Combined Haplotypes of CaSR Gene Sequence Variants and Their Associations with Growth Traits in Cattle

The calcium-sensing receptor (CaSR) is a Class C G-protein coupled receptor that regulates food intake and assimilation. However, studies on the relationship between CaSR gene and growth traits in cattle are deficient. The aim of this study was to examine the association of the CaSR polymorphism with growth traits in cattle breeds. Four novel single nucleotide polymorphisms (SNPs) and one previously reported SNP (NC_007299.5: g.67630865T>C, 67638409G>C, 67660395G>C, 67661546C>G, and 67661892A>C) were identified in the bovine CaSR gene using DNA sequencing and PCR-SSCP methods in 520 individuals from three representative breeds. The three SNP P4_2, P7_1, and P7_4 in LX, QC, and JX cattle populations belonged to intermediate genetic diversity (0.25?相似文献   

Novel SNPs of the bovine <Emphasis Type="Italic">GAD1/gad67</Emphasis> gene and their association with growth traits in three native Chinese cattle breeds

In this study, polymorphism in the exon 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and 11 of bovine NUCB2 gene was detected by PCR-SSCP and DNA sequencing methods in 686 individuals from three Chinese cattle breeds. Two haplotypes (M and N), three observed genotypes (MM, MN and NN) and two SNPs (NC_007313: g. 27451G>A, NC_007313: g. 27472T>C) were detected. The frequencies of haplotypes M and N in inland Chinese three breeds were 0.531–0.721 and 0.279–0.469 respectively. The studied showed that Nanyang, Jiaxian Red and Qinchuan cattle populations were in Hardy–Weinberg equilibrium at SNPs locus of NUCB2 gene (P > 0.05). Polymorphism of the NUCB2 gene was shown to be associated with growth traits in Qingchuan and Nanyang cattle breed. The linkage of two mutant sites in the bovine NUCB2 gene had significant effects on body length, body weight, heart girth, and average daily gain at 24 months (P < 0.05). Results of this study suggested that the NUCB2-gene-specific SNP may be a useful marker for growth traits in future marker-assisted selection programmes in inland Chinese cattle.     

Novel SNPs of the bovine <Emphasis Type="Italic">NUCB2</Emphasis> gene and their association with growth traits in three native Chinese cattle breeds

In this study, polymorphism in the exon 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and 11 of bovine NUCB2 gene was detected by PCR-SSCP and DNA sequencing methods in 686 individuals from three Chinese cattle breeds. Two haplotypes (M and N), three observed genotypes (MM, MN and NN) and two SNPs (NC_007313: g. 27451G>A, NC_007313: g. 27472T>C) were detected. The frequencies of haplotypes M and N in inland Chinese three breeds were 0.531–0.721 and 0.279–0.469 respectively. The studied showed that Nanyang, Jiaxian Red and Qinchuan cattle populations were in Hardy–Weinberg equilibrium at SNPs locus of NUCB2 gene (P > 0.05). Polymorphism of the NUCB2 gene was shown to be associated with growth traits in Qingchuan and Nanyang cattle breed. The linkage of two mutant sites in the bovine NUCB2 gene had significant effects on body length, body weight, heart girth, and average daily gain at 24 months (P < 0.05). Results of this study suggested that the NUCB2-gene-specific SNP may be a useful marker for growth traits in future marker-assisted selection programmes in inland Chinese cattle.     

Back fat thickness and meat tenderness are associated with a 526 T→A mutation in the exon 1 promoter region of the MyF-5 gene in Chinese Bos taurus

Qualitative trait loci (QTL) for growth and meat quality traits in cattle (Bos taurus) have been previously mapped to three chromosome regions, 0 to 30, 55 to 70, and 70 to 80 cM on chromosome 5. We evaluated the allele frequencies and gene-specific single nucleotide polymorphisms (SNPs) of bovine myogenic factor 5 (MyF-5) in the QTL regions and their associations with live weight and meat characteristics in indigenous Chinese cattle breeds. PCR-SSCP methodology showed a T>A mutation at 526 bp. Least square analysis revealed a significant association of this SNP with backfat thickness and meat tenderness (P < 0.05), while no significant association was found with live weight, loin eye height, loin eye area, rib area, or water holding capacity. Allele frequencies of MyF-5-A/B in the five breeds were 0.760/0.239, 0.752/0.247, 0.629/0.370, 0.715/0.284, and 0.750/0.250, for JiaXian red, Luxi, Nanyang, Qinchuan, and XiaNan crossbreed, respectively. The genotype distributions for these alleles in two of the Chinese cattle breeds (Luxi and Qinchuan) were not in Hardy-Weinberg equilibrium (P < 0.05); while those for the other three breeds (JiaXian red, Nanyang, and XiaNan) were in agreement with Hardy-Weinberg equilibrium (P > 0.05). The genotypic frequencies among all five cattle breeds showed moderate diversity (0.25 < polymorphism information content < 0.5). Based on our findings, we suggest that the MyF-5 gene influences back fat thickness and meat tenderness in Chinese Bos taurus. This SNP could be useful for marker-assisted selection for meat quality traits in these cattle.     

