits in cattle.     

Haplotype distribution in the GLI3 gene and their associations with growth traits in cattle

The glioma-associated oncogene family zinc finger 3 gene (GLI3) mediates in all vertebrates hedgehog (Hh) signaling that plays an essential role in the induction and patterning of numerous cell types during invertebrate and vertebrate development. In this study, a total of 6 single nucleotide polymorphisms (SNPs: 1–6) were identified by polymerase chain reaction–single stranded conformational polymorphism (PCR–SSCP) and DNA pool sequencing, including all 13 exons and 12 exon–intron boundaries within the bovine GLI3 gene. 16 haplotypes and 13 combined genotypes were revealed and the linkage disequilibrium was assessed in 708 individuals representing three main cattle breeds from China. The statistical analyses indicated that the SNP2, 3 and 4 are associated with the body weight at birth and 6 months in Nanyang cattle population (P < 0.05). No significant association was detected between 11 combined genotypes and body weight at five different ages. Our results provide evidence that polymorphisms in the GLI3 gene are associated with growth traits, and may be used for marker-assisted selection in beef cattle breeding program.     

Assessment of association between variants and haplotypes of the IGF2 gene in beef cattle

Insulin-like growth factor 2 (IGF2) is a fetal growth and differentiation factor that plays an important role in muscle growth and in myoblast proliferation and differentiation. The aim of this study was to examine the association of the IGF2 polymorphism with growth traits in beef cattle breed. Four single nucleotide polymorphisms (SNPs: 1–4) were identified in the bovine IGF2 by sequencing pooled DNA samples (Pool-Seq) and forced polymerase chain reaction–restriction fragment length polymorphism (Forced PCR–RFLP) methods. The result of haplotype analysis of four SNPs showed that eight haplotypes and eighteen combined genotypes were revealed, and the linkage disequilibrium and evolutionary relationship were assessed in 1522 individuals representing four purebred cattle breeds from China. The statistical analyses indicated that the 4 SNPs and 18 combined genotypes or haplotypes are associated with the body weight at 18 and 24 months in Jiaxian cattle population (P < 0.05 or P < 0.01). 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.     

Novel SNPs in the bovine Transmembrane protein 18 gene, their linkage and their associations with growth traits in Nanyang cattle

Transmembrane protein 18 (TMEM18) gene is expressed in the central nervous system that has recently been linked to human obesity and body mass index (BMI) in genome wide association studies (GWAS). In this study, two novel single nucleotide polymorphisms (SNPs), g.3835 G > A (aa. Gly > Ser) and g.3865 A > G were detected in cattle TMEM18 gene by DNA sequencing. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and forced PCR-RFLP methods were used to genotype the two SNPs in 1218 Chinese native cattle individuals. The association between novel SNPs and growth traits (especially on body weight and body height) in Nanyang cattle showed that individuals with GG genotype was higher than those with AA genotype at g.3835G>A locus (P < 0.05) in Nanyang cattle. Significant association also revealed that individuals of AA genotype at g. 3865 A>G locus were higher in terms of body weight, average daily gain, chest circunmference, body length (P < 0.05), body height and hucklebone width (P < 0.01) than GG genotypes in Nanyang cattle. Moreover, the effect of XspI-MluI combinations with growth traits in Nanyang cattle revealed that AAGG type had higher body weight, body length, chest circumference and average daily gain (P < 0.05) than GGAG in Nanyang cattle aged at 6 months.     

A novel single-nucleotide polymorphism of thevisfatin gene and its associations with performance traits in the chicken

Visfatin is a peptide that is predominantly expressed in visceral adipose tissue and is hypothesized to be related to obesity and insulin resistance. In this study, a novel silent single-nucleotide polymorphism (SNP) was found in exon 7 of the chickenvisfatin gene (also known asPBEF1) by single-stranded conformation polymorphism (SSCP) and DNA sequencing. In total, 836 chickens forming an F₂ resource population of Gushi chicken crossed with Anka broiler were genotyped by XbaI forced RFLP, and the associations of this polymorphism with chicken growth, carcass characteristics, and meat quality were analyzed. Significant associations were found between the polymorphism and 4-week body weight (BW4), 6-week body weight (BW6), 4-week body slanting length (BSL4), fat bandwidth (FBW), breast muscle water loss rate (BWLR) and breast muscle fiber density (BFD) (P < 0.05), as well as 4-week breastbone length (BBL4) (P < 0.01). These observations suggested that the polymorphism in exon7 of thevisfatin gene had significant effects on the early growth traits of chicken.     

