The Implications of Ancient Maize Selection and Demography for Future Improvement

Maize domestication involved a population bottleneck followed by rapid expansion, both of which left a pronounced mark on genetic diversity across the genome. We studied the consequences of this demographic history using whole genome sequencing data from 23 landrace maize and 13 teosinte individuals. We estimate that at the onset of the bottleneck, maize population size was reduced to approximately 5% that of teosinte, but that subsequently maize has expanded to be several-fold larger than teosinte. We observe that purifying selection, as opposed to hard sweeps on new mutations, has been the primary force driving maize evolution. Importantly, maize’s recent expansion has led to an increased efficiency of purifying selection at purging deleterious alleles from the gene pool. Based on these observations, we predict that polygenic selection may have also played an important role in shaping the genome of modern maize. To investigate the importance of polygenic selection, we describe a simple statistic, applicable to multi-generation breeding or experimental populations, to test for selection on polygenic traits that may not be significant based on genome-wide association studies or selection mapping. We demonstrate the applicability of this test using the Wisconsin Quality Synthetic breeding population.