Genome-Wide Association Studies in Arabidopsis thaliana: Statistical Analysis and Network-Based Augmentation of Signals

2020 ◽  
pp. 187-210
Author(s):  
Tak Lee ◽  
Insuk Lee
Keyword(s):  
Arabidopsis Thaliana ◽  
Statistical Analysis ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Genome-Wide Association Study Reveals Key Genes for Differential Lead Accumulation and Tolerance in Natural Arabidopsis thaliana Accessions

2021 ◽  
Vol 12 ◽  
Author(s):  
Sílvia Busoms ◽  
Laura Pérez-Martín ◽  
Miquel Llimós ◽  
Charlotte Poschenrieder ◽  
Soledad Martos
Keyword(s):  
Arabidopsis Thaliana ◽  
Cell Walls ◽  
Association Studies ◽  
Root Cell ◽  
Genome Wide Association ◽  
Chromosome 1 ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Pb Accumulation ◽  
Root Cell Walls

Soil contamination by lead (Pb) has become one of the major ecological threats to the environment. Understanding the mechanisms of Pb transport and deposition in plants is of great importance to achieve a global Pb reduction. We exposed a collection of 360 Arabidopsis thaliana natural accessions to a Pb-polluted soil. Germination rates, growth, and leaf Pb concentrations showed extensive variation among accessions. These phenotypic data were subjected to genome wide association studies (GWAs) and we found a significant association on chromosome 1 for low leaf Pb accumulation. Genes associated with significant SNP markers were evaluated and we selected EXTENSIN18 (EXT18) and TLC (TRAM-LAG1-CLN8) as candidates for having a role in Pb homeostasis. Six Pb-tolerant accessions, three of them exhibiting low leaf Pb content, and three of them with high leaf Pb content; two Pb-sensitive accessions; two knockout T-DNA lines of GWAs candidate genes (ext18, tlc); and Col-0 were screened under control and high-Pb conditions. The relative expression of EXT18, TLC, and other genes described for being involved in Pb tolerance was also evaluated. Analysis of Darwinian fitness, root and leaf ionome, and TEM images revealed that Pb-tolerant accessions employ two opposing strategies: (1) low translocation of Pb and its accumulation into root cell walls and vacuoles, or (2) high translocation of Pb and its efflux to inactive organelles or intracellular spaces. Plants using the first strategy exhibited higher expression of EXT18 and HMA3, thicker root cell walls and Pb vacuolar sequestration, suggesting that these genes may contribute to the deposition of Pb in the roots. On the other hand, plants translocating high amounts of Pb showed upregulation of TLC and ABC transporters, indicating that these plants were able to properly efflux Pb in the aerial tissues. We conclude that EXT18 and TLC upregulation enhances Pb tolerance promoting its sequestration: EXT18 favors the thickening of the cell walls improving Pb accumulation in roots and decreasing its toxicity, while TLC facilitates the formation of dictyosome vesicles and the Pb encapsulation in leaves. These findings are relevant for the design of phytoremediation strategies and environment restoration.

scholarly journals A tutorial on conducting genome-wide association studies: Quality control and statistical analysis

2018 ◽  
Vol 27 (2) ◽  
pp. e1608 ◽  
Author(s):  
Andries T. Marees ◽  
Hilde de Kluiver ◽  
Sven Stringer ◽  
Florence Vorspan ◽  
Emmanuel Curis ◽  
...  
Keyword(s):  
Quality Control ◽  
Statistical Analysis ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Genome-wide association mapping within a single Arabidopsis thaliana population reveals a richer genetic architecture for defensive metabolite diversity

2021 ◽  
Author(s):  
Andrew D Gloss ◽  
Amelie Vergnol ◽  
Timothy C Morton ◽  
Peter J Laurin ◽  
Fabrice Roux ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Architecture ◽  
Biochemical Characterization ◽  
Association Studies ◽  
Causal Variant ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Continental Scale ◽  
Mapping Panel ◽  
Genome Wide

A paradoxical finding from genome-wide association studies (GWAS) in plants is that variation in metabolite profiles typically maps to a small number of loci, despite the complexity of underlying biosynthetic pathways. This discrepancy may partially arise from limitations presented by geographically diverse mapping panels. Properties of metabolic pathways that impede GWAS by diluting the additive effect of a causal variant, such as allelic and genic heterogeneity and epistasis, would be expected to increase in severity with the geographic range of the mapping panel. We hypothesized that a population from a single locality would reveal an expanded set of associated loci. We tested this in a French Arabidopsis thaliana population (< 1 km transect) by profiling and conducting GWAS for glucosinolates, a suite of defensive metabolites that have been studied in depth through functional and genetic mapping approaches. For two distinct classes of glucosinolates, we discovered more associations at biosynthetic loci than previous GWAS with continental-scale mapping panels. Candidate genes underlying novel associations were supported by concordance between their observed effects in the TOU-A population and previous functional genetic and biochemical characterization. Local populations complement geographically diverse mapping panels to reveal a more complete genetic architecture for metabolic traits.

