Abstract
Understanding the genetic architecture of complex traits is a major objective in biology. The standard approach for doing so is genome-wide association studies (GWAS), which aim to identify genetic polymorphisms responsible for variation in traits of interest. In human genetics, consistency across studies is commonly used as an indicator of reliability. However, if traits are involved in adaptation to the local environment, we do not necessarily expect reproducibility. On the contrary, results may depend on where you sample, and sampling across a wide range of environments may decrease the power of GWAS because of increased genetic heterogeneity. In this study, we examine how sampling affects GWAS in the model plant species Arabidopsis thaliana. We show that traits like flowering time are indeed influenced by distinct genetic effects in local populations. Furthermore, using gene expression as a molecular phenotype, we show that some genes are globally affected by shared variants, whereas others are affected by variants specific to subpopulations. Remarkably, the former are essentially all cis-regulated, whereas the latter are predominately affected by trans-acting variants. Our result illustrate that conclusions about genetic architecture can be extremely sensitive to sampling and population structure.
Highlights
After the expression data analysis, reported plant responses were confirmed and hypotheses related to endodermis as a barrier against pathogen invasion could be tested at gene expression level and later confirmed via fluorescence confocal microscospy and A. thaliana mutant infection
Infection by P. parasitica led to the major number of up-regulated genes in all cell layers, whereas down-regulation was higher in the rhizodermis and the endodermis of plants infected by V. longisporum
Results coming from RNA sequencing (RNAseq) data analysis provided a general overview of gene induction across root cell layers of A. thaliana plants infected by one mutualistic and two pathogenic fungi
Summary
A. thaliana is probably the best known plant model organism. This species has been playing a decisive role in all fields of plant biology since it was suggested as an ideal model organism (Laibach, 1943). Given its wide geographic distribution across contrasting environments, local adaptation for many traits in A. thaliana might be expected, highlighting flowering time (Agren et al, 2017; Fournier-Level et al, 2011) and seed dormancy (Kronholm et al, 2012; Postma and Ågren, 2016). These two traits have an enormous impact on fitness due to the importance of fine-tuning of germination to avoid desiccation and flower formation in order to ensure reproduction. Despite all these evidence for local adaptation, the genetic basis underlying this process remains hidden
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