Single nucleotide polymorphisms

Polymorphism analysis of the intron one of insulin-like growth factor 2 receptor gene (IGF2R) in FFRC strain common carp (Cyprinus carpio L.) and its relationship with growth performance

Z. J. Dong, Su, S. Y., Zhu, W. B., Zhang, C. F., Ding, M., Chen, W. X., Yuan, X. H., and Xie, Z., “Polymorphism analysis of the intron one of insulin-like growth factor 2 receptor gene (IGF2R) in FFRC strain common carp (Cyprinus carpio L.) and its relationship with growth performance”, vol. 14, pp. 407-418, 2015.

The insulin-like growth factor 2 receptor gene (IGF2R) encodes a transmembrane protein receptor and acts to sequester and degrade excess circulating insulin-like growth factor 2, which is critical for normal mammalian growth and development. Thus, IGF2R may serve as a candidate gene underlying growth trait in the common carp. In this study, we isolated the intron one of common carp IGF2R and detected the diversity in 3 continuous generations of FFRC strain common carp.

Single nucleotide polymorphisms in the mitochondrial displacement loop and age-at-onset of non-small cell lung cancer

W. X. Hu, Ding, C. M., Li, R. J., Fan, H. Y., Guo, Z. J., and Liu, W., “Single nucleotide polymorphisms in the mitochondrial displacement loop and age-at-onset of non-small cell lung cancer”, vol. 14, pp. 2512-2517, 2015.

The associations between single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) and cancer risk and disease outcome have been extensively analyzed. We investigated the association between age-at-onset and SNPs in the mitochondrial D-loop using a population-based series of non-small cell lung cancer (NSCLC) patients. The D-loop region of mtDNA from NSCLC patients was amplified and sequenced.

Relationship between EPHX2 gene polymorphisms and essential hypertension in Uygur, Kazakh, and Han

X. L. Zhu, Wang, L., Wang, Z., Chen, S. Z., Zhang, W. Q., and Ma, M. M., “Relationship between EPHX2 gene polymorphisms and essential hypertension in Uygur, Kazakh, and Han”, vol. 14, pp. 3474-3480, 2015.

We investigated the association between rs751141 polymorphisms in the EPHX2 gene and essential hypertension in Uygur, Kazakh, and Han subjects in Xinjiang, China. A total of 302 essential hypertensive patients in Uygur, 267 in Kazakh, and 368 in Han, as well as 323 normotensive controls in Uygur, 284 in Kazakh, and 348 in Han were enrolled in this study. The TaqMan assay was used to detect the rs751141 G/A gene polymorphism in EPHX2.

Genome-wide polymorphisms between the parents of an elite hybrid rice and the development of a novel set of PCR-based InDel markers

K. Wang, Zhuang, J. Y., Huang, D. R., Ying, J. Z., and Fan, Y. Y., “Genome-wide polymorphisms between the parents of an elite hybrid rice and the development of a novel set of PCR-based InDel markers”, vol. 14, pp. 3209-3222, 2015.

Genome-wide re-sequencing of the Zhenshan 97 (ZS97) and Milyang 46 (MY46) parents of an elite three-line hybrid rice developed in China resulted in the generation of 9.91 G bases of data with an effective sequencing depth of 11.66x and 11.51x, respectively. Detection of genome-wide DNA polymorphisms, single nucleotide polymorphisms (SNPs), short insertions/deletions (InDels; 1-5 bp), and structural variations (SVs), which is an invaluable variation resource for genetic research and molecular marker-assisted breeding, was conducted by comparing whole-genome re-sequencing data.

Association of TUSC3 gene polymorphisms with non-syndromic mental retardation based on nuclear families in the Qinba mountain area of China

M. J. Zhang, Xing, L. X., Cui, M., Yang, X., Shi, J. G., Li, J., Zhang, K. J., Zheng, Z. J., Zhang, F. C., Li, J. L., and Gao, X. C., “Association of TUSC3 gene polymorphisms with non-syndromic mental retardation based on nuclear families in the Qinba mountain area of China”, vol. 14, pp. 5022-5030, 2015.

TUSC3 interacts with the protein phosphatase 1 and magnesium ion transport system, which plays an important role in learning and memory. Abnormal conditions of learning and memory are common clinical characteristics of mental retardation (MR). However, the association of TUSC3 genetic polymorphisms with MR remains unknown. A total of 456 DNA samples including 174 nuclear families containing MR were collected in the Qinba mountain area of China. The genotypes of eight tag single nucleotide polymorphisms of TUSC3 were evaluated with traditional genetic methods.

