scholarly journals Mitochondrial Haplotype Analysis of <i>Pomoxis nigromaculatus</i> Inhabiting Three Georgian Lakes

2017 ◽  
Vol 07 (03) ◽  
pp. 105-116
Author(s):  
Michael A. Erwin ◽  
Bagie George
Keyword(s):  
Haplotype Analysis ◽  
Mitochondrial Haplotype ◽  
Pomoxis Nigromaculatus

scholarly journals Mitochondrial Haplotype Analysis as a Tool for Differentiating Isolates of Verticillium dahliae

2010 ◽  
Vol 100 (11) ◽  
pp. 1231-1239 ◽  
Author(s):  
Frank N. Martin
Keyword(s):  
Phylogenetic Analysis ◽  
Verticillium Dahliae ◽  
Haplotype Analysis ◽  
Geographic Origin ◽  
Mitochondrial Haplotype ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Additional Tool ◽  
Mitochondrial Haplotypes ◽  
Compatibility Group

The ability to monitor mitochondrial background in Verticillium dahliae may provide an additional tool for population studies and monitoring clonal populations. Published mitochondrial genome sequences of V. dahliae (DQ351941) were used to design primers for amplification of spacer regions for assessment of mitochondrial haplotype differences among isolates. Five regions were examined (5,229 bp, or 19% of the total genome size) for 30 isolates representing a range in vegetative compatibility group (VCG), host, and geographic origin. Observed differences among isolates were due to single nucleotide polymorphisms, different numbers of bases in specific homopolymeric regions, and copies of subrepeated sequences. When the differences observed for each locus were totaled there were 28 total groupings; when the results of each locus for individual isolates were combined there were 15 mitochondrial haplotypes. Some of the observed groupings correlated with VCG. For example, five VCG-1A and VCG-1B isolates from California, Spain, and Greece had identical haplotypes; however, this was not observed for VCG-2 or VCG-4 isolates. While some VCG-2 isolates also were identical and fell into a single haplotype, five haplotypes were found for this group (five other haplotypes were observed for other isolates that had not been characterized to VCG but grouped with VCG-2 isolates in the phylogenetic analysis). Likewise, five VCG-4 isolates fell into four mitochondrial haplotypes, one of which was identical to the largest VCG-2 grouping. A heterokaryon self-incompatible isolate that was reported in the literature to cluster with VCG-2 isolates by amplified fragment length polymorphism analysis was identical with VCG-1 isolates for four of the five loci, but was intermediate between VCG-1 and VCG-2 in the haplotype analysis. Phylogenetic analysis with these regions revealed the mitochondrial background of VCG-1 and VCG2-B to be monophyletic but VCG-2A and VCG-4 could not be separated. The results obtained indicate that there is variation in mitochondrial haplotypes and this type of analysis may be a useful for characterization of isolates. While data from all five regions was used for the haplotype separation in this study, depending on the VCG or the level of variability observed within a population it is possible to use fewer loci.

scholarly journals Association Between SSCP Haplotypes at the Bovine Growth Hormone Gene and Milk Protein Percentage

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 945-951
Author(s):  
A Lagziel ◽  
E Lipkin ◽  
M Soller
Keyword(s):  
Growth Hormone ◽  
Candidate Gene ◽  
Milk Protein ◽  
Haplotype Analysis ◽  
Bos Taurus ◽  
Bovine Growth Hormone ◽  
Growth Hormone Gene ◽  
Protein Percentage ◽  
Quantitative Genetic ◽  
Positive Effect

Abstract The bovine Growth Hormone gene (bGH) is an attractive candidate gene for milk production in cattle. Single-strand conformation polymorphisms at bGH were identified and used to define haplotype configurations at this gene in the Israeli Holstein dairy cattle population (Bos taurus) and in the parent animals of the International Bovine Reference Family Panel (a collection of B. taurus and B. indicus crosses). B. taurus and B. indicus haplotypes at the bGH gene differed qualitatively, confirming the previously proposed long evolutionary separation of these cattle subraces. Only a small number of bGH haplotypes were present in the Israel Holstein population. One of the haplotypes, apparently of B. indicus origin, was found to have a highly significant positive effect on milk protein percentage. This illustrates the utility of the haplotype approach for uncovering candidate gene involvement in quantitative genetic variation in agricultural populations. The strong effect of an indicine haplotype in a taurine background raises the possibility that indicine alleles at other candidate genes may comprise a genetic resource for improvement of taurine populations. It is proposed that haplotype analysis may be a useful adjunct to measures of genetic distance for evaluating rare breeds with respect to gene conservation.

