Biology subjects

Zwiener, M.

Publications and source records attributed to Zwiener, M..

3 recordsLinked to original sources

bioRxiv2023

Grain Utilization by the Gut Microbiome as a Human Health Phenotype to Identify Multiple Effect Loci in Genome-Wide Association Studies of Sorghum bicolor

A growing epidemic of complex lifestyle diseases such as obesity and metabolic diseases are explained in part by dysbiosis of the human gut microbiome. The gut microbiome, comprising trillions of microorganisms, contributes to functions ranging from digestion to the immune system. Diet plays a critical role in determining the species composition and functionality of the gut microbiome. Substantial functional metabolic diversity exists within the cultivated grain crops which directly or indirectly provide more than half of all calories consumed by humans around the globe, however much of this diversity is poorly characterized and the effects of such diversity on the human gut microbiome is not well studied. We employed a quantitative genetics approach to identify genetic variants in sorghum that alter the composition and function of human gut microbes. Using an automated high-throughput phenotyping method based on in vitro microbiome fermentation of grain from a diverse population of Sorghum bicolor cultivars, we demonstrate sorghum genetics can explain effects of grain variation on fermentation patterns of bacterial taxa across multiple human microbiomes. In a genome-wide analysis using a sorghum association panel, we identified fifteen multiple-effect loci (MEL) where different alleles in the sorghum genome produced changes in seed that affect the abundance of multiple bacterial taxa across two human microbiomes in automated in vitro fermentations. In a number of cases parallel genome-wide association studies conducted for biochemical and agronomic traits identified seed traits potentially causal for the link between sorghum genetics and human microbiome outcomes. This work demonstrates that genetic factors affecting sorghum seed can drive significant effects on human gut microbes, particularly bacterial taxa considered beneficial. Understanding these relationships will enable targeted crop breeding strategies to improve human health through gut microbiome modulation.

genomics↗

bioRxiv2022

Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel

Access to biologically available nitrogen is a key constraint on plant growth in both natural and agricultural settings. Variation in tolerance to nitrogen deficit stress and productivity in nitrogen limited conditions exists both within and between plant species. Here we quantified variation in the metabolic, physiological, and morphological responses of a sorghum association panel assembled to represent global genetic diversity to long term, moderate, nitrogen deficit stress and the relationship of these responses to grain yield under both conditions. Grain yield exhibits substantial genotype by environment interaction while many other morphological and physiological traits exhibited consistent responses to nitrogen stress across the population. Large scale nontargeted metabolic profiling for a subset of lines in both conditions identified a range of metabolic responses to long term nitrogen deficit stress as well as several metabolites associated with variation in the degree of yield plasticity specific sorghum genotypes exhibited in response to nitrogen deficit stress.

plant biology↗

bioRxiv2021

3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves

Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quantification of the angle of each leaf for each plant. The resulting measurements are both heritable and correlated with manually collected leaf angles. This automated and scaleable reconstruction approach was employed to measure leaf-by-leaf angles for a population of 366 sorghum plants at multiple time points, resulting in 971 successful reconstructions and 3,376 leaf angle measurements from individual leaves. A genome wide association study conducted using aggregated leaf angle data identified a known large effect leaf angle gene, several previously identified leaf angle QTL from a sorghum NAM population, and novel signals. Genome wide association studies conducted separately for three individual sorghum leaves identified a number of the same signals, a previously unreported signal shared across multiple leaves, and signals near the sorghum orthologs of two maize genes known to influence leaf angle. Automated measurement of individual leaves and mapping variants associated with leaf angle reduce the barriers to engineering ideal canopy architectures in sorghum and other grain crops.

plant biology↗