Breeding Potential of European Flint Maize Landraces Evaluated by their Testcross Performance

There exists extraordinary morphological and genetic diversity among the maize landraces that have been developed by pre-Columbian cultivators. To explain this high level of diversity in maize, several authors have proposed that maize landraces were the products of multiple independent domestications from their wild relative (teosinte). We present phylogenetic analyses based on 264 individual plants, each genotyped at 99 microsatellites, that challenge the multiple-origins hypothesis. Instead, our results indicate that all maize arose from a single domestication in southern Mexico about 9,000 years ago. Our analyses also indicate that the oldest surviving maize types are those of the Mexican highlands with maize spreading from this region over the Americas along two major paths. Our phylogenetic work is consistent with a model based on the archaeological record suggesting that maize diversified in the highlands of Mexico before spreading to the lowlands. We also found only modest evidence for postdomestication gene flow from teosinte into maize.

Maize and its closest wild relatives, the teosintes, differ strikingly in the morphology of their female inflorescences or ears. Despite their divergent morphologies, several studies indicate that some varieties of teosinte are cytologically indistinguishable from maize and capable of forming fully fertile hybrids with maize. Molecular analyses identified one form of teosinte (Zea mays ssp. parviglumis) as the progenitor of maize. Analyses of the inheritance of the morphological traits that distinguish maize and teosinte indicates that they are under the control of multiple genes and exhibit quantitative inheritance. Nevertheless, these analyses have also identified a few loci of large effect that appear to represent key innovations during maize domestication. Remaining challenges are to identify additional major and minor effect genes, the polymorphisms within these genes that control the phenotypes, and how the combination of the individual and epistatic effects of these genes transformed teosinte into maize.

Background Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. Results The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. Conclusions The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.