Frequency of the delta Phe508 mutation and correlation with XV.2c/KM-19 haplotypes in an American population of cystic fibrosis patients: results of a collaborative study

1990 ◽  
Vol 36 (10) ◽  
pp. 1741-1746 ◽  
Author(s):  
W E Highsmith ◽  
G L Chong ◽  
H T Orr ◽  
T R Perry ◽  
D Schald ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Haplotype Analysis ◽  
Screening Program ◽  
Collaborative Study ◽  
Population Based ◽  
Carrier Status ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Phenylalanine Residue ◽  
Test Result

Abstract The cystic fibrosis (CF) gene has been recently cloned, and a deletion of 3 basepairs (bp) of DNA was found on most of the CF chromosomes. This deletion leads to the synthesis of a protein that lacks a phenylalanine residue at position 508. Using two polymerase chain reaction protocols to study the frequency of this mutation in a series of 192 CF patients, we found the mutation on 72% of affected chromosomes. We then used this value to calculate the predictive value of a negative test result in a population-based screening program for CF carrier status. Haplotype analysis with the polymorphic markers XV.2c and KM-19 on 239 CF chromosomes revealed that 90.7% of CF chromosomes with the deletion had a single haplotype. This haplotype was also associated with 60.4% of CF chromosomes with unknown mutations. These values can be used to calculate the probability of whether an individual from the general population is a carrier of any CF mutation.

scholarly journals Haplotype analysis on correlation between transcription factor 7-like 2 gene polymorphism and breast cancer risk

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yang Wang ◽  
Xiaojuan Men ◽  
Yongxue Gu ◽  
Huidong Wang ◽  
Zhicai Xu
Keyword(s):  
Breast Cancer ◽  
Transcription Factor ◽  
Logistic Regression ◽  
Abdominal Obesity ◽  
Haplotype Analysis ◽  
Environment Interaction ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Locus Model ◽  
Gene Environment

Abstract Background Up to now, limited researches focused on the association between transcription factor 7-like 2 gene (TF7L2) gene single nucleotide polymorphisms (SNPs) and breast cancer (BC) risk. The aim of this study was to evaluate the associations between TF7L2 and BC risk in Chinese Han population. Methods Logistic regression model was used to test the correlation between polymorphisms and BC risk. Strength of association was evaluated by odds ratio (OR) and 95% confidence interval (CI). Generalized multifactor dimensionality reduction (GMDR) was applied to analyze the SNP-SNP and gene-environment interaction. Results Logistic regression analysis indicated that the BC risk was obviously higher in carriers of rs1225404 polymorphism C allele than that in TT genotype carriers (TC or CC versus TT), adjusted OR (95%CI) =1.40 (1.09–1.72). Additionally, we also discovered that people with rs7903146- T allele had an obviously higher risk of BC than people with CC allele (CT or TT versus CC), adjusted OR (95%CI) =1.44 (1.09–1.82). GMDR model was used to research the effect of interaction among 4 SNPs and environmental factors on BC risk. We discovered an important two-locus model (p = 0.0100) including rs1225404 and abdominal obesity, suggesting a potential gene–environment correlation between rs1225404 and abdominal obesity. In general, the cross-validation consistency of two-locus model was 10 of 10, and the testing accuracy was 0.632. Compared with subjects with normal waist circumference (WC) value and rs1225404 TT genotype, abdominal obese subjects with rs1225404 TC or CC genotype had the highest BC risk. After covariate adjustment, OR (95%CI) was 2.23 (1.62–2.89). Haplotype analysis indicated that haplotype containing rs1225404-T and rs7903146-C alleles were associated with higher BC risk. Conclusions C allele of rs1225404 and T allele of rs7903146, interaction between rs1225404 and abdominal obesity, rs1225404-T and rs7903146-C haplotype were all related to increased BC risk.

scholarly journals The Independent Domestication of Timopheev’s Wheat: Insights from Haplotype Analysis of the Brittle rachis 1 (BTR1-A) Gene

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 338
Author(s):  
Moran Nave ◽  
Mihriban Taş ◽  
John Raupp ◽  
Vijay K. Tiwari ◽  
Hakan Ozkan ◽  
...  
Keyword(s):  
Promoter Region ◽  
Haplotype Analysis ◽  
Common Ancestor ◽  
Triticum Turgidum ◽  
Tetraploid Wheat ◽  
Wheat Species ◽  
Loss Of Function ◽  
Brittle Rachis ◽  
Gene Level ◽  
Large Panel