Candidate SNP of CACNA2D1 Gene Associated with Clinical Mastitis and Production Traits in Sahiwal (Bos taurus indicus) and Karan Fries (Bos taurus taurus × Bos taurus indicus)

The present study was conducted to identify polymorphisms in CACNA2D1 gene and their association with clinical mastitis and production traits. Exon 18 and its flanking regions were screened for the presence of SNPs. Statistical analysis was performed to identify association of period of birth, breed, and genotype with mastitis incidence on randomly selected 103 Sahiwal and 102 Karan Fries cattle. PCR-RFLP analysis revealed that g.38819398G?>?A mutation in exon 18 (269?bp amplicon) of CACNA2D1 gene resolved into AA, AG, and GG genotypes in Sahiwal and Karan Fries cattle. Wald chi-square analysis revealed that the period of birth, breed, and genotype were significantly associated with mastitis incidence. GG genotyped cattle were found to be less susceptible to mastitis. Least square analysis revealed that GG and AG genotype animals of G38819398A SNP of CACNA2D1 gene in Sahiwal as well as in Karan Fries cattle were associated with higher average milk yields during 1st, 2nd, and 3rd lactations (P?<?0.01). These observations and their differential association with the incidence of mastitis and production traits can be utilized as an aid to selection for simultaneous improvement of both antagonistic traits; however, validation of results on large number of animals is warranted.     

A novel 18-bp deletion mutation of the AMPD1 gene affects carcass traits in Qinchuan cattle

The objectives of the present study were focused on detecting deletion mutation in bovine AMPD1 gene, and analyzing its effect on body measurement and carcass traits in Qinchuan cattle by using DNA sequencing and agarose electrophoresis methods. The 198-bp PCR products of AMPD1 gene exhibited three genotypes and two alleles were revealed: A and B. The frequencies of genotype AA/AB/BB in Qinchuan populations was 0.7163, 0.2233 and 0.0605. The χ²-test analysis demonstrated that the breed was not in agreement with Hardy–Weinberg equilibrium (P < 0.05). The association of the 18-bp deletion mutation of AMPD1 gene with body measurement and carcass traits of Qinchuan cattle were analyzed. The cattle with AA genotype had slaughter weight and carcass weight than those with genotype AB (P < 0.01 or P < 0.05). These results suggest that the 18-bp deletion mutation may influence the carcass traits in Qinchuan cattle.     

Associations between newly discovered polymorphisms in the Bos taurusgrowth hormone receptor gene and performance traits in Holstein–Friesian dairy cattle

Variations in the growth hormone receptor (GHR) gene sequence are associated with performance traits in cattle. For example, the single nucleotide polymorphism (SNP) F279Y in transmembrane exon 8 has a strong association with milk yield. In this study, 32 previously unreported, putative novel SNPs (31 in the 5′ non‐coding region) were identified by resequencing ～19 kb of the GHR gene in genomic DNA from 22 cattle of multiple breeds. A population of 848 Holstein–Friesian AI sires was subsequently genotyped for the 32 putative novel SNPs and seven published SNPs (including F279Y, one in exon 1A promoter and five in exon 10). Associations between each segregating SNP and genetic merit for performance were quantified in the 848 Holstein–Friesians using weighted animal linear mixed models. Six of the published SNPs and seven of the novel SNPs were associated with at least one of the traits – milk yield, fat yield, protein yield, fat percentage, protein percentage, somatic cell score, calving interval, survival and growth and size traits. Even when the allelic substitution effect (P < 0.001) of F279Y was accounted for, the allelic substitution effect of one of the novel SNPs (GHR4.2) in the 5′ non‐coding region of GHR was associated with a lactation milk yield of 37.46 kg (P < 0.001). GHR4.2 and F279Y were not in linkage disequilibrium (r² = 0.00, D’ = 0.04) in the 848 Holstein–Friesians, indicating that their association with milk yield was independent.