Genetics of phenotypic plasticity: QTL analysis in barley, Hordeum vulgare

Abstract

Phenotypic plasticity is the variation in phenotypic traits produced by a genotype in different environments. In contrast, environmental canalization is defined as the insensitivity of a genotype's phenotype to variation in environments. Despite the extensive literature on the evolutionary significance and potential genetic mechanisms driving plasticity and canalization, few studies tried to unravel the genetic basis of this phenomenon. Using both simulations and real data from barley (Hordeum vulgare), we used QTL mapping to obtain insights into the genetics of phenotypic plasticity. We explored two ways of quantifying phenotypic plasticity, namely the phenotypic variance across environments and the Finlay-Wilkinson's regression slope. Each relates to a different concept of stability. Through QTL detection with real and simulated data, we show that each measure of plasticity detects specific types of plasticity QTL. Most of the plasticity QTLs were detected in the data set with the lowest number of environments. All plasticity QTL co-located with loci showing QTL Â E interaction and there were no QTL that only affected plasticity. The number of environments that are considered and their homogeneity is a key to interpret the genetic control of phenotypic plasticity. Regulatory pathways of plasticity may vary from one set of environments to another due to unique features of each environment. Therefore, with an increasing number of environments, it may become impossible to detect a single 'consistent' regulatory pathway for all environments.

Epigenetic Basis of Morphological Variation and Phenotypic Plasticity inArabidopsis thaliana

“…Similar results were obtained in drought and nutrient stress experiments, in which phenotypic plasticity was much higher in epiRILs than in the Col-0 wild type and highly heritable (Zhang et al, 2013). However, PP is also observed in conventional RIL populations (Lacaze et al, 2009;Tétard-Jones et al, 2011;ElSoda et al, 2014). It is difficult to compare the epigenetic with the genetic contribution to phenotypic plasticity, as epigenetic variation might contribute to phenotypic variation in conventional RIL populations when the epigenetic variation associates with the genetic markers (Schmitz et al, 2013a).…”

“…All PP QTLs coincided with QTLs explaining variation in the same morphological traits under control conditions. This indicates that the regulatory gene(s) underlying the QTLs are sensitive to variation in the environment and that modification of methylation profiles determines to some extent plasticity (Lacaze et al, 2009). In rice (Oryza sativa), a mutation in a gene leading to increased DNA methylation on repetitive sequences and decreased histone acetylation resulted in high expression variation in different environments, illustrating the regulation of PP through epigenetic processes .…”

“…Phenotypic plasticity is defined as the ability of a genotype to express alternative phenotypes in different environments (Schlichting, 1986). Phenotypically plastic genotypes are able to display a variety of phenotypes, in both morphology and physiology, in response to changes in the environment and as such can have improved growth and reproduction (Lacaze et al, 2009). It has been proposed that this plasticity is hidden in wild-type plants through DNA methylation, and when unlocked, could be valuable for the improvement of plant performance in unfavorable conditions (Mirouze and Paszkowski, 2011).…”

Quantitative evaluation of plastic root responses to contiguous water gradient in rice

“…By comparing Nipponbare with CSSLs, we confirmed that root plasticity was affected by the intensities of drought stress and also affected by the genotypes indicating that such plastic root response is genetically controlled (Niones et al 2015). By using these tools, the genetic control of phenotypic plasticity has been clarified through the precise quantitative evaluation and measurement of root plasticity with minimal ef f ects of genetic confounding (Lacaze et al 2009, Sandhu et al 2016.…”

Plant Responses to Elevated Temperatures: A Field Study on Phenological Sensitivity and Fitness Responses to Simulated Climate Warming

“…some genes are expressed only under some circumstances, or some gene function is only relevant under some environments) (Gardner & Latta, 2006;Lacaze et al, 2008). Alternatively, it may be due to the existence of a 'plasticity gene' that affects the magnitude of the plastic response independent of the QTL that affect variation in trait value (Schlichting & Pigliucci, 1993).…”