Adaptation to Plant Communities across the Genome of Arabidopsis thaliana

Abstract

Despite the importance of plant-plant interactions on plant community dynamics and crop yield, our understanding of the adaptive genetics underlying these interactions is still limited and deserves to be investigated in the context of complex and diffuse interactions occurring in plant assemblages. Here, based on 145 natural populations of Arabidopsis thaliana located in southwest of France and characterized for plant communities, we conducted a Genome-Environment Association analysis to finely map adaptive genomic regions of A. thaliana associated with plant community descriptors. To control for correlated abiotic environment effects, we also characterized the populations for a set of biologically meaningful climate and soil variables. A non-negligible fraction of top SNPs was associated with both plant community descriptors and abiotic variables, highlighting the importance of considering the actual abiotic drivers of plant communities to disentangle genetic variants for biotic adaptation from genetic variants for abiotic adaptation. The adaptive loci associated with species abundance were highly dependent on the identity of the neighboring species suggesting a high degree of biotic specialization of A. thaliana to members of its plant interaction network. Moreover, the identification of adaptive loci associated with α-diversity and composition of plant communities supports the ability of A. thaliana to interact simultaneously with multiple plant neighbors, which in turn can help to understand the role of community-wide selection. Altogether, our study highlights that dissecting the genetic basis underlying plant-plant interactions at a regional scale while controlling for abiotic confounding factors, can help understanding the adaptive mechanisms modulating natural plant assemblages.

A complex network of additive and epistatic quantitative trait loci underlies natural variation of Arabidopsis thaliana quantitative disease resistance to Ralstonia solanacearum under heat stress

“…Given that most of the A. thaliana natural populations located in France are genetically diverse (Le Corre, 2005; Platt et al ., 2010; Brachi et al ., 2013; Frachon et al ., 2018; Frachon et al ., 2019), it would be interesting to investigate the level of genetic variation of QDR to R. solanacearum GMI1000 (or to other strains) within those populations. This would provide valuable information on the local dynamics of QDR to a bacterial pathogen in A. thaliana at the metapopulation level (Ding et al ., 2007; Vetter et al ., 2012; Karasov et al ., 2014; Roux and Bergelson, 2016).…”

Temporal environmental variation may impose differential selection on both genomic and ecological traits

“…Still, all this genomic background determines standing genetic variation, which in turn will constrain which individual phenotypes are possible and thus a population's evolutionary potential. With the increasing availability of exhaustive genetic data, considering detailed genetic factors in eco‐evolutionary models has become more feasible, especially for model species (Exposito‐Alonso et al 2019, Frachon et al 2019). Indeed, there is an increasing amount of genetic data at the population or even at the individual level (Domingues et al 2012, Alonso‐Blanco et al 2016).…”

Genetic variation associated with plastic and homeostatic growth responses to drought in Arabidopsis

“…The online tool GWAPP (http://gwas.gmi.oeaw.ac.at/) was employed using a linear regression model (Seren et al, 2012). While the linear regression model does not address confounding effects of population stratification, family structure and cryptic relatedness (Price et al, 2010), it was employed here because those issues were minimized by our choice of a regional (Iberian) population (Frachon et al, 2018; Tabas-Madrid et al, 2018; Frachon et al, 2019).…”