Patterns and Consequences of Breeding-Induced Metagenome Variation in Maize.

Genetically enhancing plants to attract more beneficial microbes from their environment is a promising avenue for sustainable agriculture research. Recent research has shown that plant-associated microbiomes are partially heritable and can dramatically alter host health. However, most studies to date have used arbitrarily chosen genotypes and descriptive approaches that only minimally improve our ability to predict how microbiomes might respond to specific genetic changes in the host. To address this problem, we apply predictions from quantitative genetics to measurements of microbiome composition in field-grown maize lines from various stages of real, ongoing breeding programs.

First, we present experimental evidence that the introgression of disease-resistance alleles into elite inbred lines has side effects on non-pathogenic microbial endophytes. We compared leaf microbiome composition of a disease-susceptible inbred line to near-isogenic lines with introgressed multiple-disease-resistance (MDR) loci. Fungal microbiome diversity was 7% to 40% higher in MDR near-isogenic lines relative to their disease-susceptible inbred parent, with which they shared >90% genome identity. Over 16% of leaf-associated fungi responded to the introgression of MDR alleles, increasing or decreasing in abundance by 4-fold to 64-fold.

Second, we describe ongoing experiments to compare the leaf- and root-associated microbiomes of F1 hybrids to those of their inbred parental lines. Despite the tremendous value of hybrid vigor, and although hybridization is the basis of many breeding techniques, it is unknown whether microbiome composition exhibits heterosis like many other quantitative traits in maize. High-throughput amplicon sequencing, shotgun metagenome sequencing, and re-inoculation experiments will test whether the maize microbiome contributes to the superior performance of hybrid lines. Together, these experiments will improve our ability to predict interactions between plant genomic variation, microbiome diversity, and crop health.