Detection of epistatic interactions between exotic alleles introgressed from wild barley (H. vulgare ssp. spontaneum)

2010 ◽  
Vol 121 (8) ◽  
pp. 1455-1464 ◽  
Author(s):  
Maria von Korff ◽  
Jens Léon ◽  
Klaus Pillen
Keyword(s):  
Wild Barley ◽  
Epistatic Interactions ◽  
Exotic Alleles

scholarly journals Plasmotype condition nuclear pleiotropic effects on clock and fitness in barley

2021 ◽  
Author(s):  
Eyal Bdolach ◽  
Manas Ranjan Prusty ◽  
Lalit Dev Tiwari ◽  
Khalil Kashkush ◽  
Eyal Fridman
Keyword(s):  
Elevated Temperatures ◽  
Wild Barley ◽  
Reproductive Traits ◽  
Pleiotropic Effects ◽  
Clock Period ◽  
Gradual Reduction ◽  
Epistatic Interactions ◽  
Dh Population ◽  
Hordeum Vulgare Ssp

In plants, the role of chloroplasts and mitochondria (plasmotype) in controlling circadian clock plasticity and overall plant robustness has not been elucidated. In this study, we investigated the rhythmicity of chlorophyll fluorescence (Chl F) clock output , and fitness in the field at optimal and elevated temperatures, in three different barley populations. First, we examined a reciprocal DH population between two wild barley (Hordeum vulgare ssp. spontaneum), in which we identified two pleiotropic QTLs (frp2.1 and amp7.1) that modulate clock and fitness including conditioning of these effects by plasmotype diversity. In the second population, a complete diallel consisting of 11 genotypes (reciprocal hybrids differing in plasmotype), we observed a gradual reduction in plasmotype, ranging from 26% and 15% for Chl F and clock measurements to 5.3% and 3.7% for growth and reproductive traits, respectively. The third population studied was a collection of cytolines in which nine different wild plasmotypes replaced the cultivated Noga (H. vulgare) plasmotype. Here, the order and magnitude of the effects of the plasmotypes differed from what we observed in the diallel population, with the greatest effect of plasmotype diversity observed for clock period and amplitude. Comparison of the chloroplast sequences suggests several candidate genes in the plastid-encoded RNA polymerase (PEP) complex that may be responsible for the observed plasmotype effects. Overall, our results unravel previously unknown cytonuclear epistatic interactions that controls clock performance while also having pleiotropic effects on a plant field characteristics.

Multilocus Analysis of Genetic Susceptibility to Myocardial Infarction in Russians: Replication Study

Acta Naturae ◽  
2017 ◽  
Vol 9 (4) ◽  
pp. 74-83
Author(s):  
N. G. Kukava ◽  
B. V. Titov ◽  
G. J. Osmak ◽  
N. A. Matveeva ◽  
O. G. Kulakova ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
Genetic Markers ◽  
Prognostic Significance ◽  
Cumulative Effect ◽  
Mthfr Gene ◽  
Composite Model ◽  
Replication Study ◽  
Epistatic Interactions ◽  
Multilocus Analysis ◽  
Lipid Metabolism Genes

In search of genetic markers of myocardial infarction (MI) risk, which have prognostic significance for Russians, we performed a replication study of MI association with genetic variants of PCSK9 (rs562556), APOE (epsilon polymorphism, rs7412 and rs429358), LPL (rs320), MTHFR (rs1801133), eNOS (rs2070744), and the 9p21 region (rs1333049) in 405 patients with MI and 198 controls. Significant MI association was observed with variants of the lipid metabolism genes (PCSK9, APOE and LPL), and of eNOS. The SNPs in the MTHFR gene and the 9p21 region were not significantly associated with MI one by one but were included in several different MI-associated allelic combinations identified by multilocus analysis. Since we have not revealed nonlinear epistatic interactions between the components of the identified combinations, we postulate that the cumulative effect of genes that form a combination arises from the summation of their small independent contributions. The prognostic significance of the additive composite model built from the PCSK9, APOE, LPL, and eNOS genes as genetic markers was assessed using ROC analysis. After we included these markers in the previously published composite model of individual genetic risk of MI, the prognostic efficacy in our sample reached AUC = 0.676. However, the results obtained in this study certainly need to be replicated in an independent sample of Russians.

Mapping and Epistatic Interactions of QTLs for Pericarp Thickness in Sweet Corn

2015 ◽  
Vol 41 (3) ◽  
pp. 359 ◽  
Author(s):  
Yong-Tao YU ◽  
Gao-Ke LI ◽  
Xi-Tao QI ◽  
Chun-Yan LI ◽  
Ji-Hua MAO ◽  
...  
Keyword(s):  
Sweet Corn ◽  
Epistatic Interactions ◽  
Pericarp Thickness

EpiPen: An R Package to Investigate Two-Locus Epistatic Models

2014 ◽  
Vol 17 (4) ◽  
Author(s):  
Raymond K. Walters ◽  
Charles Laurin ◽  
Gitta H. Lubke
Keyword(s):  
Power Analysis ◽  
R Package ◽  
Simulation Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Epistatic Interactions ◽  
Model Interpretation ◽  
Genome Wide ◽  
Using Data ◽  
Power Analyses

Epistasis is a growing area of research in genome-wide studies, but the differences between alternative definitions of epistasis remain a source of confusion for many researchers. One problem is that models for epistasis are presented in a number of formats, some of which have difficult-to-interpret parameters. In addition, the relation between the different models is rarely explained. Existing software for testing epistatic interactions between single-nucleotide polymorphisms (SNPs) does not provide the flexibility to compare the available model parameterizations. For that reason we have developed an R package for investigating epistatic and penetrance models, EpiPen, to aid users who wish to easily compare, interpret, and utilize models for two-locus epistatic interactions. EpiPen facilitates research on SNP-SNP interactions by allowing the R user to easily convert between common parametric forms for two-locus interactions, generate data for simulation studies, and perform power analyses for the selected model with a continuous or dichotomous phenotype. The usefulness of the package for model interpretation and power analysis is illustrated using data on rheumatoid arthritis.

scholarly journals Genetic Screens for Factors Involved in the Notum Bristle Loss of Interspecific Hybrids Between Drosophila melanogaster and D. simulans

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 269-282
Author(s):  
Toshiyuki Takano-Shimizu
Keyword(s):  
Drosophila Melanogaster ◽  
Interspecific Cross ◽  
Species Variation ◽  
Genetic Screens ◽  
Pure Species ◽  
Epistatic Interactions ◽  
X Chromosomes ◽  
Powerful Means ◽  
Different Populations ◽  
Deficiency Screening

Abstract Interspecific cross is a powerful means to uncover hidden within- and between-species variation in populations. One example is a bristle loss phenotype of hybrids between Drosophila melanogaster and D. simulans, although both the pure species have exactly the same pattern of bristle formation on the notum. There exists a large amount of genetic variability in the simulans populations with respect to the number of missing bristles in hybrids, and the variation is largely attributable to simulans X chromosomes. Using nine molecular markers, I screened the simulans X chromosome for genetic factors that were responsible for the differences between a pair of simulans lines with high (H) and low (L) missing bristle numbers. Together with duplication-rescue experiments, a single major quantitative locus was mapped to a 13F–14F region. Importantly, this region accounted for most of the differences between H and L lines in three other independent pairs, suggesting segregation of H and L alleles at the single locus in different populations. Moreover, a deficiency screening uncovered several regions with factors that potentially cause the hybrid bristle loss due to epistatic interactions with the other factors.

Sign in / Sign up

Export Citation Format

Share Document