scholarly journals Variance heterogeneity genome‐wide mapping for cadmium in bread wheat reveals novel genomic loci and epistatic interactions

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Waseem Hussain ◽  
Malachy T. Campbell ◽  
Diego Jarquin ◽  
Harkamal Walia ◽  
Gota Morota
Keyword(s):  
Bread Wheat ◽  
Variance Heterogeneity ◽  
Epistatic Interactions ◽  
Genome Wide

scholarly journals Variance heterogeneity genome-wide mapping for cadmium in bread wheat reveals novel genomic loci and epistatic interactions

2019 ◽  
Author(s):  
Waseem Hussain ◽  
Malachy Campbell ◽  
Diego Jarquin ◽  
Harkamal Walia ◽  
Gota Morota
Keyword(s):  
Linear Model ◽  
Bread Wheat ◽  
Generalized Linear Model ◽  
Genome Wide Association Study ◽  
Mean Value ◽  
Genome Wide Association ◽  
Variance Heterogeneity ◽  
Epistatic Interactions ◽  
Genome Wide ◽  
The Mean

AbstractGenome-wide association mapping identifies quantitative trait loci (QTL) that influence the mean differences between the marker genotypes for a given trait. While most loci influence the mean value of a trait, certain loci, known as variance heterogeneity QTL (vQTL) determine the variability of the trait instead of the mean trait value (mQTL). In the present study, we performed a variance heterogeneity genome-wide association study (vGWAS) for grain cadmium (Cd) concentration in bread wheat. We used double generalized linear model and hierarchical generalized linear model to identify vQTL associated with grain Cd. We identified novel vQTL regions on chromosomes 2A and 2B that contribute to the Cd variation and loci that affect both mean and variance heterogeneity (mvQTL) on chromosome 5A. In addition, our results demonstrated the presence of epistatic interactions between vQTL and mvQTL, which could explain variance heterogeneity. Overall, we provide novel insights into the genetic architecture of grain Cd concentration and report the first application of vGWAS in wheat. Moreover, our findings indicated that epistasis is an important mechanism underlying natural variation for grain Cd concentration.

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 Genome-Wide Association and Prediction of Male and Female Floral Hybrid Potential Traits in Elite Spring Bread Wheat Genotypes

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 895
Author(s):  
Samira El Hanafi ◽  
Souad Cherkaoui ◽  
Zakaria Kehel ◽  
Ayed Al-Abdallat ◽  
Wuletaw Tadesse
Keyword(s):  
Genomic Selection ◽  
Bread Wheat ◽  
Genome Wide Association ◽  
Hybrid Breeding ◽  
Floral Traits ◽  
Phenotypic Variance ◽  
Spring Bread Wheat ◽  
Genome Wide ◽  
Anther Length ◽  
Anther Extrusion

Hybrid wheat breeding is one of the most promising technologies for further sustainable yield increases. However, the cleistogamous nature of wheat displays a major bottleneck for a successful hybrid breeding program. Thus, an optimized breeding strategy by developing appropriate parental lines with favorable floral trait combinations is the best way to enhance the outcrossing ability. This study, therefore, aimed to dissect the genetic basis of various floral traits using genome-wide association study (GWAS) and to assess the potential of genome-wide prediction (GP) for anther extrusion (AE), visual anther extrusion (VAE), pollen mass (PM), pollen shedding (PSH), pollen viability (PV), anther length (AL), openness of the flower (OPF), duration of floret opening (DFO) and stigma length. To this end, we employed 196 ICARDA spring bread wheat lines evaluated for three years and genotyped with 10,477 polymorphic SNP. In total, 70 significant markers were identified associated to the various assessed traits at FDR ≤ 0.05 contributing a minor to large proportion of the phenotypic variance (8–26.9%), affecting the traits either positively or negatively. GWAS revealed multi-marker-based associations among AE, VAE, PM, OPF and DFO, most likely linked markers, suggesting a potential genomic region controlling the genetic association of these complex traits. Of these markers, Kukri_rep_c103359_233 and wsnp_Ex_rep_c107911_91350930 deserve particular attention. The consistently significant markers with large effect could be useful for marker-assisted selection. Genomic selection revealed medium to high prediction accuracy ranging between 52% and 92% for the assessed traits with the least and maximum value observed for stigma length and visual anther extrusion, respectively. This indicates the feasibility to implement genomic selection to predict the performance of hybrid floral traits with high reliability.

