Extent and Distribution of Genetic Variation in U.S. Maize: Historically Important Lines and Their Open‐Pollinated Dent and Flint Progenitors

Abstract

Ancestral open‐pollinated populations of U.S. maize (Zea mays L.) are a resource to broaden the genetic base of modern maize and to ensure long‐term gains in maize breeding. We report the extent and distribution of simple sequence repeat (SSR) variation in a comprehensive study of Northern Flints (NFs), Southern Dents (SDs), Corn Belt Dents (CBDs), and historically important inbred lines, and address their implications for maize improvement and conservation. We found that the loss of rare alleles in open‐pollinated cultivars from elite gene pools resulted in the divergence of inbred lines as a distinct group apart from their progenitor races. In contrast, the Corn Belt Dent cultivars retained high levels of genetic variation that approximated or exceeded that found in their NF and SD progenitors. Within open‐pollinated varieties, the absence of any clear pattern of population differentiation indicates frequent admixture, a relatively recent time of divergence, or poor correlation between the degree of divergence at neutral marker loci and quantitative trait variation. This research suggests that the inbred lines currently used by breeders as the primary genetic resource for line improvement do not represent the genetic variation available in the temperate races from which they are derived: only 56% of the alleles found in the Corn Belt Dents were displayed in a diverse set of inbred lines. Extensive sampling targeted at a limited number of Corn Belt Dent cultivars is a promising approach toward the identification and introgression of rare alleles that were lost during early inbred development or the maintenance of open‐pollinated populations.