Genetic interactions matter more in less-optimal environments: a Focused Review of "Phenotype uniformity in combined-stress environments has a different genetic architecture than in single-stress treatments" (Makumburage and Stapleton, 2011)

Abstract

An increase in the distribution of data points indicates the presence of genetic or environmental modifiers. Mapping of the genetic control of the spread of points, the uniformity, allows us to allocate genetic difference in point distribution to adjacent, cis effects or to independently segregating, trans genetic effects. Our genetic architecture-mapping experiment elucidated the "environmental context specificity" of modifiers, the number and effect size of positive and negative alleles important for uniformity in single and combined stress, and the extent of additivity in estimated allele effects in combined stress environments. We found no alleles for low uniformity in combined stress treatments in the maize mapping population we examined. The major advances in this research area since early 2011 have been in improved methods for modeling of distributions and means and detection of important loci. Double hierarchical general linear models and, more recently, a likelihood ratio formulation have been developed to better model and estimate the genetic and environmental effects in populations. These new methods have been applied to real data sets by the method authors and we now encourage additional development of the software and wider application of the methods. We also propose that simulations of genetic regulatory network models to examine differences in uniformity and systematic exploration of models using shared simulations across communities of researchers would be constructive avenues for developing further insight into the genetic mechanisms of variation control.

Keywords: QTL; abiotic stress; combined stress effects; crop; genotype-environment interaction; modifier; uniformity; variance heterogeneity.

Figure 1

Hypothetical example of a modifier effect on a plasticity allele. This illustration is formulated like Figure 1 in Ronnegard and Valdar (2012), except that our focus is on environmental factors rather than allele interactions. The y axis is the measured amount of a phenotype, and the x axis indicates the effect of a single allele of a plastic, environmentally-sensitive locus. (A) The stress-sensitivity is apparent in the difference in the mean (dashed line) contribution to the phenotype of the allele, with high phenotype effect in the normal control setting and low contribution in the stress environment. The spread of the points also differs for this allele, with a tight clustering of points around the mean in the control and a wider spread in the stress environment. (B) A modifier allele is illustrated by color-coding the phenotype effect estimates. In this example the modifier confers a higher mean (yellow points) and the plasticity allele retains its sensitivity to environmental stress (blue points). The mean difference is still visible in this example, though with the modifier identified the mean plasticity of the focus allele would be even larger than originally estimated from part (A).