scholarly journals A Genome-Wide Association Study of Non-Photochemical Quenching in response to local seasonal climates in Arabidopsis thaliana

2019 ◽  
Author(s):  
Tepsuda Rungrat ◽  
Andrew A. Almonte ◽  
Riyan Cheng ◽  
Peter J. Gollan ◽  
Tim Stuart ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Association Studies ◽  
Excess Energy ◽  
Genome Wide Association ◽  
Photochemical Quenching ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
A Genome ◽  
Significant Difference ◽  
Non Photochemical Quenching

AbstractField-grown plants have variable exposure to sunlight as a result of shifting cloud-cover, seasonal changes, canopy shading, and other environmental factors. As a result, they need to have developed a method for dissipating excess energy obtained from periodic excessive sunlight exposure. Non-photochemical quenching (NPQ) dissipates excess energy as heat, however the physical and molecular genetic mechanics of NPQ variation are not understood. In this study, we investigated the genetic loci involved in NPQ by first growing different Arabidopsis thaliana accessions in local and seasonal climate conditions, then measured their NPQ kinetics through development by chlorophyll fluorescence. We used genome-wide association studies (GWAS) to identify 15 significant quantitative trait loci (QTL) for a range of photosynthetic traits, including a QTL co-located with known NPQ gene PSBS (AT1G44575). We found there were large alternative regulatory segments between the PSBS promoter regions of the functional haplotypes and a significant difference in PsbS protein concentration. These findings parallel studies in rice showing recurrent regulatory evolution of this gene. The variation in the PSBS promoter and the changes underlying other QTLs could give insight to allow manipulations of NPQ in crops to improve their photosynthetic efficiency and yield.B.P. & J.B. conceived the project; B.P., J.B., P.W. and T.R. designed the research plan and analysis; P.W. supervised the experiments; T.R. performed most of the experiments and analysis; P.G., T.S., A.A. & E.A. designed and undertook experimental design, experiments and analysis for Figure 4; R.C. did the GWAS analysis; P.W., T.R. & A.A. wrote the article with contributions of all the authors.

scholarly journals Genotype networks of 80 quantitative Arabidopsis thaliana phenotypes reveal phenotypic evolvability despite pervasive epistasis

2020 ◽  
Author(s):  
Gabriel Schweizer ◽  
Andreas Wagner
Keyword(s):  
Arabidopsis Thaliana ◽  
Fundamental Problem ◽  
Association Studies ◽  
Genome Wide Association ◽  
Phenotypic Change ◽  
Genome Wide Association Studies ◽  
Network Representation ◽  
Genome Wide ◽  
Additive Interactions ◽  
Evolutionary Paths

AbstractWe study the genotype-phenotype maps of 80 quantitative phenotypes in the model plant Arabidopsis thaliana, by representing the genotypes affecting each phenotype as a genotype network. In such a network, each vertex or node corresponds to an individual’s genotype at all those genomic loci that affect a given phenotype. Two vertices are connected by an edge if the associated genotypes differ in exactly one nucleotide. The 80 genotype networks we analyze are based on data from genome-wide association studies of 199 A. thaliana accessions. They form connected graphs whose topography differs substantially among phenotypes. We focus our analysis on the incidence of epistasis (non-additive interactions among mutations) because a high incidence of epistasis can reduce the accessibility of evolutionary paths towards high or low phenotypic values. We find epistatic interactions in 67 phenotypes, and in 51 phenotypes every pairwise mutant interaction is epistatic. Moreover, we find phenotype-specific differences in the fraction of accessible mutational paths to maximum phenotypic values. However, even though epistasis affects the accessibility of maximum phenotypic values, the relationships between genotypic and phenotypic change of our analyzed phenotypes are sufficiently smooth that some evolutionary paths remain accessible for most phenotypes, even where epistasis is pervasive. The genotype network representation we use can complement existing approaches to understand the genetic architecture of polygenic traits in many different organisms.Author summaryHow genotypic change relates to phenotypic change is a fundamental problem in evolutionary biology. A smooth relationship between genotypic and phenotypic change facilitates phenotypic evolution, whereas a rugged one hampers it, because evolutionary change on a rugged landscape does not allow a monotonic increase or decrease in phenotypic value. We use data from multiple genome-wide association studies for 80 different phenotypes in the thale cress Arabidopsis thaliana to construct 80 genotype-phenotype maps for these phenotypes. We use a network representation for each map, where a vertex corresponds to a genotype, and where two vertices are connected if they differ in a single nucleotide. We study the incidence of non-additive interactions between mutations as a proxy for the ease to reach extreme phenotypic values of these maps. This incidence varies greatly among phenotypes, but even where it is highest, some monotonic pathways to high or low phenotypic values exist for the vast majority of phenotypes, such that the underlying phenotypes are accessible to adaptive evolution.

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