Detection of Bovine Central Nervous System Tissue as Bovine Spongiform Encephalopathy Risk Material by Real-Time Reverse Transcriptase-PCR in Raw and Cooked Beef Products

PCR-SSCP and DNA sequencing methods were applied to reveal single nucleotide polymorphisms (SNPs) in the bovine VEGF-B gene in 675 samples belonging to three native Chinese cattle breeds. We found 3 SNPs and a duplication NC_007330.5: g. [782 A>G p. (Gly112 =) (;) 1000-1001dup CT (;) 1079 C>T (;) 2129 G>A p. (Arg184Gln)]. We also observed a statistically significant association of the polymorphism (1000-1001dup CT) in intron 3 of the VEGF-B gene with the body weight of the Nanyang cattle (p < 0.05). This polymorphisms of VEGF-B gene need to be verified among a larger cattle population before it can be identified as a marker for bovine body weight.     

Haplotype combination of SREBP-1c gene sequence variants is associated with growth traits in cattle

The aim of this study was to examine the association of the SREBP-1c polymorphism with growth traits in cattle breeds. Five sequence variants (SVs) were identified within the bovine sterol regulatory element-binding protein-1c gene (SREBP-1c), using DNA sequencing, PCR, PCR–RFLP, and forced PCR–RFLP methods. These polymorphisms include three missense mutations (SV1, SV4, and SV5) in exons 7, 9, and 12, a silent mutation (SV3) in exon 9, and a large deletion (SV2) in intron 7. Overall, we report the validation of polymorphisms within the bovine SREBP-1c gene, and the haplotype variability and extent of linkage disequilibrium (LD) in 1061 individuals representing the five main cattle breeds from China. We also investigated haplotype frequencies and LD coefficients for five SVs in all study populations. LD and haplotype structure of SREBP-1c were different between breeds. The result of haplotype analysis of five SVs showed that 27 different haplotypes were identified by all breeds. Two haplotypes (Hap1 and Hap2) shared by all five populations accounted for 42.75%, 35.68%, 36.44%, 25.43%, and 96.26% of all haplotypes observed in the cattle breeds Nanyang, Qinchuan, Jiaxian, Jinnan, and Chinese Holstein, respectively. The statistical analyses indicated that one single SV and 38 combined haplotypes were significantly associated with growth traits in the Nanyang cattle population (P < 0.05 or P < 0.01). The results of this study suggest that the SREBP-1c gene possibly is a strong candidate gene that affects growth traits in the Chinese beef cattle breeding program.     

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.     

Identification and genetic effect of haplotype in the bovine BMP7 gene

Bone morphogenetic proteins (BMPs) are peptide growth factors belonging to the transforming growth factor-beta (TGF-β) superfamily, and some members of the BMP family support white adipocyte differentiation. In this study, we focused on the BMP7 which singularly promotes the differentiation of brown preadipocytes. Haplotypes involving 5 single nucleotide polymorphism (SNP) sites in the bovine BMP7 gene were identified and their effect on body weight was analyzed. 16 haplotypes and 18 combined haplotypes were revealed and the linkage disequilibrium was assessed in the cattle population with 602 individuals representing three main cattle breeds from China. The results showed that haplotypes 3, 10 and 14 were predominant and accounted for 75.64%, 69.85%, and 83.36% in Nanyang, Qinchuan and Jiaxian cattle breeds, respectively. The statistical analyses indicated that the SNP 1, 4, and 5 are associated with the body weight, body length, and heart girth at 12 and 24 months in Nanyang cattle population (P < 0.05), whereas there is no significant association between their 16 haplotypes and 18 combined haplotypes. Our results provide evidence that some SNPs and haplotypes in BMP7 are associated with growth traits, and may be utilized as a genetic marker in marker-assisted selection for beef cattle breeding programs.     

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.     

