Sequence characterization and polymorphism detectionin AQP7 gene of Murrah buffalo

2016 ◽  
Author(s):  
Ragini Kumari ◽  
K.P. Ramesha ◽  
Rakesh Kumar ◽  
Divya Divya ◽  
Anjali Kumari ◽  
...  
Keyword(s):  
Semen Quality ◽  
Single Strand Conformation Polymorphism ◽  
Sscp Analysis ◽  
Reference Sequence ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Single Nucleotide ◽  
Sequence Characterization ◽  
Murrah Buffalo ◽  
Aquaporin 7

Aquaporin 7 (AQP7) gene is a member of aqua-glyceroporins which transports glycerol and water to spermatids. The present study aimed to investigate the polymorphisms within exons 2, 3, 4, 5 and their flanking intronic regions in AQP7 gene of Murrah bulls. Genomic DNA was extracted from 69 Murrah bulls blood samples and was subjected to polymerase chain reaction- single strand conformation polymorphism (PCR-SSCP) analysis. PCR-SSCP analysis revealed a total of eight different variants for amplicons of exons 4 and 5. Amplicon of exon 4 revealed three different patterns viz. E4P1, E4P2 and E4P3 with the frequency of 0.30, 0.22 and 0.48, respectively. Analysis of exon 5 revealed five unique SSCP patterns viz. E5P1, E5P2, E5P3, E5P4 and E5P5, with the frequency of 0.10, 0.37, 0.20, 0.20 and 0.13, respectively. Sequence analysis showed 16 single nucleotide polymorphisms, 7 of which were observed in coding region. Amplicons of exons 2 and 3 showed monomorphic patterns. However, compared to the reference sequence of taurine cattle one transition (C6878T) in exon 3 and 4 transitions (G2099A, C2116T, A2117G, G6848C) in intron 2 were observed for all the bulls under study. The genetic variability identified in the AQP7 gene may serve as potential genetic marker(s) for semen quality traits in buffalo.

SSCP Analysis of cDNA Markers Provides a Dense Linkage Map of theAedes aegyptiGenome

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 715-726 ◽  
Author(s):  
Ruth E Fulton ◽  
Michael L Salasek ◽  
Nancy M DuTeau ◽  
William C Black
Keyword(s):  
Population Genetics ◽  
Drosophila Melanogaster ◽  
Linkage Map ◽  
Single Strand Conformation Polymorphism ◽  
Genome Project ◽  
Sscp Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
F2 Progeny ◽  
Conformation Polymorphism

AbstractAn intensive linkage map of the yellow fever mosquito, Aedes aegypti, was constructed using single-strand conformation polymorphism (SSCP) analysis of cDNA markers to identify single nucleotide polymorphisms (SNPs). A total of 94 A. aegypti cDNAs were downloaded from GenBank and primers were designed to amplify fragments <500 bp in size. These primer pairs amplified 94 loci, 57 (61%) of which segregated in a single F1 intercross family among 83 F2 progeny. This allowed us to produce a dense linkage map of one marker every 2 cM distributed over a total length of 134 cM. Many A. aegypti cDNAs were highly similar to genes in the Drosophila melanogaster genome project. Comparative linkage analysis revealed areas of synteny between the two species. SNP polymorphisms are abundant in A. aegypti genes and should prove useful in both population genetics and mapping studies.

Single nucleotide polymorphisms of CBF4 locus region of Arabidopsis thaliana correspond to drought tolerance

2004 ◽  
Vol 1 (3) ◽  
pp. 181-190 ◽  
Author(s):  
Hao Gang-Ping ◽  
Wu Zhong-Yi ◽  
Chen Mao-Sheng ◽  
Cao Ming-Qing ◽  
Dominique Brunel ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Drought Tolerance ◽  
World Wide ◽  
Nucleotide Variation ◽  
Nucleotide Polymorphisms ◽  
Water Deficiency ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Adaptation To Drought

