[Show abstract][Hide abstract] ABSTRACT: We looked for novel genetic variations within the Six6 gene by PCR-SSCP, DNA sequencing and forced RFLP-PCR and estimated their associations with production traits in 2132 goats of eight indigenous Chinese breeds. A novel single nucleotide polymorphism (NM_001104993.1: g.232T>C) within the goat Six6 gene was identified. The frequencies of allele "C" varied from 0.8621 to 1.000, which were in Hardy-Weinberg equilibrium. Genotype and allele frequencies were found to be significantly different in the breeds. Association analysis revealed a significant relationship between genotypes and cannon circumference in Hainan black goats (P = 0.047); adult individuals with genotype CT showed higher cannon circumference than those with genotype CC. Another significant association of genotypes with five-year-old fiber length was found in Inner Mongolia white cashmere goats (P = 0.002). In addition, individuals with genotype CT had longer fiber length than those with genotype CC. The data revealed that the Six6 gene positively affects growth traits and cashmere traits. Polymorphism of Six6-PstI could be useful as a DNA marker for goat breeding and genetics via marker-assisted selection.
[Show abstract][Hide abstract] ABSTRACT: As a transcriptional regulatory gene of the SIX family, SIX6 (also known as OPTX2, SIX9), probably affects pituitary development and secretion of hormones, suggesting that this gene is a potential candidate gene for studying association with growth trait in animals. Therefore, this study is first of all focused on detecting sequence variations in a bovine SIX6 gene and on its effects on growth traits in 1087 cattle from five Chinese cattle breeds using DNA sequencing and HhaI-ACRS-PCR methods. Herein, a novel mutation (NC_007308: g 2015T > C) in the TGA stop-codon of a bovine SIX6 gene was found, which leads to an ORF shift and extension of the encoded protein for four amino acids (Arg223-Gln224-Arg225-Val226). The frequency of allele "C" varied from 0.255 (Chinese Holsteins) to 0.614 (Hasake). They all were in the Hardy-Weinberg equilibrium except Jiaxian Red and Hasake cattle. Using amino acid sequence alignment and online prediction software, a new helix in the C-terminal domain of the mutated bovine SIX6 protein was revealed, which possibly affects pituitary development and hormone secretion. So, relationship analysis between this polymorphism and growth traits in the Nanyang breed was carried out based on a proper linear model. Although no statistically significant associations were observed (P > 0.05), the presented work preliminarily demonstrated a novel mutation in the TGA stop-codon which extends the spectrum of genetic variations of the bovine SIX6 gene and might be of interest in terms of its association with other biophysical and biochemical indexes.
[Show abstract][Hide abstract] ABSTRACT: The Kruppel-like factor KLF7 gene was studied as a candidate for genetic markers of growth traits. We investigated the growth traits at different ages of 1002 Chinese cattles belonging to four breeds and applied artificially created restriction site (ACRS)-PCR-RFLP and DNA sequencing methods to reveal three SNPs: NC_007300:g.41401C>T (p.F54F), 42025T>C and 42075A>G. The statistical results indicated there was a strong linkage not only between C41401T and T42025C in Jiaxian, but also between T42025C and A42075G in Qinchuan, Nanyang and Chinese Holstein respectively (r2>0.33). Significant statistical differences in genotypic frequencies at the three loci displayed that the polymorphisms were remarkably correlated with cattle breeds by χ2 test (P
[Show abstract][Hide abstract] ABSTRACT: As a zinc-finger protein, PR domain containing 16 (PRDM16) controls brown fat determination by stimulating brown fat-selective genes expression while suppressing the expression of genes selective for white fat cells, whose mutations were associated with myelodysplastic syndrome (MDS) and leukemogenesis in human and murine model of leukemia. To date, no polymorphisms of PRDM16 gene in bovine had been reported. Herein, PCR-SSCP and DNA sequencing methods were employed to screen the genetic variation within PRDM16 gene in 1031 Chinese indigenous bovine. The results revealed two novel silent mutations: XM_001788152: m.1641T>C (547aa), 1881G>A (627aa). Hence, we described the PvuII and HaeIII forced PCR-RFLP methods for detecting these mutations, respectively. In the forced PCR-RFLP analysis with PvuII, the frequencies of bovine PRDM16-C allele varied from 0.044 to 0.506 in four Chinese native breeds. In the forced PCR-RFLP analysis with HaeIII, the frequencies of bovine PRDM16-G allele were 0.474, 0.494, 0.576 and 0.906 for Jiaxian (JX), Nanyang (NY), Qinchuan (QC) and Chinese Holstein (CH) population. Significant statistical differences between genotypic frequencies implied that both of the polymorphic loci were significantly associated with cattle breeds by the chi square test (chi2 = 190.058, P < 0.001 and chi2 = 118.239, P < 0.001 for PvuII; chi2 = 209.842, P < 0.001 and chi2 = 108.711, P < 0.001 for HaeIII). The associations of the PvuII and HaeIII forced PCR-RFLPs of bovine PRDM16 loci with growth traits were analyzed in Nanyang breed. The two SNPs were associated with body weight and average daily gain in Nanyang aged 12 months, individuals with genotype TT and AA showed significantly better body weight (P < 0.05) and average daily gain (P < 0.01) at 12 months, respectively.