Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize.

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.

The genetic architecture of maize height.

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.

Comprehensive genotyping of the USA national maize inbred seed bank.

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.

Identification and heritability of fumonisin insensitivity in Zea mays.

Landraces of maize (Zea mays ssp. mays) and its wild teosinte relatives (Zea mays spp. parviglumis and mexicana) were surveyed for sensitivity to fumonisin B(1), a phytotoxin produced by the maize pathogen Gibberella moniliformis. Only two of 42 Z. mays samples were highly insensitive to FB(1) (ED(50) = ca. 200 microM). The teosintes and 76% of the maize landraces were moderately or highly sensitive to FB(1) (ED(50) < or = 30 microM), which indicates that FB(1) sensitivity is likely to be an ancestral trait in Z. mays. F(1) generations derived from crosses between FB(1)-sensitive maize inbred B73 and insensitive landraces were significantly less sensitive than B73. Thus, our data indicate that FB(1)-insensitivity is a relatively rare but heritable trait in maize. We also report the sensitivity of maize to other Gibberella toxins - beauvericin, diacetoxyscirpenol, and moniliformin.