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

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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 × 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.