Time series analysis in a maize landrace reveals rapid fixation of beneficial alleles

Identifying loci in the genome that allow a population to respond to selection pressure is essential to understand evolution and improve crops. Temporally consecutive generations under selection offer the opportunity to identify signatures of selection. Maize, as one of the most important crops worldwide is rich in genetic diversity and a model for breeding advances. Therefore, it is an ideal system to study genetic changes in response to selection. Here, we study the genetic changes in two replicates of a selection experiment in a European maize landrace, which showed rapid trait improvement over three cycles of selection. We identified an increase in genetic divergence across successive doubled-haploid populations derived from each selection cycle, consistent with the effect of strong directional selection. The genetic divergence observed between the replicates was greater than that between generations. In addition to the genome-wide signal, we identified multiple candidate loci under selection through temporal FST outlier analysis comparing the original landrace population to subsequent cycles. These loci showed a significant overlap with genomic regions, controlling intentionally selected traits and other traits. The significant overlap of selected loci between the two replicates shows the importance of major loci in response to directional selection, while the large number of non-overlapping loci demonstrates the polygenic response. Our work shows that the temporal dimension in plant breeding time-series enables the identification of candidate loci under selection and the genome-wide dynamics of change in response to selection.