Genetic Regulation of Grain Protein in Maize Following Long-term Selection

Identification of genetic mechanisms underlying phenotypic variation between and within populations is essential to understanding natural selection and evolution.  Changes in gene expression are an important source of phenotypic variation and may arise due to a combination of cis- and trans-regulatory variation within complex genetic networks.  This complexity has hindered identification of genomic targets of both natural and artificial selection.  Long-term phenotypic selection experiments in plants and animals provide an invaluable resource for studying evolutionary change in natural populations, with implications for enhancing the efficiency of genetic gain in plant and animal breeding.  The Illinois Long Term Selection Experiment for grain composition is a classic in plant genetics, and although conducted for more than a century, the tools for studying genome-wide responses to selection are just becoming available.  Previous QTL mapping studies suggest that changes in protein concentration in the Illinois experiment are governed by many genes of small effect, but these studies are limited by insufficient marker density to capture local changes in linkage disequilibrium.  Here we investigate the contribution of cis- and trans-regulatory variation in the Illinois Protein Strains using functional genomics approaches.  We provide evidence for at least one major-effect factor contributing to high seed protein concentration in Illinois High Protein (IHP), and another major-effect factor associated with the response to reverse selection from IHP, which acts by a distinct regulatory mechanism.  Ongoing QTL mapping utilizes floury2-mRFP expression as a phenotype that tracks expression of an individual 22-kD α-zein gene and GBS for high density marker generation.