Graphical Tests for Hardy-Weinberg Equilibrium Based on the Ternary Plot

Graffelman, Jan; Camarena, Jair Morales

doi:10.1159/000108939

Cited by 72 publications

(54 citation statements)

References 27 publications

(18 reference statements)

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“…First, markers were filtered for Hardy–Weinberg equilibrium (HWE) in R using the function ‘HWChisqMat’ in the package ‘Hardy–Weinberg’ [77]. This provided 4029 markers of which 3279 had complete information (no missing data).…”

Section: Methodsmentioning

confidence: 99%

Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)

Allwright

Payne

Emiliani

et al. 2016

Biotechnol Biofuels

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BackgroundSecond generation (2G) bioenergy from lignocellulosic feedstocks has the potential to develop as a sustainable source of renewable energy; however, significant hurdles still remain for large-scale commercialisation. Populus is considered as a promising 2G feedstock and understanding the genetic basis of biomass yield and feedstock quality are a research priority in this model tree species.ResultsWe report the first coppiced biomass study for 714 members of a wide population of European black poplar (Populus nigra L.), a native European tree, selected from 20 river populations ranging in latitude and longitude between 40.5 and 52.1°N and 1.0 and 16.4°E, respectively. When grown at a single site in southern UK, significant Site of Origin (SO) effects were seen for 14 of the 15 directly measured or derived traits including biomass yield, leaf area and stomatal index. There was significant correlation (p < 0.001) between biomass yield traits over 3 years of harvest which identified leaf size and cell production as strong predictors of biomass yield. A 12 K Illumina genotyping array (constructed from 10,331 SNPs in 14 QTL regions and 4648 genes) highlighted significant population genetic structure with pairwise FST showing strong differentiation (p < 0.001) between the Spanish and Italian subpopulations. Robust associations reaching genome-wide significance are reported for main stem height and cell number per leaf; two traits tightly linked to biomass yield. These genotyping and phenotypic data were also used to show the presence of significant isolation by distance (IBD) and isolation by adaption (IBA) within this population.ConclusionsThe three associations identified reaching genome-wide significance at p < 0.05 include a transcription factor; a putative stress response gene and a gene of unknown function. None of them have been previously linked to bioenergy yield; were shown to be differentially expressed in a panel of three selected genotypes from the collection and represent exciting, novel candidates for further study in a bioenergy tree native to Europe and Euro-Asia. A further 26 markers (22 genes) were found to reach putative significance and are also of interest for biomass yield, leaf area, epidermal cell expansion and stomatal patterning. This research on European P. nigra provides an important foundation for the development of commercial native trees for bioenergy and for advanced, molecular breeding in these species.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0603-1) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.)

Allwright

Payne

Emiliani

et al. 2016

Biotechnol Biofuels

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“…Despite the indeterminacy of the homozygote vertices, the plot remains highly informative, as now minor allele frequency, genotype frequencies and equilibrium status are visualized simultaneously for many markers in just one plot. Graffelman and Morales-Camarena (2008) …”

Section: The Ternary Plotmentioning

confidence: 99%

Exploring Diallelic Genetic Markers: TheHardyWeinbergPackage

Graffelman¹

2015

J. Stat. Soft.

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198

159

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Testing genetic markers for Hardy-Weinberg equilibrium is an important issue in genetic association studies. The HardyWeinberg package offers the classical tests for equilibrium, functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Functions for testing equilibrium in the presence of missing data by using multiple imputation are provided. The package also supplies various graphical tools such as ternary plots with acceptance regions, log-ratio plots and Q-Q plots for exploring the equilibrium status of a large set of diallelic markers. Classical tests for equilibrium and graphical representations for diallelic marker data are reviewed. Several data sets illustrate the use of the package.

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“…For a more extensive elaboration, we refer to the literature, e.g., textbooks of biochemistry and related fields, or to recent publications in the field of medicine, e.g. (5)(6)(7).…”

Section: Treatment Of Urine Datamentioning

confidence: 99%