Triticum turgidum and T. timopheevii are two tetraploid wheat species sharing T. urartu as a common ancestor, and domesticated accessions from both of these allopolyploids exhibit nonbrittle rachis (i.e., nonshattering spikes). We previously described the loss-of-function mutations in the Brittle Rachis 1 genes BTR1-A and BTR1-B in the A and B subgenomes, respectively, that are responsible for this most visible domestication trait in T. turgidum. Resequencing of a large panel of wild and domesticated T. turgidum accessions subsequently led to the identification of the two progenitor haplotypes of the btr1-A and btr1-B domesticated alleles. Here, we extended the haplotype analysis to other T. turgidum subspecies and to the BTR1 homologues in the related T. timopheevii species. Our results showed that all the domesticated wheat subspecies within T. turgidum share common BTR1-A and BTR1-B haplotypes, confirming their common origin. In T. timopheevii, however, we identified a novel loss-of-function btr1-A allele underlying a partially brittle spike phenotype. This novel recessive allele appeared fixed within the pool of domesticated Timopheev’s wheat but was also carried by one wild timopheevii accession exhibiting partial brittleness. The promoter region for BTR1-B could not be amplified in any T. timopheevii accessions with any T. turgidum primer combination, exemplifying the gene-level distance between the two species. Altogether, our results support the concept of independent domestication processes for the two polyploid, wheat-related species.

scholarly journals An actionable KCNH2 Long QT Syndrome variant detected by sequence and haplotype analysis in a population research cohort

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Shona M. Kerr ◽  
Lucija Klaric ◽  
Mihail Halachev ◽  
Caroline Hayward ◽  
Thibaud S. Boutin ◽  
...  
Keyword(s):  
Long Qt Syndrome ◽  
Haplotype Analysis ◽  
Long Qt ◽  
Population Research ◽  
Qt Syndrome

Broader Clinical Spectrum of Fukuyama-Type Congenital Muscular Dystrophy Manifested by Haplotype Analysis

1999 ◽  
Vol 14 (11) ◽  
pp. 711-715 ◽  
Author(s):  
Mieko Yoshioka ◽  
Tatsushi Toda ◽  
Shigekazu Kuroki ◽  
Kenzo Hamano
Keyword(s):  
Muscular Dystrophy ◽  
Haplotype Analysis ◽  
Congenital Muscular Dystrophy ◽  
Clinical Spectrum

Haplotype analysis in western European patients with mal de Meleda: founder effect for the W15R mutation in theSLURP1gene

2013 ◽  
Vol 168 (6) ◽  
pp. 1372-1374 ◽  
Author(s):  
R.G.L. Nellen ◽  
P.M. Steijlen ◽  
H.C. Hennies ◽  
J. Fischer ◽  
C.S. Munro ◽  
...  
Keyword(s):  
Founder Effect ◽  
Haplotype Analysis ◽  
Western European ◽  
Mal De Meleda

The Atlas Massif separates a northern and a southern mitochondrial haplotype group of North African water frogs Pelophylax saharicus (Anura: Ranidae) in Morocco

2015 ◽  
Vol 36 (4) ◽  
pp. 437-443 ◽  
Author(s):  
Aziza Lansari ◽  
Miguel Vences ◽  
Susanne Hauswaldt ◽  
Ralf Hendrix ◽  
David Donaire ◽  
...  
Keyword(s):  
Mitochondrial Haplotype ◽  
North African ◽  
High Atlas ◽  
Water Frog ◽  
The North ◽  
Water Frogs ◽  
Atlas Mountains ◽  
High Atlas Mountains ◽  
Gene Coi ◽  
Area North

We assessed the genetic variation of 47 Moroccan populations of the North African water frog (Pelophylax saharicus) using partial sequences of the mitochondrial cytochrome oxidase subunit I gene (COI). All 239 samples belonged to the main haplotype clade previously identified from Morocco, with no haplotypes of the Algerian/Tunisian clades among our samples. Altogether 40 haplotypes were found, with a maximum of 13 mutational steps between them. Two weakly divergent haplogroups separated by a minimum of six mutational steps were distributed (i) in the Anti-Atlas and the Sahara (south of the High Atlas Mountains) versus (ii) in the Middle Atlas, the High Atlas, and in the Rif area north of the Atlas Massif. Haplotypes of the northern haplogroup were found at the southernmost locality, which might be due to human translocation, and co-occurrence of the two haplogroups was recorded at three sites within the range of the northern haplogroup.

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