Polymorphisms in a myostatin gene and associations with growth in a hybrid of Culter alburnus and Ancherythroculter nigrocauda

L. Cheng and Sun, Y. H., “Polymorphisms in a myostatin gene and associations with growth in a hybrid of Culter alburnus and Ancherythroculter nigrocauda”, vol. 14, pp. 5615-5620, 2015.

Myostatin (MSTN) is a member of the transforming growth factor-β superfamily that negatively regulates skeletal muscle development and growth. In the present study, partial genomic frag­ments of MSTN were screened for single nucleotide polymorphisms (SNPs) in a hybrid of Culter alburnus (♀) x Ancherythroculter nigro­cauda (♂) individuals from a commercial hatchery population, and two non-synonymous SNPs (c.6T>C and c.162G>A) and two synonymous SNPs (c.152G>A and c.155G>A) in exon 2 were identified.

FSHR gene Thr307Ala and Asn680Ser polymorphisms in infertile men: an association study in North China and meta-analysis

X. Q. Wu, Xu, S. M., Wang, Y. Q., Li, Q., Wang, Z. Q., Zhang, C. L., and Shen, Y., “FSHR gene Thr307Ala and Asn680Ser polymorphisms in infertile men: an association study in North China and meta-analysis”, vol. 14, pp. 5592-5601, 2015.

Male infertility is a complex multifactorial and polygenic disease, and genetic factors play an important role in its formation and development. Recently, the association between follicle stimulating hormone receptor (FSHR) gene polymorphisms and male infertility risk has attracted widespread attention due to the unique biological functions of FSH. The aim of this study was to further explore the associations between the Thr307Ala and Asn680Ser polymorphisms of the FSHR gene and male infertility.

Association between polymorphisms in exons 4 and 10 of the BPI gene and immune indices in Sutai pigs

Z. C. Wu, Liu, Y., Zhao, Q. H., Zhu, S. P., Huo, Y. J., Zhu, G. Q., Wu, S. L., and Bao, W. B., “Association between polymorphisms in exons 4 and 10 of the BPI gene and immune indices in Sutai pigs”, vol. 14, pp. 6048-6058, 2015.

The bactericidal/permeability-increasing protein (BPI) gene has been identified as a candidate gene for disease-resistance breeding. We evaluated whether polymorphisms in exons 4 and 10 of the BPI gene are associated with immune indices [interleukin-2 (IL-2), IL-4, IL-6, interferon-b (IFN-b), IL-10, and IL-12]. In this study, we identified one mutation (C522T) in the BPI exon 4 site and two mutations (A1060G and T1151G) in the BPI exon 10 site.

Association study of c.910A>G and c.1686C>G polymorphisms in XRCC1 gene with risk of hepatocellular carcinoma in the Chinese population

W. F. Xia, Ma, X. P., Li, X. R., Dong, H., and Yi, J. L., “Association study of c.910A>G and c.1686C>G polymorphisms in XRCC1 gene with risk of hepatocellular carcinoma in the Chinese population”, vol. 13, pp. 1314-1322, 2014.

XRCC1 (human X-ray repair complementing defective repair in Chinese hamster cell 1) gene is considered a potentially important gene influencing the risk of hepatocellular carcinoma (HCC). Our analyses detected two allelic variants of XRCC1, c.910A>G and c.1686C>G. We aimed to investigate whether these polymorphisms influence the risk of HCC. The association between the XRCC1 polymorphisms and the risk of HCC was analyzed in 719 patients and 662 controls by polymerase chain reaction-restriction fragment length polymorphism.

Adjacent SNPs in the transcriptional regulatory region of the FADS2 gene associated with fatty acid and growth traits in chickens

S. K. Zhu, Tian, Y. D., Zhang, S., Chen, Q. X., Wang, Q. Y., Han, R. L., and Kang, X. T., “Adjacent SNPs in the transcriptional regulatory region of the FADS2 gene associated with fatty acid and growth traits in chickens”, vol. 13, pp. 3329-3336, 2014.

Delta-6 fatty acid desaturases are rate-limiting desaturases involved in metabolic processes of fatty acids, and they are encoded by the FADS2 gene. In the current study, an F2 resource population of Gushi chickens crossed with Anak broilers was used to investigate the genetic effects of the chicken FADS2.

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