SNPs

Study of lipid metabolism-related genes as candidate genes of sexual precocity in Nellore cattle

M. M. Dias, Souza, F. R. P., Takada, L., Feitosa, F. L. B., Costa, R. B., Diaz, I. D. P. S., Cardoso, D. F., Tonussi, R. L., Baldi, F., Albuquerque, L. G., and Oliveira, H. N., “Study of lipid metabolism-related genes as candidate genes of sexual precocity in Nellore cattle”, vol. 14, pp. 234-243, 2015.

The objective of this study was to identify associations between known polymorphisms in genes related to adipose tissue and sexual precocity in Nellore cattle. A total of 1689 precocious and non-precocious heifers belonging to farms participating in Conexão Delta G breeding program were studied. SNPs from the Illumina High-Density Bovine SNP BeadChip were used. This chip contains 777,000 SNPs located within the region of the candidate genes at a distance of up to 5 kb, considering that linkage disequilibrium (LD) exists at this distance.

Transcriptional co-activator PGC-1α gene is associated with chicken skeletal muscle fiber types

J. T. Shu, Xu, W. J., Zhang, M., Song, W. T., Shan, Y. J., Song, C., Zhu, W. Q., Zhang, X. Y., and Li, H. F., “Transcriptional co-activator PGC-1α gene is associated with chicken skeletal muscle fiber types”, vol. 13, pp. 895-905, 2014.

The peroxisome proliferators-activated receptor-γ coactivator-1α (PGC-1α) is a candidate gene for meat quality traits because of its prominent role in muscle fiber type switching and determination. We investigated the effects of the PGC-1α gene on chicken skeletal muscle fiber type switching and on other meat quality traits. Single nucleotide polymorphisms were detected by PCR-SSCP and DNA sequencing, and then genotyping was performed by PCR-ligation detection reaction methods.

Correlation analysis between starch properties and single nucleotide polymorphisms of waxy genes in common rye (Secale cereale L.)

M. Meng, Gao, X., Han, L. J., Li, X. Y., Wu, D., Li, H. Z., and Chen, Q. J., “Correlation analysis between starch properties and single nucleotide polymorphisms of waxy genes in common rye (Secale cereale L.)”, vol. 13, pp. 2574-2589, 2014.

To understand the relationships between single nucleotide polymorphisms (SNPs) in the waxy gene and starch parameters in common rye, we performed sequence characterization, enzyme activity testing, amylopectin/amylose ratio evaluation, starch property testing, and correlation analysis. Specific primers were used to clone waxy from 20 rye cultivars. Sequence analysis showed that waxy was 2852 bp, including 11 exons, and sequence similarity across the 20 cultivars was over 98%.

Role of XRCC1 and ERCC5 polymorphisms on clinical outcomes in advanced non-small cell lung cancer

D. Liu, Wu, J., Shi, G. Y., Zhou, H. F., and Yu, Y., “Role of XRCC1 and ERCC5 polymorphisms on clinical outcomes in advanced non-small cell lung cancer”, vol. 13, pp. 3100-3107, 2014.

We aimed to assess the role of polymorphisms of the XRCC1 Arg194Trp, XRCC1 Arg399Gln, ERCC5 His1104Asp, and ERCC5 His46His genes on clinical outcomes of advanced non-small cell lung cancer (NSCLC) patients receiving platinum-based chemotherapy regimens. A total of 378 NSCLC patients were asked to participate within 1 month after diagnosis between January 2005 and January 2006, and they were followed up until November 2011. Genomic DNA of the four genes was extracted using the Qiagen Blood Kit.

A case-control study indicates that the TRIB1 gene is associated with pancreatic cancer

X. X. Lu, Hu, J. J., Fang, Y., Wang, Z. T., Xie, J. J., Zhan, Q., Deng, X. X., Chen, H., Jin, J. B., Peng, C. H., Liu, J., Li, H. W., and Shen, B. Y., “A case-control study indicates that the TRIB1 gene is associated with pancreatic cancer”, vol. 13, pp. 6142-6147, 2014.

Pancreatic cancer is a malignant neoplasm originating from transformed cells arising in tissues that form the pancreas. To investigate whether the tribbles homolog 1 (Drosophila) gene (TRIB1) is associated with pancreatic cancer in the Chinese Han population, we conducted this case-control study and genotyped 3 single nucleotide polymorphisms (rs2980879, rs2980874, and rs2235108) of the TRIB1 gene in 182 patients and 359 normal controls of Chinese Han origin and analyzed their association.