Sequence variants in the bovine PRDM16 gene associated with body weight in Chinese cattle breeds

As a zinc-finger protein, PR domain containing 16 (PRDM16) controls brown fat determination by stimulating brown fat cell production while suppressing the expression of genes for production of white fat cells; mutations in this domain are associated with myelodysplastic syndrome and leukemogenesis. In our study, polymorphisms in exons 2, 3, 4, 5, 7, 8, and 9 of the PRDM16 gene were detected by PCR-SSCP, DNA sequencing and CRS-PCR-RFLP methods in 1031 cattle of the Chinese breeds: Jiaxian, Nanyang, Qinchuan, and Chinese Holstein. Three mutations (NC_007314.3: g.577 G>T, 614 T>C, 212237 T>C) were detected. Animals with the homozygote genotype had lower body weight and average daily gain than those with the other genotypes. PRDM16 gene-specific SNPs may be useful markers for growth traits for marker-assisted selection programs.     

Genetic Variant of MYLK4 Gene and its Association with Growth Traits in Chinese Cattle

As a member of MYLK family, MYLK4 gene may play a vital role in muscle development. In this study, one novel single-nucleotide polymorphism (SNP) was identified the bovine MYLK4 by sequencing pooled DNA samples (pool-Seq) and forced polymerase chain reaction-restriction fragment length polymorphism (forced PCR-RFLP) methods. Overall, we reported one mutation (SNP1) in the intron 10 region within the bovine MYLK4 gene in 559 individuals representing five main cattle breeds from China (Nanyang, NY; Qinchuan; Jiaxian, JX; Pinan cattle; and Caidamu cattle, CDM). Genotype AA and allele A were predominant in the QC, PN, and XN populations. Association analysis with growth traits in the QC breed showed that the animals with genotype GG had significantly greater chest breadth and hip width (P?<?0.05). Meanwhile, the genotype GG was strongly associated with withers height and body length than those with genotype AA (P?<?0.01 or P?<?0.05) at 12 months in the NY breed. These statistical results exhibited that the MYLK4 gene might be a potential candidate gene to improve cattle’s growth traits, and the SNP could be used as molecular markers in early marker-assisted selection (MAS) in beef cattle breeding program.     

Novel genetic variants of sine oculis homeobox homolog 3 gene are associated with body weight and average daily gain in Bos taurus

Sine oculis homeobox homolog 3 (Six3) gene is responsible for normal mammalian pituitary development, and its genetic variations or deficiency will cause hypopituitarism, suggesting that this gene is a potential candidate gene for studying association with growth traits in animals. Herein, genetic variants within bovine Six3 gene was screened in 1031 individuals from four Chinese indigenous cattle breeds. Two novel polymorphisms (NC_007309:g.2515G>A and NC_007309:g.2607T>C) locating at positions nt1707 and nt1799 of intron 1 in bovine Six3 gene, were found, and could be genotyped by TaqI ACRS PCR-RFLP and Alw26I PCR-RFLP, respectively. The frequencies of allele “A” of TaqI locus varied from 0.004 to 0.309, as well as the frequencies of allele “C” of Alw26I locus waved from 0.025 to 0.340. Association analysis revealed no significant association of TaqI locus with growth traits in Nanyang breed. However, significant relationships between Alw26I locus and body weight (BW) and average daily gain (ADG) in Nanyang breed was found (p<0.05). The individuals with genotype TC had greater body weight and average daily gain than those with genotype TT at 18 months old. Furthermore, based on combinated genotypes from these two loci, diplotypes was found to be associated with growth traits (p<0.05).The individuals with dihaplotype GG-TC had greater body weight and average daily gain at 18 month-old than those of other dihaplotypes. Therefore, the TaqI and Alw26I genetic variants of bovine Six3 gene were recommended as DNA markers related to growth traits through marker-assisted selection for genetics and breeding 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.     

A TaqI PCR-RFLP Detecting a Novel SNP in Exon 2 of the Bovine POU1F1 Gene

PCR-SSCP and DNA sequencing methods were applied to reveal three novel single nucleotide polymorphisms (SNPs) in exon 2 of the POU1F1 gene in 963 Chinese cattle belonging to eight breeds. Among them, a silent SNP (NM_174579:c.545G > A) detected by TaqI endonuclease is described. Frequencies of the POU1F1-G allele varied from 0.685 to 1.000. The association of TaqI polymorphism with growth traits was analyzed in 251 Nanyang cattle. No significant associations of the TaqI polymorphism with body weight and average daily gain for different growth periods (6, 12, 18, and 24 months old) were observed (P > 0.05), as well as for body sizes (P > 0.05).