AbstractThe levels of drought tolerance and nucleotide polymorphism at the CBF4 locus were examined in a world-wide sample of 17 core accessions of Arabidopsis thaliana. The results showed that different accessions exhibited considerable differences in adaptation to drought stress. Compared with Columbia accession, the frequency of nucleotide polymorphism at the CBF4 locus of 25av, 203av and 244av accessions, including single nucleotide polymorphism (SNP) and insertion/deletion (Indel), was high, on average 1 SNP per 35.8 bp and 1 Indel per 143 bp. No significance in all regions of Tajima's D test indicated that the neutral mutation hypothesis could explain the nucleotide polymorphism in this CBF4 gene region. The higher polymorphism was the result of purification selection. Nucleotide polymorphism in the non-coding region was three times higher than in the coding region. This might indicate a recent relaxation of selection pressures on the non-coding region of CBF4 gene. In the coding region of CBF4, SNP frequency was 1 SNP per 96.4 bp and one non-synonymous mutation was detected from 25av, 203av and 244av accessions: the amino acid variation gly↔val at position 205, caused by the nucleotide variation G↔T at position 1034 (corresponding to the nucleotide at position 19 696 of GenBank accession no. AB015478 as 1). Furthermore, four differential SNPs were discovered in haplotype 6 constituted by 203av, one of them located in the 3′ non-coding region (A↔C at position 1106) and the others in the 5′ non-coding region (A↔G, A↔C and G↔A at positions 27, 129 and 171, respectively). The drought tolerance assay indicated that accession 203av was the best at tolerating water deficiency. We propose that haplotype 6 is consistent with its drought tolerance.

scholarly journals Screening of Three Different Alleles of mtDNA (G709A, G3496T, A3537G) in Subpopulation of UKM Students

2018 ◽  
Vol 5 (1) ◽  
pp. 37-40
Author(s):  
Seri Mirianti Ishar ◽  
Jeyaganesan Pillay a/l Balaraman ◽  
Muhammad Jefri Mohd Yusof ◽  
Khairul Osman ◽  
Lee Loong Chuen
Keyword(s):  
Uv Light ◽  
Forensic Genetics ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Documentation System ◽  
Single Nucleotide ◽  
National University ◽  
Pcr Products ◽  
Malay Population ◽  
Mutation Allele

Human DNA consists of nucleus DNA (nDNA) and mitochondrial DNA (mtDNA). Both are valuable in medicine and forensic genetics but in this project, single nucleotide polymorphisms (SNPs) in mtDNA are used to trace the mutation occurred. Mutations in the sequence of alleles can lead to haplogroup variation and also certain diseases. The purpose of this study is to screen of mutations on alleles G709A, G3496T, and A3537G in Malay population of The National University of Malaysia (UKM) students. These SNPs lie in the ND1 (nitrogen dehydrogenase subunit 1) coding region, and the reports state that these three alleles are prone to mutate. From MitoMap Web site, the mutations of these alleles are reported to have potential in causing several diseases with the collaboration of other SNPs mutation. Allele G709A is reported to have an association with hearing loss and Leber Hereditary Optic Neuropathy (LHON) while allele G3496T is associated to LHON only. Allele A3537G is related to diabetes. A total of 100 DNA samples were collected from Malay students of UKM and preserved on FTA card to be purified later. The concentration of the DNA on the purified FTA card was between 10μM to 20μM. An attempt was made by amplifying those three loci from the genomic DNA. The amplified product was detected and separated using 1% gel electrophoresis. Before sequencing, the PCR products were visualized under UV light using gel documentation system. All PCR products were sequenced to detect the mutation on every single position chosen. From the alignment of sequencing results, allele G709A and allele G3496T showed no mutation. Meanwhile four samples from alleles A3537G has the mutation. From the results obtained, it seems that mutations are rare in all selected alleles. It is recommended to increase the sample size and alleles selected in the future to increase the strength of the study. This study also should be applied to other populations in Malaysia such as Chinese and Indian.  

scholarly journals An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes

2021 ◽  
Author(s):  
Thomas K. F. Wong ◽  
Teng Li ◽  
Louis Ranjard ◽  
Steven Wu ◽  
Jeet Sukumaran ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Real Data ◽  
Reference Sequence ◽  
Nucleotide Polymorphisms ◽  
Data Set ◽  
Single Nucleotide ◽  
Short Read ◽  
Pooled Samples ◽  
Haplotype Information

AbstractA current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogenetic tree according to the SNP patterns. AFPhyloMix adopts a Bayesian model of inference to estimates the phylogeny of the haplotypes and their relative frequencies, given that the number of haplotypes is known. In our simulations, AFPhyloMix achieved at least 80% accuracy at recovering the phylogenies and frequencies of the constituent haplotypes, for mixtures with up to 15 haplotypes. AFPhyloMix also worked well on a real data set of kangaroo mitochondrial DNA sequences.

