Biology subjects

Boyles, R. E.

Publications and source records attributed to Boyles, R. E..

4 recordsLinked to original sources

bioRxiv2026

The Sorghum Lipid Database (SoLD): population-scale lipidomics linking environmental and genetic variation in the Sorghum Association Panel

Sorghum (Sorghum bicolor) is a climate-resilient crop whose acclimation to nutrient limitation and low temperature likely involves extensive lipidome reconfiguration. Lipids are key membrane components, carbon and energy stores, and mediators of stress signaling, yet population-scale lipidomics data for sorghum are limited. We present the Sorghum Lipid Database (SoLD), a curated lipidomics resource from the Sorghum Association Panel grown under two field regimes: (i) a nutrient-sufficient with usual planting date environment (control) and (ii) a low-input treatment with reduced nitrogen and phosphorus, earlier planting, and no application of insecticides, herbicides, or pesticides (low-input). Using high-resolution LC-MS, we quantified 244 lipid species and detected broad, largely conserved compositional shifts across field trials. However, there were four major low-input-associated lipid signatures relative to control: (i) depletion of sulfoquinovosyldiacylglycerol, (ii) triacylglycerol enrichment, (iii) phospholipid redistribution centered on phosphatidylserine, and (iv) coordinated lysophospholipid remodeling, reflected in altered lysophosphatidylcholine-to-lysophosphatidylethanolamine ratios. Analyses of lipid chemical space and lipid ontology enrichment supported these compositional changes. GWAS of lipid species, class sums, and class ratios revealed recurrent, environment-specific loci. Control-associated loci were enriched for genes involved in lipid and isoprenoid metabolism, developmental regulation, and cell-wall biosynthesis and modification. Low-input-associated loci were enriched for genes involved in nutrient-stress signaling, cell-wall remodeling, defense, developmental control, and cold-related barrier formation and proteostasis. Thus, SoLD provides a framework connecting sorghum lipid diversity with environmental and genetic variation. All information regarding the database and the experiment is freely accessible through a Shiny application: https://nirwan.shinyapps.io/SAP-Lipidomics-Database/. The database enables users to move from lipid-class to individual molecular species and associated candidate loci, for hypothesis generation, comparative analyses, and prioritization of targets for functional validation.

plant biology↗

bioRxiv2025

Developing future resilience from signatures of adaptation across the sorghum pangenome

While the green revolution adapted a handful of crops to homogenous and high-input industrialized agriculture, much of the global population still relies on local food production from low-input smallholder farms that grow highly variable crop cultivars. The high diversity of the grain and bioenergy crop sorghum 1-4, and many other crops that were not homogenized during the green revolution 5, not only provides the raw materials for breeders to make substantial gains in cultivar improvement, but also constrains breeding efforts due to highly specialized locally adapted plant phenotypes 6. Here, we construct a 33-member pangenome and identify trait-associated variants in 1,988 cultivars and landraces. We then apply these resources to explore the complex interplay between historical contingency, ongoing adaptation, and the potential for future gains through climate-aware genome-enabled breeding. Specifically, our analyses conclusively demonstrate that multiple nested, deeply diverged, and previously uncharacterized structural variants in the domestication gene SHATTERING1 distinguish the previously established multicentric origin of sorghum. We then apply landscape genomics tests to reveal how gene flow, adaptation, and secondary contact created the complex genetic mosaic in current global breeding networks. Further analysis of climate-gene associations highlights candidate loci underlying adaptation, including the biosynthetic gene cluster for the cyanogenic glucoside dhurrin. Combined, the pangenome-informed variants developed here will enable both trait discovery and subsequent marker assays to accelerate breeding and provide a framework for similar applications in other diverse and non-model crops.

genomics↗

bioRxiv2023

Bearded or Smooth? Awns Improve Yield when Wheat Experiences Heat Stress During Grain Fill

The presence or absence of awns - whether wheat heads are "bearded" or "smooth"- is the most visible phenotype distinguishing wheat cultivars. Previous studies suggest that awns may improve yields in heat or water-stressed environments, but the exact contribution of awns to yield differences remains unclear. Here we leverage historical phenotypic, genotypic, and climate data to estimate the yield effects of awns under different environmental conditions over a 12-year period in the Southeast US. Lines were classified as awned or awnless based on sequence data, and observed heading dates were used to associate grain fill periods of each line in each environment with climatic data and grain yield. In most environments, awn suppression was associated with higher yields, but awns were associated with better performance in heat-stressed environments more common at southern locations. Wheat breeders in environments where awns are only beneficial in some years may consider selection for awned lines to reduce year-to-year yield variability, and with an eye towards future climates.

genetics↗

bioRxiv2020

Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum

Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate both pleiotropy and genotype by environment interactions. Here we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome wide association studies conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35-43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations.

plant biology↗