Genomewide Selection and Marker‐Assisted Recurrent Selection in Doubled Haploid versus F 2 Populations

Molecular markers have been previously found useful for increasing genetic gain in maize ( Zea mays L.). The use of doubled haploids (DHs) instead of F 2 plants (or, equivalently, F 3 families) may permit a better estimation of marker–trait associations. Our objective was to determine the usefulness of DH versus F 2 populations in marker‐assisted recurrent selection (MARS) and genomewide selection. We simulated testcrosses from a DH population and an F 2 population from the same cross between two inbreds and studied genetic models defined by the number of quantitative trait loci (QTL) and trait heritability ( H ). Equal‐time comparisons of selection response were between Cycle 3 with an F 2 population and Cycle 2 with a DH population. For the genetic model of 100 QTL, H = 0.20 and a population size of N = 100, the ratio of response to selection in DH versus F 2 populations was R DH:F2 = 109% for genomewide selection and 128% for MARS. For the genetic model of 20 QTL, H = 0.80 and N = 100 these values decreased to 99% for genomewide selection and 109% for MARS. Although genomewide selection was superior to MARS for a given type of population, the advantage of using DH instead of F 2 populations was greater in MARS than in genomewide selection. We concluded that DH populations are most useful in genomewide selection and MARS when many QTL control the trait, H is low, and N is small.