Genome‐wide interaction study reveals epistatic interactions for beef lipid‐related traits in Nellore cattle

2021 ◽  
Author(s):  
S. T. Amorim ◽  
N. B. Stafuzza ◽  
S. Kluska ◽  
E. Peripolli ◽  
A. S. C. Pereira ◽  
...  
Keyword(s):  
Interaction Study ◽  
Epistatic Interactions ◽  
Genome Wide ◽  
Nellore Cattle

scholarly journals Genome-Wide Association Mapping for Stomata and Yield Indices in Bread Wheat under Water Limited Conditions

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1646
Author(s):  
Hafiz Ghulam Muhu-Din Ahmed ◽  
Muhammad Nouman Iqbal ◽  
Muhammad Arslan Iqbal ◽  
Yawen Zeng ◽  
Aziz Ullah ◽  
...  
Keyword(s):  
Grain Yield ◽  
Bread Wheat ◽  
Significant Snps ◽  
Water Shortage ◽  
Genome Wide Association ◽  
Yield Potential ◽  
Strong Positive Correlation ◽  
Leaf Venation ◽  
Genome Wide ◽  
Stomata Size

Genome-wide association study (GWAS) was performed for stomata- and yield-related attributes with high-density Illumina 90 K Infinium SNP (single nucleotide polymorphism) array in bread wheat to determine genetic potential of germplasm for scarce water resources with sustainable yield potential. Major yield and stomata attributes were phenotyped on a panel of Pakistani and foreign accessions grown in non-stressed and water shortage environments during two seasons. Highly significant variations were shown among accessions in both conditions for examined characteristics. Water shortage conditions reduced the overall wheat yield and strong positive correlation existed among stomatal frequency, leaf venation and grain yield per plant. Population structure analyses based on 90,000 SNP data classified the accessions into four sub-populations which indicated the presence of genetic variability. Marker-trait association (MTA) analyses revealed that 422 significant SNPs at p ≤ 10−3, after crossing the false discovery rate (FDR) <0.05 threshold, were linked with examined attributes. Pleiotropic loci (wsnp_Ex_c8913_14881924 and Tdurum_contig10598_304) were associated with flag leaf area (FLA), stomata size (SS), stomata frequency (SF), leaf venation (LV), number of grain per spike (NGS) and grain yield per plant (GYP), which were located on chromosome 4B and 6B at the positions 173.63cM and 229.64cM, respectively, under water shortage conditions. Pleotropic loci wsnp_Ex_c24167_33416760, wsnp_Ex_c5412_9564046 and Tdurum_contig81797_369 on chromosomes 7A, 2A and 4B at the positions 148.26cM, 261.05cM and 173.63cM, respectively, were significantly linked with stomata and yield indices such as FLA, SS, SF, LV, NGS and GYP under normal and water shortage conditions. The current experiment not only validated several MTAs for studied indices reported in other studies but also discovered novel MTAs significant under water shortage environments. Associated and significant SNPs will be useful in discovering novel genes underpinning water shortage tolerance in bread wheat for producing high-yielding and drought tolerant wheat varieties to fulfill the wheat demand for growing populations.

scholarly journals Multi-locus interactions and the build-up of reproductive isolation

2020 ◽  
Vol 375 (1806) ◽  
pp. 20190543 ◽  
Author(s):  
I. Satokangas ◽  
S. H. Martin ◽  
H. Helanterä ◽  
J. Saramäki ◽  
J. Kulmuni
Keyword(s):  
Reproductive Isolation ◽  
Empirical Work ◽  
Hybrid Fitness ◽  
Epistatic Interactions ◽  
Genome Scans ◽  
Theoretical Approaches ◽  
Genome Wide ◽  
Experimental Approaches ◽  
Polymorphism Data

All genes interact with other genes, and their additive effects and epistatic interactions affect an organism's phenotype and fitness. Recent theoretical and empirical work has advanced our understanding of the role of multi-locus interactions in speciation. However, relating different models to one another and to empirical observations is challenging. This review focuses on multi-locus interactions that lead to reproductive isolation (RI) through reduced hybrid fitness. We first review theoretical approaches and show how recent work incorporating a mechanistic understanding of multi-locus interactions recapitulates earlier models, but also makes novel predictions concerning the build-up of RI. These include high variance in the build-up rate of RI among taxa, the emergence of strong incompatibilities producing localized barriers to introgression, and an effect of population size on the build-up of RI. We then review recent experimental approaches to detect multi-locus interactions underlying RI using genomic data. We argue that future studies would benefit from overlapping methods like ancestry disequilibrium scans, genome scans of differentiation and analyses of hybrid gene expression. Finally, we highlight a need for further overlap between theoretical and empirical work, and approaches that predict what kind of patterns multi-locus interactions resulting in incompatibilities will leave in genome-wide polymorphism data. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

Genome-wide association analysis of resistance to wheat spindle streak mosaic virus in bread wheat

2018 ◽  
Vol 68 (3) ◽  
pp. 609-616 ◽  
Author(s):  
D. Hourcade ◽  
M. Bogard ◽  
M. Bonnefoy ◽  
F. Savignard ◽  
F. Mohamadi ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Bread Wheat ◽  
Association Analysis ◽  
Genome Wide Association ◽  
Genome Wide Association Analysis ◽  
Genome Wide
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