Genetic Architecture of Stability of Genetically Complex Traits in Lettuce

Over evolutionary time, plants adapt to changing environments through genetic variation.  Short term adaptation to environmental variability occurs through modulating gene expression leading to developmental and morphological changes.  Although phenotypic plasticity may be adaptive to natural populations, maintaining a stable phenotype for many agronomic and horticultural traits across environments is a key, but elusive, breeding goal.  To examine the genetic architecture and molecular mechanisms underlying trait stability, a lettuce recombinant inbred line (RIL) population was grown in multiple environments over several years and locations to observe genotype x environment interactions.  The phenotypes of the RIL population were obtained for genetically complex traits including seed germination, antioxidant and vitamin content of leaves.    

Strikingly different germination capacity and nutritional content for a given RIL family across production years was observed.  Assessment of genes encoding key genes associated with these traits (light signaling, hormone synthesis and metabolism) revealed different expression profiles for the same genotypes across production environments.   Plasticity loci were located in unique genomic regions as well as those that collocated with phenotypic quantitative trait loci.  The data indicated that expression profiles were correlated to germination phenotypes and that transcript levels varied broadly across the RIL population.  Gene expression can be modulated by methylation, and we observed dynamic methylation of genotypes over production years.  In summary, our observations for a number of genetically complex traits with a highly inbred lettuce RIL population indicate stress-induced plasticity, which may be modulated by both genetic and epigenetic mechanisms.