Experimental evolution in maize with replicated divergent selection identifies plant-height associated SNPs

Experimental evolution studies are common in agricultural research, where they are often deemed “long term selection”. These are often used to perform selection mapping, which involves identifying markers which were putatively under selection based on finding signals of selection left in the genome. A challenge of previous selection mapping studies, especially in agricultural research, has been the specification of robust significance thresholds. This is in large part because long term selection studies are rarely replicated. Usually, significance thresholds in long term selection experiments are based on outliers from an empirical distribution or based on drift simulations. Both of these approaches are prone to missing true positives or including false positives. Under laboratory conditions with model species, replicated selection has been shown to be a powerful tool, especially for the specification of significance thresholds. In this study, we conducted divergent, replicated selection for short and tall plant-height in a random mating maize population under real field conditions. Selection of the 5% tallest or shortest plants was conducted for three generations. Significance thresholds were specified using the false discovery rate for selection (FDRfS) based on a single marker-based statistic leveraging replicated selection ( F _ST Sum ). Overall, we found 44 significant SNPs. Thirty-four were located within a region of 1.02 Mb comprising the coding region of the plant-height genes Dwarf1 and iAA8 . We applied a window-based analysis and haplotype block analysis to further dissect the pattern of selection in significant regions of the genome. We observed patterns of strong selection in the subpopulations selected for short plant height.