Four SNPs of insulin-induced gene 1 associated with growth and carcass traits in Qinchuan cattle in China

Y. Liu, Liu, X. L., He, H., and Gu, Y. L., “Four SNPs of insulin-induced gene 1 associated with growth and carcass traits in Qinchuan cattle in China”, vol. 11, pp. 1209-1216, 2012.

The insulin-induced gene 1 (Insig-1) is a regulator of lipid metabolism and plays an important role in the sterol-mediated regulation of SREBP, SCAP and HMG-CoA reductase. We used PCR-RFLP and DNA sequencing to detect polymorphisms of the Insig-1 gene in 215 individuals of the Qinchuan cattle breed. Four SNPs [4366(A>G), 4534(T>C), 5001(T>C), and 5235(G>A)] were indentified. The association of the genetic viariation with growth and carcass traits (body length, withers height, hip width, slaughter weight, and carcass weight) was analyzed.

Low prevalence of glucokinase gene mutations in gestational diabetic patients with good glycemic control

H. R. Frigeri, Santos, I. C. R., Réa, R. R., Almeida, A. C. R., Fadel-Picheth, C. M. T., Pedrosa, F. O., Souza, E. M., Rego, F. G. M., and Picheth, G., “Low prevalence of glucokinase gene mutations in gestational diabetic patients with good glycemic control”, vol. 11, pp. 1433-1441, 2012.

Glucokinase (GCK) plays a key role in glucose homeostasis. Gestational diabetes mellitus increases the risk of gestational complications in pregnant women and fetuses. We screened for mutations in coding and flanking regions of the GCK gene in pregnant women with or without gestational diabetes in a Brazilian population. A sample of 200 pregnant women classified as healthy (control, N = 100) or with gestational diabetes (N = 100) was analyzed for mutations in the GCK gene.

Novel single nucleotide polymorphisms of the bovine methyltransferase 3b gene and their association with meat quality traits in beef cattle

X. Liu, Guo, X. Y., Xu, X. Z., Wu, M., Zhang, X., Li, Q., Ma, P. P., Zhang, Y., Wang, C. Y., Geng, F. J., Qin, C. H., Liu, L., Shi, W. H., Wang, Y. C., and Yu, Y., “Novel single nucleotide polymorphisms of the bovine methyltransferase 3b gene and their association with meat quality traits in beef cattle”, vol. 11, pp. 2569-2577, 2012.

DNA methylation is essential for adipose deposition in mammals. We screened SNPs of the bovine DNA methyltransferase 3b (DNMT3b) gene in Snow Dragon beef, a commercial beef cattle population in China. Nine SNPs were found in the population and three of six novel SNPs were chosen for genotyping and analyzing a possible association with 16 meat quality traits. The frequencies of the alleles and genotypes of the three SNPs in Snow Dragon beef were similar to those in their terminal-paternal breed, Wagyu.

Association of CD14 G(-1145)A and C(-159)T polymorphisms with reduced risk for tuberculosis in a Chinese Han population

M. Y. Zhao, Xue, Y., Zhao, Z. Q., Li, F. J., Fan, D. P., Wei, L. L., Sun, X. J., Zhang, X., Wang, X. C., Zhang, Y. X., and Li, J. C., “Association of CD14 G(-1145)A and C(-159)T polymorphisms with reduced risk for tuberculosis in a Chinese Han population”, vol. 11, pp. 3425-3431, 2012.

Although the role of CD14 in mediating signals from Toll-like receptors to recognize Mycobacterium tuberculosis is known, how polymorphisms in this gene affect the susceptibility to develop tuberculosis are still not clear. We examined whether single nucleotide polymorphisms at positions -1145 and -159 in the promoter region of the CD14 gene are associated with tuberculosis in a Chinese Han population in a case-control study of 432 Chinese patients with tuberculosis and 404 ethnically matched healthy controls.

Novel SNPs of the mannan-binding lectin 2 gene and their association with production traits in Chinese Holsteins

Z. L. Zhao, Wang, C. F., Li, Q. L., Ju, Z. H., Huang, J. M., Li, J. B., Zhong, J. F., and Zhang, J. B., “Novel SNPs of the mannan-binding lectin 2 gene and their association with production traits in Chinese Holsteins”, vol. 11, pp. 3744-3754, 2012.

The mannan-binding lectin gene (MBL) participates as an opsonin in the innate immune system of mammals, and single nucleotide polymorphisms (SNPs) in MBL cause various immune dysfunctions. In this study, we detected SNPs in MBL2 at exon 1 using polymerase chain reaction single-strand conformation polymorphism analysis and DNA sequencing techniques in 825 Chinese Holstein cows. Four new SNPs with various allele frequencies were also found. The g.1164 G>A SNP was predicted to substitute arginine with glutamine at the N-terminus of the cysteine-rich domain.