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Associations of six SNPs of POU1F1-PROP1-PITX1-SIX3 pathway genes with growth traits in two Chinese indigenous goat breeds

gene expression of growth hormone, prolactin, and thyrotropin. Endocrin. Metab. Clin., 25: 523-540. Daga C., Paludo M., Luridiana S., Mura M.C., Bodano S., Pazzola M., Dettori M.L., Vacca G.M., Carcangiu V. (2013). Identification of novel SNPs in the Sarda breed goats POU1F1 gene and their association with milk productive performance. Mol. Biol. Rep., 40: 2829-2835. Emigh T.H. (1980). Acomparison of tests for Hardy-Weinberg equilibrium. Biometrics, 36: 627-642. Fang X.T., Xu H.X., Zhang C.L., Zhang J.M., Lan X.Y., Gu C

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Detection of single nucleotide polymorphisms at major prolificacy genes in the Mehraban sheep and association with litter size

Abstract

The present study aimed to investigate the presence of polymorphisms at four known genes controlling ovine prolificacy i.e. BMP15, GDF9, BMPR1B and B4GALNT2 in a sample of 115 Iranian Mehraban ewes and their association with litter size (LS) and lambs’ birth weight (BW) traits. Using Sanger sequencing of exons and polymorphism specific genotyping, ten SNPs (Single Nucleotide Polymorphisms) were observed in only two genes, GDF9 and BMPR1B. Seven SNPs were found in the GDF9 gene on the chromosome 5. Among them, six were already described in the coding sequence, and a new one (g.41840985C>T) was found in the 3’UTR. In the BMPR1B gene on the chromosome 6, three novel SNPs were detected in the exon 7 (g.29382184G>A; g.29382337G>A and g.29382340G>A). Allelic frequencies were established for six SNPs among the ten identified and they were in Hardy-Weinberg equilibrium. A significant association was found between the novel SNPs found in the exon 7 of BMPR1B and LS. Present results indicate the potential role of the BMPR1B locus in controlling prolificacy of Mehraban sheep and provide genetic markers for further exploitation in selection to improve reproductive efficiency.

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RTN4 AND FBXL17 GENES ARE ASSOCIATED WITH CORONARY HEART DISEASE IN GENOME-WIDE ASSOCIATION ANALYSIS OF LITHUANIAN FAMILIES

ABSTRACT

Coronary heart disease (CHD) is a complex and heterogeneous cardiovascular disease. There are many genome-wide association studies (GWAS) performed worldwide to extract the causative genetic factors. Moreover, each population may have some exceptional genetic characteristic. Thus, the background of our study is from the previous Lithuanian studies (the LiVicordia Project), which demonstrated the differences of the atherosclerosis process between Lithuanian and Swedish male individuals. In this study we performed GWAS of 32 families of Lithuanian origin in search of significant candidate genetic markers [single nucleotide polymorphisms (SNPs)] of CHD in this population. After careful clinical and biochemical phenotype evaluation, the ~770K SNPs genotyping (Illumina HumanOmniExpress- 12 v1.0 array) and familial GWAS analyses were performed. Twelve SNPs were found to be significantly associated with the CHD phenotype (p value <0.0001; the power >0.65). The odds ratio (OR) values were calculated. Two SNPs (rs17046570 in the RTN4 gene and rs11743737 in the FBXL17 gene) stood out and may prove to be important genetic factors for CHD risk. Our results correspond with the findings in other studies, and these two SNPs may be the susceptibility loci for CHD

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Association of Single Nucleotide Polymorphism in Chromosome 11 with Autism Spectrum Disorder

Abstract

Several genetic loci in chromosomes 11 and 15 have recently been associated with non-syndromic autism spectrum disorder (ASD) in populations from North America and Europe. The aim of the present study was to investigate whether such an association exists in a Latvian population. Ninety-five patients with ASD in the age range 3–20 years (mean age 8 years, SD 3.18) participated in the study. The control group consisted of 161 healthy, non-related individuals without ASD randomly selected from the Latvian Genome Database. Four single nucleotide polymorphisms (SNPs) — rs11212733, SNP rs1394119, rs2421826, rs1454985 — were genotyped by the TaqMan method. Allele frequency differences between ASD patients and control subjects were compared for each SNP using a standard chi-square test with Bonferroni correction. The level of statistical significance was set at 0.05 for nominal association. Only the genetic marker rs11212733, localised on the long arm of chromosome 11 in locus 22.3, was found to be strongly associated with the ASD patient group (χ2 6.982, Padjusted 0.033, odds ratio 1.625). Our data demonstrating a significant relationship between the SNP rs11212733 and the development of ASD in a Latvian population suggest that it is not a population-specific relationship. Thus, future studies focusing on the DDX10 gene and related genetic loci are needed.

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Relationship between vitamin D receptor gene polymorphisms and anemia in postmenopausal Vietnamese women

Abstract

Background: Both in vitro and in vivo studies have shown that calcitriol, the active form of vitamin D, is involved in hematopoiesis. Vitamin D receptor (VDR) gene has been suggested as one of the candidate genes for anemia. Objective: Investigate relationship between anemia and the commonly studied polymorphisms of VDR gene (FokI, BsmI, ApaI and TaqI) in terms of genotype and haplotype in Vietnamese. Methods: A case-control study including 132 postmenopausal women without chronic kidney diseases was designed to investigate the relationship between VDR polymorphism and anemia. Four single nucleotide polymorphisms (SNPs) FokI (rs2228570), BsmI (rs1544410), ApaI (rs7975232), and TaqI (rs731236) were typed by polymerase chain reaction and restriction fragment length polymorphism method. Results: Genotype distributions of four SNPs were in Hardy-Weinberg equilibrium in both anemia and control groups. The SNPs at the 3’end of the VDR gene (BsmI, ApaI and TaqI) exhibited a strong linkage disequilibrium. There was no significant association between anemia and VDR polymorphism in terms of allele, genotype, and haplotype in the analyses unadjusted or adjusted for the covariates (age, body mass index, educational level, serum ferritin, iron and albumin). Conclusion: VDR gene did not influence anemia in postmenopausal women without chronic kidney disease. For further study on the association between VDR gene and anemia, the use of larger sample size, a prospective study design, and additional markers would enhance the reliability and validity of findings.