Promoter region single nucleotide polymorphism of siglec-8 gene associates with susceptibility to allergic asthma

2020 ◽  
Vol 17 (3) ◽  
pp. 195-201 ◽  
Author(s):  
Mohammad Sajay-asbaghi ◽  
Mahnaz Sadeghi-shabestrai ◽  
Amir Monfaredan ◽  
Narges Seyfizadeh ◽  
Alireza Razavi ◽  
...  
Keyword(s):  
Allergic Asthma ◽  
Normal Subjects ◽  
Single Strand Conformation Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Potential Therapeutic Target ◽  
Single Nucleotide ◽  
Study Materials ◽  
Protective Allele ◽  
Conformation Polymorphism

Aim: Siglec-8 is exclusively expressed on mast cells, eosinophils and basophils. Possible association of six siglec-8 single nucleotide polymorphisms (SNPs) with susceptibility to allergic asthma in the Azeri population of Iran was investigated in this study. Materials & methods: A total of 194 patients and 190 normal subjects were enrolled. PCR single strand conformation polymorphism (PCR-SSCP) was used to determine the genotypes of the studied SNPs. Results: The rs36498 showed significant association with allergic asthma (odds ratio [OR]: 0.65; p = 0.022) and the T allele was found as a protective allele (OR: 0.61; p = 0.008). Also, eosinophil count in the CC genotype was significantly higher than that in the other genotypes (p = 0.026). Conclusion: The rs36498 is thought to influence the expression level of siglec-8. Siglec-8 could be a potential therapeutic target for allergic asthma.

scholarly journals Narrowing a region on rat chromosome 13 that protects against hypertension in Dahl SS-13BN congenic strains

2011 ◽  
Vol 300 (4) ◽  
pp. H1530-H1535 ◽  
Author(s):  
Carol Moreno ◽  
Jan M. Williams ◽  
Limin Lu ◽  
Mingyu Liang ◽  
Jozef Lazar ◽  
...  
Keyword(s):  
Congenic Strain ◽  
Region Of Interest ◽  
Differentially Expressed ◽  
Brown Norway ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Single Nucleotide ◽  
Chromosome 13 ◽  
Protein Excretion ◽  
Sequencing Studies

Transfer of chromosome 13 from the Brown Norway (BN) rat onto the Dahl salt-sensitive (SS) genetic background attenuates the development of hypertension, but the genes involved remain to be identified. The purpose of the present study was to confirm by telemetry that a congenic strain [SS.BN-(D13Hmgc37-D13Got22)/Mcwi, line 5], carrying a 13.4-Mb segment of BN chromosome 13 from position 32.4 to 45.8 Mb, is protected from the development of hypertension and then to narrow the region of interest by creating and phenotyping 11 additional subcongenic strains. Mean arterial pressure (MAP) rose from 118 ± 1 to 186 ± 5 mmHg in SS rats fed a high-salt diet (8.0% NaCl) for 3 wk. Protein excretion increased from 56 ± 11 to 365 ± 37 mg/day. In contrast, MAP only increased to 152 ± 9 mmHg in the line 5 congenic strain. Six subcongenic strains carrying segments of BN chromosome 13 from 32.4 and 38.2 Mb and from 39.9 to 45.8 Mb were not protected from the development of hypertension. In contrast, MAP was reduced by ∼30 mmHg in five strains, carrying a 1.9-Mb common segment of BN chromosome 13 from 38.5 to 40.4 Mb. Proteinuria was reduced by ∼50% in these strains. Sequencing studies did not identify any nonsynonymous single nucleotide polymorphisms in the coding region of the genes in this region. RT-PCR studies indicated that 4 of the 13 genes in this region were differentially expressed in the kidney of two subcongenic strains that were partially protected from hypertension vs. those that were not. These results narrow the region of interest on chromosome 13 from 13.4 Mb (159 genes) to a 1.9-Mb segment containing only 13 genes, of which 4 are differentially expressed in strains partially protected from the development of hypertension.

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