Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe

Abstract

Plants face a variety of challenges within their ever-changing environment. Diverse metabolites are central to the plants ability to overcome these challenges. Understanding the environmental and genetic factors influencing the variation in specialized metabolites is the key to understand how plants survive and develop under changing environments. Here we measure the variation in specialized metabolites across a population of 797 natural Arabidopsis thaliana accessions. We show a combination of geography, environmental parameters, demography, and different genetic processes that creates a specific pattern in their accumulation and distribution. By identifying and tracking causal polymorphisms at multiple loci controlling metabolites variation we show that each locus displays extensive allelic heterogeneity with signatures of both parallel and convergent evolutionary processes. These loci combine epistatically and show differing relationships to environmental parameters leading to different distributions. This provides a detailed perspective about the complexity of the forces and mechanisms that shape the accumulation and distribution of a family of specialized metabolites critical for plant fitness.

A New Catalog of Structural Variants in 1,301 A. thaliana Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response Genes

“…2001 ; Kliebenstein 2004 ) that multiple losses have occurred over evolutionary time across Eurasia. ( Katz et al. 2020 ).…”

Revisiting a GWAS peak inArabidopsis thalianareveals possible confounding by genetic heterogeneity

“…However, several GWAS identified a strong peak roughly 1 Mb from FRI , a peak which stood out because it was not obviously associated with a known flowering time gene (Brachi et al ., 2010; Atwell et al ., 2010; Li et al ., 2010; Zan and Carlborg, 2019). Instead, this peak appeared to pinpoint the highly variable and adaptively important ALKENYL HYDROXALKYL PRODUCING ( AOP ) cluster (Atwell et al ., 2010; Kerwin et al ., 2011; Katz et al ., 2020), containing three tandemly duplicated genes involved in the synthesis of glucosinolates, secondary metabolites that play important role in defense against herbivory (Kliebenstein et al ., 2001). In the Swedish population, the strongest association was found for the SNP at chr4:1355057, 961 bp upstream of AOP2 , and strongly correlated both with flowering time and FLC expression (Figs.…”

Images carried before the fire: The power, promise, and responsibility of latent phenotyping in plants

“…This makes the application of latent phenotyping more challenging for basic biological questions than for prediction. Despite these challenges, latent phenotyping approaches have been used to successfully identify genetic loci linked with tomato fruit and leaves (Chitwood et al., 2012; Li, Frank, et al., 2018; Wang et al., 2019), rice grains (Iwata et al., 2015), the maize, rice, and soybean ionomes (Chu et al., 2016; Fikas et al., 2019; Liu et al., 2021), the Brassica defensive metabolome (D'Oria et al., 2021; Katz et al., 2021), oat seed fatty acid concentrations (Carlson et al., 2019), inflorescence development in maize and sorghum (Leiboff & Hake, 2019; Rice et al., 2020), carrot shoot and roots (Turner et al., 2018), response to drought in Setaria (Ubbens et al., 2020), and strawberry fruit shape (Nagamatsu et al., 2021). Some of these successful examples have relied on prior information from preceding univariate analyses to validate the loci discovered using latent phenotyping and to aid their interpretation of those newly discovered loci (Fikas et al., 2019; Katz et al., 2021; Ubbens et al., 2020).…”

“…In these examples, dimension reduction enhances the biological signal of “branching angle of lateral organs” while not explicitly double‐ or triple‐counting the same trait. Similarly, researchers have implicitly posited that latent traits also include the plant ionome (the profile of ions in the plant, Fikas et al., 2019) the defense metabolome (the profile of specialized metabolites that participate in herbivory and pathogen responses, Katz et al., 2021), and the composition of seed fatty acids (Carlson et al., 2019).…”