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The Association Between Novel Polymorphisms of Gremlin Genes and Egg-Laying Performance Traits in Chinese Village Dagu Hens

differentiation factor-9 genes with egg production traits in local chinese Dagu hens. Poultry Sci., 94: 88-95. Qu L.J., Wu G.Q., Li X.Y., Yang N. (2004). Conservation efficiency of local chicken breeds in different farms as revealed by microsatellite markers. Yi Chuan Xue Bao., 31: 591-595. Rothschild M.F., Soller M. (1997). Candidate gene analysis to detect genes controlling traits of economic importance in domestic livestock. Probe, 8: 13-20. Sambrook J., Russell D.W. (2001). Molecular Cloning: A Laboratory Manual, 3rd ed. Cold

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Effects of LEP, GYS1, MYOD1, and MYF5 polymorphisms on pig economic traits

traits. Anim Biotechnol., 26: 156-163. Matsumoto T., Okumura N., Uenishi H., Hayashi T., Hamasima N., Awata T. (2012). Porcine single nucleotide polymorphism (SNP) development and population structure of pigs assessed by validated SNPs. Biochem. Genet., 50: 428-439. Park H.K., Ahima R.S. (2014). Leptin signaling. F1000Prime Rep., 6, p. 73. Perez- Montarelo D., Fernandez A., Folch J.M., Pena R.N., Ovilo C., Rodri-guez C., Silio L., Fernandez A.I. (2012). Joint effects of porcine leptin and leptin receptor polymorphisms on

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A novel single nucleotide polymorphism of the POU1F1 gene associated with meat quality traits in rabbits

Abstract

The purpose of this research was to investigate the effect of the POU1F1 gene on meat quality traits in the Hyla, Champagne, and Tianfu Black rabbit breeds. We detected one single nucleotide polymorphism and the SNP was located at 536 bp in intron 5 of this gene. Chi-square tests showed that the genotypic frequencies in the three rabbit populations were not in Hardy-Weinberg equilibrium. The PIC values indicated that the three populations had intermediate levels of genetic diversity. Rabbits with the CC genotype had a significantly greater pH0h than those with the CT genotype in the biceps femoris muscle. The least squares means for cooking loss in CT and CC rabbits were significantly higher than those for TT rabbits. Rabbits with the CC genotype had a significantly higher intramuscular fat content in the longissimus dorsi and biceps femoris muscles than those with genotype TT and CT. Thus, the results here indicate that this POU1F1 SNP may be of potential use in marker assisted selection for meat quality traits in rabbits.

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Genomic prediction by considering genotype × environment interaction using different genomic architectures

3395. Daetwyler H.D., Pong - Wong R., Villanueva B., Woolliams J.A. (2010). The impact of genetic architecture on genome-wide evaluation methods. Genetics, 185: 1021-1031. De Roos A.P.W., Hayes B.J., Goddard M.E. (2009). Reliability of genomic predictions across multiple populations. Genetics, 183: 1545-1553. Dekkers J.C.M. (2007). Prediction of response to marker-assisted and genomic selection using selection index theory. J. Anim. Breed. Genet., 124: 331-341. Falconer D.S., Mac Kay T.F.C. (1996

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The number of PON1 mutant alleles, but not PON1 phenotype, is associated with Gensini score of coronary damage

Abstract

Objectives. The aim of this study was to examine the effects of single nucleotide polymorphisms (SNPs) of PON1 gene at the level of promoter region (‒909 and ‒832) and of first exon (+575, A20352G, resulting Q192R substitution) on paraoxonase-1 (PON1) activities in 53 patients with angiographycally proven coronary heart disease (CHD) and 17 free-CHD subjects. Methods and Results. Serum PON1 arylesterase (Ar-ase) and salt-stimulated paraoxonase (ssPO-ase) activities were assessed with manual spectrophotometric methods, by using phenyl acetate and paraoxon as substrates. Common serum biochemical markers were assayed by enzymatic methods using commercial kits, on a Roche/Hitachi 912 Auto Analyzer. PON1 genotypes were determined by PCR and nucleotide sequencing of the amplicons with an ABI PRISMTM 310 Genetic Analyzer and a BigDye® Terminator v3.1 Cycle Sequencing Kit. The severity of coronary artery stenosis was assessed and classified using the Gensini score. We found no significant differences in the PON1 activities and -909(G→C), -832(G→A) and +575(A→G) PON1 polymorphisms between CHD and CHD-free groups. Considering all investigated subjects, we found that -909(G→C) and +575(A→G) SNPs had statistically significant effects on Ar-ase activity and PO-ase activity, respectively. In a multiple regression model we found that diabetes, LDL-cholesterol and the number of mutant alleles were significant independent determinants of the Gensini score. A significant positive correlation was observed only between the Gensini score and the number of mutant alleles. Conclusions. There are no differences between CHD and CHD-free groups regarding PON1 genotypes and phenotypes but the increasing number of PON1 mutant alleles is an important factor in determining the severity of coronary damage.

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