Characteristics Of Single Nucleotide Polymorphisms Research Articles

Genome-wide association study reveals candidate genes critical for skin pigmentation in common carp (Cyprinus carpio) strains including koi

The differentiation and variation of body color in fish is an important component of biological evolution and phylogenetic research, and is influenced by several factors such as heredity, nutrition, physiological hormones and rearing conditions, with heredity being the most critical factor. An improved comprehension of the genetic regulation in different carp populations will facilitate future applications of precision breeding and pigment cell development-related genes editing. In this study, we used restriction site-associated DNA sequencing (2d-RAD) to determine the distribution characteristics of single nucleotide polymorphisms (SNPs) in eight common carp strains including six koi strains, i.e., Kohaku (Hb), Taisho (Dz), Showa (Zh), Golden (Hj), Matsukawabake (Sch) and Five-color (Ws), and two genetically improved breeding strains, i.e., FFRC No. 2 strain (Fr) and red FFRC strain (Hfr), and then SNP markers to resolve genetic information on the population structure and skin color formation of these strains. We found that most individuals of eight strains were clearly divided into eight clades. Genetic diversity within Fr, Sch and Ws is relatively high, while it is low within Dz, Hb and Hfr. A comparison between the populations revealed that Hfr and Ws have the highest degree of genetic differences, while Hb and Dz have the lowest. The GWAS analysis for two strategies identified several SNPs that are significantly related to skin color variation and affect melanin synthesis (ephrinb2, slc22a23, herc2, ephb2), carotenoid metabolism (oca2, bcmo1, bco2) and circadian rhythm(cipc). To summarize, our study provides some information on the genetic structure and diversity of Japanese koi and Chinese FFRC carp. Furthermore, based on the data obtained on relevant genes related to skin color differentiation and pigmentation, it can provide a theoretical basis for the subsequent integration of dominant traits and precision breeding in carps.

Two genetic variants in the SRD5A2 gene are found to be associated with sex differences in the disease characteristics of patients with chronic hepatitis B virus infection

BackgroundTo examine the expression characteristics of single nucleotide polymorphisms (SNPs) in the SRD5A2 gene and investigate their potential association with differences in the clinical characteristics between sexes in patients with chronic hepatitis B virus (HBV) infection.MethodsA total of 30 loci in six genes primarily involved in the metabolism and signaling of sex hormones/sex hormone receptors, namely AKR1C2, AKR1C3, HSD17B6, SRD5A1, SRD5A2, and ESR1, were genotyped in 1007 patients from eight counties (cities) in Northeastern China with chronic HBV infection and 1040 healthy controls, and their association with viral replication characteristics and the differences in disease severity between sexes was assessed. Western blotting was conducted to determine the hepatic SRD5A2 protein level and its relationship with the inflammatory activity and fibrosis degree in male and female patients.ResultsTwo SNP loci in the SRD5A2 gene (rs12470143 and rs7594951) exhibited significant differences in genotype and allele frequencies between sexes, with the proportion of T alleles significantly higher in males than in females. It was found that the incidence and severity of HBV-related liver fibrosis were significantly higher in patients with the T/T genotype in SRD5A2 rs12470143 and rs7594951 than those with the non-T/T genotype. Additionally, serum HBV DNA levels were significantly elevated in T/T patients compared to non-T/T patients. Female patients exhibited significantly lower serum DNA levels compared to male patients. Western blot analysis indicated that greater hepatic SRD5A2 protein levels were associated with higher METAVIR inflammation and fibrosis scores. Furthermore, multivariate analysis showed that the two genetic variants in the SRD5A2 gene (rs12470143 C > T, r7594951 C > T), together with the male sex, age > 50 years old, HBeAg positive status, elevated serum HBsAg load, high serum HBV DNA load, and HBV genotype C, were independent risk factors for HBV-related liver fibrosis.ConclusionsThis study demonstrated that two genetic variants in the SRD5A2 gene (rs12470143 C > T, r7594951 C > T) are associated with sex differences in the clinical characteristics of patients with chronic HBV infection.

Self-similar characteristics of single nucleotide polymorphisms in the rice genome

With single nucleotide polymorphism (SNP) data from the 3,000 rice genome project, we investigate the mutational characteristics of the rice genome from the perspective of statistical physics. From the frequency distributions of the space between adjacent SNPs, we present evidence that SNPs are not spaced randomly, but clustered across the genome. The clustering property is related to a long-range correlation in SNP locations, suggesting that a mutation occurring in a locus may affect other mutations far away along the sequence in a chromosome. In addition, the reliability of the existence of the long-range correlation is supported by the agreement between the results of two independent analysis methods. The highly-skewed and long-tailed distribution of SNP spaces is further characterized by a multi-fractal, showing that SNP spaces possess a rich structure of a statistical self-similarity. These results can be used for an optimal design of a microarray assay and a primer, as well as for genotyping quality control.

Relationship between polymorphisms and haplotypes of RET gene and Hirschsprung's disease.

Objective To study the relationship between polymorphisms of RET gene and the incidence of Hirschsprung's disease, investigate the haplotypes of RET gene in patients with Hirschsprung's disease, and analyze the characteristics of single nucleotide polymorphisms of RET gene in Zhejiang Han population. Methods Peripheral blood samples were collected from 123 patients with Hirschsprung's disease and 194 healthy children from 2005 to 2007 at Children's Hospital of Zhejiang University. G enomic DNA was extracted from the peripheral blood, and the genotypes were analyzed using polymerase chain reaction and direct sequencing. The frequencies of haplotypes were estimated using the PHASE software. The frequencies of RET alleles of the 194 healthy children were compared with those of other races. The correlation between RET gene and Hirschsprung's disease was analyzed using the chi-square test, and it was expressed in the form of odds ratio and 95% confidence interval.Results Increased risk of Hirschsprung's disease was observed in homozygous genotypes of the RET alleles -5AA, - 1CC, c135AA and c2307GG when compared with other genotypes ( x2 =57. 775, 20.469, 57. 040,38. 869, P ＜ 0. 05 ). Increased risk of Hirschsprung's disease was also observed in RET alleles -5A, - 1 C,c135A, c2307G when compared with other alleles ( x2 = 85.114, 53.117, 77. 005, 70. 161, P ＜0.05). There was no relationship between the frequencies of the alleles and the types of Hirschsprung's disease ( x2= 0.048,0.265, 0. 395, 0.027, P ＞ 0.05 ). The percentage of patients with haplotype ACAG was 75.2%, which was significantly higher than that of 38.7% in healthy children ( x2 = 62. 776, P ＜ 0.05 ). The frequencies of Hirschsprung's disease-associated alleles of RET - 5A, c135A and c2307G in Chinese were significantly higher than thosein the Caucasians or Yorubas (P＜0.05). Conclusions RET -5G＞A, -1A ＞C, c135G＞A and c2307T ＞ G are associated with Hirschsprung's disease and haplotype ACAG is the core one in Zhejiang Han population. There is no relationship between the frequency of allele and the types of Hirschsprung's disease. The frequencies of alleles of RET -5A, c135A and c2307G in Chinese are significantly higher than those in the Caucasians or Yorubas. Key words: Hirschsprung's disease; RET gene; Polymorphism; Haplotype