Deducing Hybrid Performance from Parental Metabolic Profiles of Young Primary Roots of Maize by Using a Multivariate Diallel Approach

Abstract

Heterosis, the greater vigor of hybrids compared to their parents, has been exploited in maize breeding for more than 100 years to produce ever better performing elite hybrids of increased yield. Despite extensive research, the underlying mechanisms shaping the extent of heterosis are not well understood, rendering the process of selecting an optimal set of parental lines tedious. This study is based on a dataset consisting of 112 metabolite levels in young roots of four parental maize inbred lines and their corresponding twelve hybrids, along with the roots' biomass as a heterotic trait. Because the parental biomass is a poor predictor for hybrid biomass, we established a model framework to deduce the biomass of the hybrid from metabolite profiles of its parental lines. In the proposed framework, the hybrid metabolite levels are expressed relative to the parental levels by incorporating the standard concept of additivity/dominance, which we name the Combined Relative Level (CRL). Our modeling strategy includes a feature selection step on the parental levels which are demonstrated to be predictive of CRL across many hybrid metabolites. We demonstrate that these selected parental metabolites are further predictive of hybrid biomass. Our approach directly employs the diallel structure in a multivariate fashion, whereby we attempt to not only predict macroscopic phenotype (biomass), but also molecular phenotype (metabolite profiles). Therefore, our study provides the first steps for further investigations of the genetic determinants to metabolism and, ultimately, growth. Finally, our success on the small-scale experiments implies a valid strategy for large-scale experiments, where parental metabolite profiles may be used together with profiles of selected hybrids as a training set to predict biomass of all possible hybrids.

Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture

“…While the underlying mechanisms remain elusive, this adds novel physiological functions to this essential signaling molecule. In case metabolite markers identified here are also valid for field-grown seed material, their diagnostic for the accumulation of lipid, protein, and starch might be used in line selection and future breeding programs (Feher et al, 2014).…”

Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis

“…Different ecotypes experience diurnal and seasonal changes in their corresponding environments, leading to differences in circadian regulation of stress-responsive gene expression. We propose that over time, 'long-term' adaptation to the local environment results in genetic and epigenetic variations between parents, which is reprogrammed in hybrids to change the expression of circadian regulators 17,48 and stress-responsive genes, and possibly metabolites 42,49 , leading to heterosis. Consistent with the role of epigenetic variation in heterosis 18 , the overall levels of CG, CHG and CHH (H ¼ A, T or C) methylation in many genes, including biotic and abiotic stress-responsive genes (Fig.…”

Development of a multiple-hybrid population for genome-wide association studies: theoretical consideration and genetic mapping of flowering traits in maize

“…The overall increase of GCA and SCA was found in NC II design between some common testers and 25 mutant lines from SP 4 derived from three inbreds carried into satellite, providing useful information for maize breeding through mutation40. A Combined Relative Level (CRL) model using 112 metabolite levels in young roots from four parental inbred lines and their diallel hybrids in maize indicates that parental metabolite profiles can be used together with selected hybrids as a training set to predict biomass of all possible hybrids41. A complete diallel series of crosses involving eight parents was developed to evaluate GCA and SCA for corn grits42.…”

“…Both diallel and NC II designs can provide elaborate information on the genetic identity of genotypes, especially on dominance-recessive relationships and some genetic interactions38. As an example, a complete diallel crosses involving eight parents was produced to evaluate GCA and SCA for corn grits41. The MHP used in this research can be used to understand combining ability, heterosis, hybrid performance and genotype × environment interaction.…”