BackgroundGenotyping 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.ResultsThe 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.ConclusionsThe 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.

Height is one of the most heritable and easily measured traits in maize (Zea mays L.). Given a pedigree or estimates of the genomic identity-by-state among related plants, height is also accurately predictable. But, mapping alleles explaining natural variation in maize height remains a formidable challenge. To address this challenge, we measured the plant height, ear height, flowering time, and node counts of plants grown in >64,500 plots across 13 environments. These plots contained >7300 inbreds representing most publically available maize inbreds in the United States and families of the maize Nested Association Mapping (NAM) panel. Joint-linkage mapping of quantitative trait loci (QTL), fine mapping in near isogenic lines (NILs), genome-wide association studies (GWAS), and genomic best linear unbiased prediction (GBLUP) were performed. The heritability of maize height was estimated to be >90%. Mapping NAM family-nested QTL revealed the largest explained 2.1 ± 0.9% of height variation. The effects of two tropical alleles at this QTL were independently validated by fine mapping in NIL families. Several significant associations found by GWAS colocalized with established height loci, including brassinosteroid-deficient dwarf1, dwarf plant1, and semi-dwarf2. GBLUP explained >80% of height variation in the panels and outperformed bootstrap aggregation of family-nested QTL models in evaluations of prediction accuracy. These results revealed maize height was under strong genetic control and had a highly polygenic genetic architecture. They also showed that multiple models of genetic architecture differing in polygenicity and effect sizes can plausibly explain a population’s variation in maize height, but they may vary in predictive efficacy.

Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Previous studies of hybrid maize have shown the contribution of within-locus complementation effects (dominance) and their differential importance across functional classes of loci. However, they have generally considered panels of limited genetic diversity, and have shown little benefit from genomic prediction based on dominance or functional enrichments. This study investigates the relevance of dominance and functional classes of variants in genomic models for agronomic traits in diverse populations of hybrid maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the U.S. (1106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1640 hybrids). We investigated three agronomic traits: days to silking (DTS), plant height (PH), and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results suggest that dominance and gene annotations improve genomic prediction across diverse populations in hybrid maize.

To determine genetic relationships among representative popcorns (Zea mays L.) of the New World, 56 maize populations from the USA and nine Latin American countries were characterized for 29 morphological traits, 18 isozyme loci, and 31 SSR loci. Cluster and principal component analyses were performed upon standardized morphological data and allelic frequencies from isozyme and SSR loci to elucidate relationships among populations within a geographical and historical context. Three groups of popcorn, with distinctive morphological characteristics and genetic profiles, were identified in the North American populations. The first group includes the North American Yellow Pearl Popcorns, which are currently the most important for U.S. commercial production. This group could be derived from introductions of the race Curagua from Chile into New England in the 19th Century. The second group includes the North American Pointed Rice Popcorns, which probably originated from the complex of traditional races of pointed popcorns from Latin America, such as Palomero Toluqueño, Confite Puntiagudo, Canguil, and Pisankalla, which diffused from the highlands of central Mexico into northern Mexico and then into southwestern USA. The third group includes the North American Early Popcorns, which show a marked influence of Northern Flint maize, from which they probably acquired the trait of early maturity. This third group also shows genetic influences of maize from northwestern Mexico and even from early European varieties of popcorn introduced late in the 19th Century. We propose that the three groups of North American popcorn identified in this study be recognized taxonomically as distinct races, and we provide characteristic traits as well as isozyme and SSR alleles to define the new races. RightsWorks produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.

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Access to high‐yielding germplasm increases agricultural productivity. Plant Variety Protection (PVP) is the most globally used form of Intellectual Property Protection. Commercially available varieties protected solely by PVP can be accessed for further breeding within the country or region of protection. Unlike the practice in most other countries, the USDA has a policy of providing parental inbred lines of hybrids into the public domain following expiration of their protection by PVP. Parental lines and varieties protected by utility patents are also available in the public domain following expiration of protection. These distributions represent fresh opportunities for researchers, hybrid seed producers and plant breeders, nationally and internationally. As a contribution to the continuing debate over ownership and access to plant germplasm we report distributions of maize (Zea mays L.) by the US National Plant Germplasm System (NPGS). During 1988–2015 the NPGS distributed 251,926 packets to 7,582 requestors, fulfilling 10,432 orders. Distributions were primarily to US entities (87%), with 32,520 (13%) to a total of 79 foreign countries. Of the total NPGS maize distributions reported here, 45,968 (18%) were expired or off‐PVP germplasm. We hope that access provided to this germplasm will act as a reminder that the primary benefit of the Multilateral System under the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) is indeed that of having facilitated global access to germplasm and that this concept will remain an important guiding principle during further implementation of the Treaty.

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