Effect of Recurrent Selection on the Genetic Structure of Two Broad-Based Spanish Maize Populations

Maize (Zea mays L.) landraces are useful materials that can introduce new diversity into breeding programs, but they will need to be selected to maximize their agronomic performance. The objective of this study was to use molecular markers to investigate the changes in the genetic diversity and structure over the cycles of a maize breeding program that combined intra- and interpopulation recurrent selection for grain yield in two broad-based Spanish maize composites. Using 76 polymorphic simple sequence repeat (SSR) markers and two flowering time related indels, this study looked at 10 populations derived from a breeding program designed to exploit the heterotic pattern northern Spain × southern Spain. Agronomic evaluations demonstrated that the selection effectively increased the yield of the composites and their crosses, but, as the molecular data from this study show, the improvement was at the expense of some variability. The genetic distance between populations increased with selection, which is accordant with the increment of heterosis found in the agronomic evaluation. The changes observed were consistent with a model in which genetic drift is the main force, although selection could also play a role in the changes observed in EPS7 and EPS13. Allele frequencies changed significantly for one marker during intrapopulation selection and three markers under interpopulation selection, pointing to regions 3.04, 7.03, 9.01, and 9.03 as quantitative trait loci (QTL) related to grain yield.