Aggregation of population‐based genetic variation over protein domain homologues and its potential use in genetic diagnostics

Background: Reperfusion following ischemia due to sudden cardiac arrest (SCA) is necessary for survival, but results in additional injury to affected tissues. Regulation of apoptosis has been shown to be important in determining the extent of reperfusion injury. Caspases (CASP) are essential enzymes in the apoptotic cascade and we therefore hypothesized that genetic variation in these enzymes might influence cardiac and brain resuscitation after SCA. To test this, we examined three genes (CASP2, CASP3, CASP9) in a population-based study of SCA survival. Methods: Subjects (mean age 67, 80% male, of European descent) were out-of-hospital SCA patients found in ventricular fibrillation (VF) and attended by paramedics in King County, WA (n=1614). To investigate cardiac resuscitation, we compared subjects who survived to hospital admission (n=827) with those who did not (n=787); for brain resuscitation, we compared subjects who survived to hospital discharge (n=448) with those who did not (n=1166). Associations of 19 SNPs were examined using logistic regression comparing each additional copy of the minor allele. Based on a priori hypotheses, models were adjusted for: age; gender; time from 911 call to arrival of emergency medical services; whether the event was witnessed; occurred in public; and whether bystander CPR was administered. We used within-gene permutation tests to adjust p-values for multiple comparisons. Results: Two SNPs in CASP3 were associated with SCA survival. The A allele of rs4647688 (minor allele frequency (MAF) 0.20) was associated with lower rates of survival to hospital admission (OR (95% CI), adjusted p-value: 0.78 (0.65, 0.93), p =0.043). The T allele of rs2705897 (MAF 0.26) was associated with a higher rate of survival to hospital admission (1.27 (1.07, 1.51), p =0.049). These two SNPs are in almost complete linkage equilibrium (r 2 =0.091). No SNPs in CASP3 were significantly associated with survival to hospital discharge, and no SNPs in CASP2 or CASP9 were significantly associated with either outcome. Conclusions: CASP3 variants are associated with SCA survival in this population. Further work is needed to explore the effect of these variants on regulation of apoptosis during reperfusion following VF arrest, and to replicate these findings in other populations.

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Evaluating the genetic variability of rubber hybrid progenies of the two crosses PB260 x RO44/71 and PB260 x RO62/54 by RAPD technique

Science and Technology Development Journal - Natural Sciences ◽

10.32508/stdjns.v2i3.751 ◽

2019 ◽

Vol 2 (3) ◽

pp. 36-43

Author(s):

Thien Minh Nguyen ◽

Tien Thi My Pham

Keyword(s):

Genetic Variation ◽

Genetic Variability ◽

Genetic Similarity ◽

Field Experiments ◽

Agronomic Traits ◽

Genetic Relationships ◽

Genetic Material ◽

Population Based ◽

Shannon Index ◽

Polymorphic Bands

The agronomic values of this population have been evaluated in the field experiments based on their phenotypic performance of agronomic traits, but the genetic variability of this population needs to be evaluated via techniques based on genetic material - DNA. In this study, the genetic variability in the investigated population of 71 hybrids and their parents was evaluated by RAPD technique, using eight selected arbitrarily primers; Genetic parameters and dendrogram expressing the genetic relationships among the investigated population were analyzed by GenALEx 6.1, Popgene 1.31 and NTSYSpc 2.1 softwares. Eight primers were used to generate the amplify products on each individual in the investigated population. From 74 genotypes, a total of 109 fragments were generated, among which, there were 89 polymorphic bands representing 81.65% with an average of 11 polymorphic bands/primer. Genetic similarity coefficient among the investigated population, based on DICE coefficient, ranged from 0.560 (LH05/0822 and PB260) to 0.991 (LH05/0781 and LH05/0841) with an average of 0,796, meaning that the genetic distance among ranged from 0.009 to 0.440 with an average of 0.231. The Shannon index and mean heterozygosity values were 0.328 and 0,176, respectively. This indicated that the progenies of the two investigated crosses possessed a relatively high range of genetic variability. The analysis of molecular variance (AMOVA) showed that genetic variation within population represented 62%, while genetic variation among two different crosses contributes 38% to the total genetic variability. Dendrogram based on DICE’s genetic similarity using UPGMA method showed that the hybrids divide into two major genetic groups (0.75), but the crosses were scattered independently of the hybrid.

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Effects of common germline genetic variation in cell cycle control genes on breast cancer survival: results from a population-based cohort

Breast Cancer Research ◽

10.1186/bcr2100 ◽

2008 ◽

Vol 10 (3) ◽

Cited By ~ 22

Author(s):

Elizabeth M Azzato ◽

Kristy E Driver ◽

Fabienne Lesueur ◽

Mitul Shah ◽

David Greenberg ◽

...

