Abstract
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.
Highlights
Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging
Inbreds were assigned to one or two testers based on known heterotic group: Stiff Stalk (SS) inbreds were crossed with PHZ51, while non-Stiff Stalk (NSS) inbreds were crossed with B47; inbreds with unknown heterotic group, as well as inbreds belonging to the Goodman association panel (Flint-Garcia et al 2005), were crossed with both testers, for a total of 1111 hybrids
Compared to Ames hybrid panel (Ames-H), NAM-H is less diverse, since it was produced by crosses between a single NSS tester (PHZ51) and biparental populations that were all derived from a cross involving B73 as a common parent (NAM recombinant inbred lines (RILs) are 50% B73)
Summary
Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Gene proximity has been linked to causal variants in maize through enrichment for QTL effects in genic regions (Wallace et al 2014), consistent with a large portion of variability of gene expression being attributed to cis polymorphisms in maize (Schadt et al 2003) Structural features such as chromatin openness and high recombination rate were associated with enrichment for QTL effects in maize inbred lines (Rodgers-Melnick et al 2016), but studies on hybrids have shown that dominance effects could locate around centromeres, where recombination is low (Larièpe et al 2012; Thiemann et al.2014, Martinez et al 2016). Our study investigated the determinants of genotypic variability in hybrid maize, based on gene action (additive and/or dominance effects) or functional enrichments (by gene proximity and structural or evolutionary features) (Figure 1)
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