Dominance effects and functional enrichments improve prediction of agronomic traits in hybrid maize

Authors: RAMSTEIN, GUILLAUME - Cornell University; LARSSON, SARA - Corteva Agriscience; COOK, JASON - Montana State University; Edwards, Jode; ERSOZ, ELHAN - Syngenta Seeds, Inc; Flint-Garcia, Sherry; Gardner, Candice; Holland, Jim - Jim; LORENZ, AARON - University Of Minnesota; McMullen, Michael; Millard, Mark; ROCHEFORD, TORBERT - Purdue University; TUINSTRA, MITCHELL - Purdue University; Bradbury, Peter; Buckler, Edward - Ed; ROMAY, CINTA - Cornell University

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/26/2020
Publication Date: 5/5/2020
Citation: Ramstein, G.P., Larsson, S.J., Cook, J.P., Edwards, J.W., Ersoz, E.S., Flint Garcia, S.A., Gardner, C.A., Holland, J.B., Lorenz, A.J., Mcmullen, M.D., Millard, M.J., Rocheford, T.R., Tuinstra, M.R., Bradbury, P., Buckler IV, E.S., Romay, M.C. 2020. Dominance effects and functional enrichments improve prediction of agronomic traits in hybrid maize. Genetics. 215:215-230. https://doi.org/10.1534/genetics.120.303025.
DOI: https://doi.org/10.1534/genetics.120.303025

Interpretive Summary: Modern corn hybrids are highly productive in large part due to the vigor observed in hybrids crosses. The genetic basis of hybrid vigor has been a very challenging problem for geneticists. Researchers with USDA ARS in collaboration with several Universities have conducted a large scale genetic analysis to better understand the genetic basis of heterosis. This study has revealed several novel insights into the genetic complexity of heterosis that will enable breeders and geneticists to design future research to improve our ability to predict and manipulate hybrid vigor. Improved prediction of hybrid vigor will benefit the seed industry, producers, and ultimately the consumers of maize products.

Technical 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.