Keyword(s):

Breast Cancer ◽

Cell Cycle ◽

Genetic Variation ◽

Cancer Survival ◽

Cell Cycle Control ◽

Population Based ◽

Breast Cancer Survival

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Population-Based Cytogenetic Banding Analysis and Phylogenetic Relationships of the Neotropical Fungus-Farming Ant Trachymyrmex holmgreni Wheeler, 1925

Cytogenetic and Genome Research ◽

10.1159/000503913 ◽

2019 ◽

Vol 159 (3) ◽

pp. 151-161 ◽

Cited By ~ 4

Author(s):

Ricardo Micolino ◽

Maykon P. Cristiano ◽

Danon C. Cardoso

Keyword(s):

Genetic Variation ◽

Phylogenetic Reconstruction ◽

Population Based ◽

Population Variation ◽

Incipient Speciation ◽

Telomeric Sequences ◽

New Information ◽

Banding Analysis ◽

Pattern Characteristic ◽

Northern Brazil

Trachymyrmex is one of the most species-rich genera within fungus-farming ants and presents intraspecific cytogenetic polymorphisms as well as possible cryptic species. This ant genus is currently paraphyletic. Therefore, to unravel systematic and taxonomic misunderstandings, it is necessary to incorporate new information. We aimed to cytogenetically and genetically examine Trachymyrmex holmgreni populations from southern and northern Brazil to identify intraspecific chromosomal variations that support incipient speciation and reveal the species' position in a molecular phylogeny. Our cytogenetic approach did not show population variation in the mapping of both 18S rDNA and the TTAGG(6) motif, presenting instead a pattern characteristic of correlated species. However, the clustered pattern of the microsatellite GA(15) showed significant differences among populations: a well-defined block in each homologue, distinctly irregular signs between homologues, and blocks in 2 pairs of homologues. Our phylogenetic reconstruction yielded unexpected results, grouping representatives of 3 former morphological groups into 1 clade, namely T. urichii, T. papulatus, and T. holmgreni. Previously, it was suggested that northern and southern populations of T. holmgreni may be undergoing incipient speciation, but we can only indicate that the southernmost population differs prominently from the others in its distribution pattern of the microsatellite GA(15). Our study also supports the uniformity of karyotypes and repetitive DNA from both telomeric sequences and ribosomal DNA in Trachymyrmex studied here. In addition, we clarify some phylogenetic uncertainties within the genus and suggest further relevant systematic changes. Finally, additional studies utilizing other probes and additional populations may allow the detection of hidden genetic variation.

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Mapping genes for growth rate and fatness in a Large White x Meishan F2 pig population

Proceedings of the British Society of Animal Science ◽

10.1017/s0308229600032207 ◽

1998 ◽

Vol 1998 ◽

pp. 7-7 ◽

Cited By ~ 2

Author(s):

G.A. Walling ◽

A.L Archibald ◽

P.M. Visscher ◽

C.S. Haley

Keyword(s):

Growth Rate ◽

Genetic Variation ◽

Experimental Design ◽

Statistical Methods ◽

Population Based ◽

Genetic Maps ◽

Large White ◽

Backcross Population ◽

Livestock Species ◽

Reproduction Traits

DNA-based markers and genetic maps of major livestock species have been developed in the last few years. These, together with experimental populations and appropriate statistical methods, provide the tools to dissect causes of economically important genetic variation in livestock. A cross between genetically diverse lines is a powerful experimental design for such a study. In an F2 or backcross population from such a cross, markers are likely to be highly informative and the genes that control the differences between the lines will be segregating. We have been developing such a resource population based on a cross between the British Large White and Chinese Meishan pigs. These breeds differ for many traits, with the Meishan being inferior for growth rate and fatness, but superior for reproduction traits. Here we report the mapping of major genetic effects on growth rate and fatness in our cross.

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Utilization of plant genetic resources in breeding for sustainability

Plant Genetic Resources ◽

10.1079/pgr20032 ◽

2003 ◽

Vol 1 (1) ◽

pp. 11-18 ◽

Cited By ~ 7

Author(s):

M. O. Humphreys

Keyword(s):

Genetic Variation ◽

Genetic Resources ◽

Related Species ◽

Plant Genetic Resources ◽

Gene Pools ◽

International Treaty ◽

Food And Agriculture ◽

United Nations Food ◽

Potential Use

AbstractUK agriculture is undergoing significant change with reduced subsidies for food production, increasing consumer demands for food safety and traceability, and environmental concerns including climate and demographic change. The International Treaty on Plant Genetic Resources for Food and Agriculture adopted by the United Nations Food and Agriculture Organisation supports the use of genetic resources for research and breeding. Mining genetic resources for useful genetic variation is perceived as a major benefit of genebanks. However, utilization by breeders may be constrained by poor characterization of genetic resources, a widening gap between improved and unimproved material, and the disruption of well- adapted genotypes during introgression. Breeders working with grasses and forage legumes for sustainable agriculture are fortunate in the wealth of genetic variation available both within the primary species of interest and among related species. New DNA technologies allow more targeted approaches to the use of these genetic resources. Possibilities for gene transfer between related species using conventional techniques expand the available gene pools while potential use of genetic transformation extend these even further.

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